# HG changeset patch # User iuc # Date 1508840999 14400 # Node ID 3bad335ccea9027a4085f587a94c6638837516cc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 diff -r 000000000000 -r 3bad335ccea9 generate_test_data.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/generate_test_data.sh Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,195 @@ +#!/usr/bin/env bash + +# 1st test +mkdir multiqc_WDir + +mkdir 'multiqc_WDir/cutadapt_0' +cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt_0/cutadapt.txt' +sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt.txt' + +mkdir -p 'multiqc_WDir/fastqc_1/data_0/file_0' +cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc_1/data_0/file_0/fastqc_data.txt' +mkdir 'multiqc_WDir/fastqc_1/data_0/file_1' +cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc_1/data_0/file_1/fastqc_data.txt' + +mkdir 'multiqc_WDir/flexbar_2' +cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar_2/flexbar.txt' + +mkdir 'multiqc_WDir/sortmerna_3' +cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna_3/sortmerna.txt' + +mkdir 'multiqc_WDir/trimmomatic_4' +cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic_4/trimmomatic.txt' + +multiqc multiqc_WDir + +mv 'multiqc_report.html' 'test-data/pre_alignment_soft_report.html' +mv 'multiqc_data/multiqc.log' 'test-data/pre_alignment_soft_log.txt' +mv 'multiqc_data/multiqc_cutadapt.txt' 'test-data/cutadapt_stats.tabular' +mv 'multiqc_data/multiqc_fastqc.txt' 'test-data/fastqc_stats.tabular' +mv 'multiqc_data/multiqc_flexbar.txt' 'test-data/flexbar_stats.tabular' +mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/pre_alignment_soft_stats.tabular' +mv 'multiqc_data/multiqc_sortmerna.txt' 'test-data/sortmerna_stats.tabular' +mv 'multiqc_data/multiqc_trimmomatic.txt' 'test-data/trimmomatic_stats.tabular' + +rm -rf 'multiqc_WDir' +rm -rf 'multiqc_data/' + +# 2nd test +mkdir multiqc_WDir + +mkdir 'multiqc_WDir/bismark_0' +cp 'test-data/bismark.txt' 'multiqc_WDir/bismark_0/bismark_SE_report.txt' + +mkdir 'multiqc_WDir/bowtie2_1' +cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2_1/bowtie2_1.txt' +cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2_1/bowtie2_2.txt' + +mkdir 'multiqc_WDir/hisat2_3' +cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2_3/hisat2_1.txt' +cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2_3/hisat2_2.txt' + +mkdir 'multiqc_WDir/kallisto_4' +cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto_4/kallisto_1.txt' +cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto_4/kallisto_2.txt' + +mkdir -p 'multiqc_WDir/salmon_5/fld_0/file_0' +cp 'test-data/salmon.txt' 'multiqc_WDir/salmon_5/fld_0/file_0/flenDist.txt' + +mkdir -p 'multiqc_WDir/star_6/log_0' +cp 'test-data/star_log.txt' 'multiqc_WDir/star_6/log_0/star_log_Log.final.out' +mkdir 'multiqc_WDir/star_6/genecounts_1' +cp 'test-data/star_counts.txt' 'multiqc_WDir/star_6/genecounts_1/star_counts_ReadsPerGene.out.tab' + +mkdir 'multiqc_WDir/tophat_7' +cp 'test-data/tophat.txt' 'multiqc_WDir/tophat_7/tophat_align_summary.txt' + +multiqc multiqc_WDir + +mv 'multiqc_report.html' 'test-data/aligner_soft_report.html' +mv 'multiqc_data/multiqc_bismark_alignment.txt' 'test-data/bismark_stats.tabular' +mv 'multiqc_data/multiqc_bowtie2.txt' 'test-data/bowtie2_stats.tabular' +mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/aligner_soft_stats.tabular' +mv 'multiqc_data/multiqc_hisat2.txt' 'test-data/hisat2_stats.tabular' +mv 'multiqc_data/multiqc_kallisto.txt' 'test-data/kallisto_stats.tabular' +mv 'multiqc_data/multiqc_star.txt' 'test-data/star_stats.tabular' +mv 'multiqc_data/multiqc_tophat.txt.txt' 'test-data/tophat_stats.tabular' + +rm -rf 'multiqc_WDir' +rm -rf 'multiqc_data/' + +# 3rd test +mkdir multiqc_WDir + +mkdir 'multiqc_WDir/bamtools_0' +cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools_0/bamtools.txt' + +mkdir 'multiqc_WDir/bcftools_1' +cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools_1/bcftools.txt' + +mkdir 'multiqc_WDir/busco_2' +cp 'test-data/busco.txt' 'multiqc_WDir/busco_2/short_summary_busco.txt' + +mkdir 'multiqc_WDir/featureCounts_3' +cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts_3/featureCounts.summary' + +mkdir 'multiqc_WDir/gatk_4' +cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk_4/gatk_BaseRecalibrator.txt' +cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk_4/gatk_varianteval.txt' + +mkdir 'multiqc_WDir/htseq_5' +cp 'test-data/htseq.txt' 'multiqc_WDir/htseq_5/htseq.txt' + +mkdir 'multiqc_WDir/picard_6' +cp 'test-data/picard_collectGcBias.txt' 'multiqc_WDir/picard_6/picard_collectGcBias.txt' +cp 'test-data/picard_CollectInsertSizeMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectInsertSizeMetrics.txt' +cp 'test-data/picard_MarkDuplicates.txt' 'multiqc_WDir/picard_6/picard_MarkDuplicates.txt' +cp 'test-data/picard_CollectBaseDistributionByCycle.txt' 'multiqc_WDir/picard_6/picard_CollectBaseDistributionByCycle.txt' +cp 'test-data/picard_CollectRnaSeqMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectRnaSeqMetrics.txt' +cp 'test-data/picard_CollectAlignmentSummaryMetrics.txt' 'multiqc_WDir/picard_6/picard_CollectAlignmentSummaryMetrics.txt' + +mkdir 'multiqc_WDir/prokka_7' +cp 'test-data/prokka_1.txt' 'multiqc_WDir/prokka_7/prokka_1.txt' +cp 'test-data/prokka_2.txt' 'multiqc_WDir/prokka_7/prokka_2.txt' + +mkdir -p 'multiqc_WDir/quast_8/file_0' +cp 'test-data/quast.tsv' 'multiqc_WDir/quast_8/file_0/report.tsv' + +#mkdir 'multiqc_WDir/rsem_9' +#cp 'test-data/rsem.txt' 'multiqc_WDir/rsem_9/rsem.cnt' + +mkdir -p 'multiqc_WDir/rseqc_10/read_gc_0' +cp 'test-data/rseqc.txt' 'multiqc_WDir/rseqc_10/read_gc_0/rseq.GC.xls' + +mkdir 'multiqc_WDir/samblaster_11' +cp 'test-data/samblaster.txt' 'multiqc_WDir/samblaster_11/samblaster.txt' + +mkdir -p 'multiqc_WDir/samtools_12/stats_0' +cp 'test-data/samtools_stats.txt' 'multiqc_WDir/samtools_12/stats_0/samtools_stats.txt' +mkdir 'multiqc_WDir/samtools_12/flagstat_1' +cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/flagstat_1/samtools_flagstat.txt' +mkdir 'multiqc_WDir/samtools_12/idxstats_2' +cp 'test-data/samtools_flagstat.txt' 'multiqc_WDir/samtools_12/idxstats_2/samtools_idxstats_idxstat' + +#mkdir 'multiqc_WDir/snpeff_13' +#cp 'test-data/snpeff.csv' 'multiqc_WDir/snpeff_13/snpeff.txt' + +mkdir -p 'multiqc_WDir/vcftools_14/tstv_by_qual_0' +cp 'test-data/vcftools.txt' 'multiqc_WDir/vcftools_14/tstv_by_qual_0/vcftools.TsTv.qual' + +multiqc multiqc_WDir + +mv 'multiqc_report.html' 'test-data/post_aligner_soft_report.html' +mv 'multiqc_data/multiqc_bamtools_stats.txt' 'test-data/bamtools_stats.tabular' +mv 'multiqc_data/multiqc_bcftools_stats.txt' 'test-data/bcftools_stats.tabular' +mv 'multiqc_data/multiqc_busco.txt' 'test-data/busco_stats.tabular' +mv 'multiqc_data/multiqc_featureCounts.txt' 'test-data/featureCounts_stats.tabular' +mv 'multiqc_data/multiqc_gatk_varianteval.txt' 'test-data/gatk_varianteval_stats.tabular' +mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/post_aligner_soft_stats.tabular' +mv 'multiqc_data/multiqc_htseq.txt' 'test-data/htseq_stats.tabular' +mv 'multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt' 'test-data/picard_AlignmentSummaryMetrics_stats.tabular' +mv 'multiqc_data/multiqc_picard_RnaSeqMetrics.txt' 'test-data/picard_RnaSeqMetrics_stats.tabular' +mv 'multiqc_data/multiqc_picard_baseContent.txt' 'test-data/picard_baseContent_stats.tabular' +mv 'multiqc_data/multiqc_picard_dups.txt' 'test-data/picard_dups_stats.tabular' +mv 'multiqc_data/multiqc_picard_insertSize.txt' 'test-data/picard_insertSize_stats.tabular' +mv 'multiqc_data/multiqc_prokka.txt' 'test-data/prokka_stats.tabular' +mv 'multiqc_data/multiqc_quast.txt' 'test-data/quast_stats.tabular' +#mv 'multiqc_data/multiqc_rsem.txt' 'test-data/rsem_stats.tabular' +mv 'multiqc_data/multiqc_rseqc.txt' 'test-data/rseqc_stats.tabular' +mv 'multiqc_data/multiqc_samblaster.txt' 'test-data/samblaster_stats.tabular' +mv 'multiqc_data/multiqc_samtools_flagstat.txt' 'test-data/samtools_flagstat_stats.tabular' +mv 'multiqc_data/multiqc_samtools_stats.txt' 'test-data/samtools_stats_stats.tabular' +#mv 'multiqc_data/multiqc_snpeff.txt' 'test-data/snpeff_stats.tabular' + +rm -rf 'multiqc_WDir' +rm -rf 'multiqc_data/' + +# 4th test +mkdir multiqc_WDir + +mkdir 'multiqc_WDir/custom_content_0' +cp 'test-data/cc_ko15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_0.tsv' +cp 'test-data/cc_wt15.bpc.tab' 'multiqc_WDir/custom_content_0/file_0_1.tsv' + +echo "custom_data:" > 'config_file' +echo " section_0:" >> 'config_file' +echo " file_format: 'tsv'" >> 'config_file' +echo " section_name: 'BPC'" >> 'config_file' +echo " title: 'Base peak chromatogram'" >> 'config_file' +echo " description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'" >> 'config_file' +echo " plot_type: 'linegraph'" >> 'config_file' +echo " pconfig:" >> 'config_file' +echo " id: 'section_0_linegraph'" >> 'config_file' +echo " ylab: 'Base Peak Intensity'" >> 'config_file' +echo " xlab: 'Retention Time'" >> 'config_file' +echo "sp:" >> 'config_file' +echo " section_0:" >> 'config_file' +echo " fn: 'file_0_*'" >> 'config_file' + +multiqc multiqc_WDir -c 'config_file' + +mv 'multiqc_report.html' 'test-data/report_manual_custom_content.html' + +rm 'config_file' +rm -rf 'multiqc_WDir' +rm -rf 'multiqc_data/' diff -r 000000000000 -r 3bad335ccea9 multiqc.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/multiqc.xml Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,994 @@ + + aggregate results from bioinformatics analyses into a single report + + 1.2 + + + + + + + + + multiqc + + mulitqc --version + +&2 ; exit 1; } && + +mkdir multiqc_WDir && + +#set $configfile="F" + +#for $i, $repeat in enumerate( $results ) + #set software_dir = 'multiqc_WDir/' + str($repeat.software_cond.software) + '_' + str($i) + mkdir $software_dir && + + #if str($repeat.software_cond.software) == "bamtools" + #set $pattern = "Stats for BAM file(s)" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "bcftools" + #set $pattern = "This file was produced by bcftools stats" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "bismark" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #set file_prefix = $software_dir + '/' + str($repeat2.type) + '_' + str($j) + #if str($repeat2.type) == "align" + #for $file in $repeat2.input + ln -s '$file' '${file_prefix}_${file.element_identifier}_SE_report.txt' && + #end for + #elif str($repeat2.type) == "dedup" + #for $file in $repeat2.input + ln -s '$file' '${file_prefix}_${file.element_identifier}_deduplication_report.txt' && + #end for + #elif str($repeat2.type) == "meth_extract" + #for $file in $repeat2.input + ln -s '$file' '${file_prefix}_${file.element_identifier}_splitting_report.txt' && + #end for + #elif str($repeat2.type) == "m_bias" + #for $file in $repeat2.input + ln -s '$file' '${file_prefix}_${file.element_identifier}_M-bias.txt' && + #end for + #elif str($repeat2.type) == "bam2nuc" + #for $file in $repeat2.input + ln -s '$file' '${file_prefix}_${file.element_identifier}.nucleotide_stats.txt' && + #end for + #end if + #end for + #elif str($repeat.software_cond.software) == "bowtie2" + #set $pattern = "reads; of these:" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "busco" + ## Searches for files "short_summary_[samplename].txt" + #for $file in $repeat.software_cond.input + ln -s '$file' '$software_dir/short_summary_${file.element_identifier}' && + #end for + #elif str($repeat.software_cond.software) == "cutadapt" + #set $pattern = "This is cutadapt" + #for $file in $repeat.software_cond.input + #set file_path = $software_dir + '/' + str($file.element_identifier) + '.txt' + ln -s '$file' '$file_path' && + ## replace header for old cutadapt release + sed -i.old 's/You are running/This is/' '$file_path' && + grep -q "$pattern" '$file_path' || die "'$pattern' or 'You are running cutadapt' not found in the file" && + #end for + #elif str($repeat.software_cond.software) == "fastqc" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #set repeat_dir = $software_dir + '/' + str($repeat2.type) + '_' + str($j) + mkdir '$repeat_dir' && + #if str($repeat2.type) == "data" + #for $k, $file in enumerate($repeat2.input) + #set file_dir = $repeat_dir + '/file_' + str($k) + mkdir '$file_dir' && + ln -s '$file' '$file_dir/fastqc_data.txt' && + #end for + #elif str($repeat2.type) == "theoretical_gc" + #for $file in $repeat2.input + ln -s '$file' '$repeat_dir/${file.element_identifier}_fastqc_theoretical_gc' && + #end for + #end if + #end for + #elif str($repeat.software_cond.software) == "featureCounts" + #for $file in $repeat.software_cond.input + #set file_prefix = $software_dir + '/' + str($file.element_identifier) + #if $file.metadata.column_names and $file.metadata.column_names.find(',') != -1 + echo '$file.metadata.column_names.replace(',','\t').replace('__ob__u','').replace('u__sq__','').replace('__sq__','').replace('__cb__','')' >> '$file_prefix.summary' && + cat '$file' >> '${file_prefix}.summary' && + #else + ln -s '$file' '${file_prefix}.summary' && + #end if + #end for + #elif str($repeat.software_cond.software) == "flexbar" + #set $pattern = "flexible barcode and adapter removal" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "gatk" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "varianteval" + #set $pattern = "#:GATKTable:TiTvVariantEvaluator" + @LN_2_FILES@ + #elif str($repeat2.type) == "base_recalibrator" + #set $pattern = "#:GATKTable:Arguments:Recalibration" + @LN_2_FILES@ + #end if + #end for + #elif str($repeat.software_cond.software) == "hicup" + #for $file in $repeat.software_cond.input + ln -s '${file}' '$software_dir/HiCUP_summary_report_${file.element_identifier}' && + #end for + #elif str($repeat.software_cond.software) == "hisat2" + #set $pattern = "HISAT2 summary stats:" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "htseq" + #set $pattern = "__too_low_aQual" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "kallisto" + #set $pattern = "finding pseudoalignments for the reads" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "picard" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #if str($repeat2.type) == "alignment_metrics" + #set $pattern = "picard.analysis.AlignmentSummaryMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "basedistributionbycycle" + #set $pattern = "picard.analysis.BaseDistributionByCycleMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "gcbias" + #set $pattern = "picard.analysis.GcBias" + @LN_2_FILES@ + #elif str($repeat2.type) == "hsmetrics" + #set $pattern = "picard.analysis.directed.HsMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "insertsize" + #set $pattern = "picard.analysis.InsertSizeMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "markdups" + #set $pattern = "picard.sam.DuplicationMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "oxogmetrics" + #set $pattern = "picard.analysis.CollectOxoGMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "pcr_metrics" + #set $pattern = "picard.analysis.directed.TargetedPcrMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "rnaseqmetrics" + #set $pattern = "Collect" + @LN_2_FILES@ + #elif str($repeat2.type) == "rrbs_metrics" + #set $pattern = "picard.analysis.RrbsSummaryMetrics" + @LN_2_FILES@ + #elif str($repeat2.type) == "wgs_metrics" + #set $pattern = "picard.analysis.CollectWgsMetrics$WgsMetrics" + @LN_2_FILES@ + #end if + #end for + #elif str($repeat.software_cond.software) == "prokka" + #set $pattern = "contigs:" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "quast" + #for $k, $file in enumerate($repeat.software_cond.input) + #set file_dir = $software_dir + '/file_' + str($k) + mkdir '$file_dir' && + ln -s '$file' '$file_dir/report.tsv' && + #end for + #elif str($repeat.software_cond.software) == "rsem" + #for $file in $repeat.software_cond.input + ln -s '$file' '$software_dir/${file.element_identifier}.cnt' && + #end for + #elif str($repeat.software_cond.software) == "rseqc" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) + mkdir '$repeat_dir' && + #if str($repeat2.type.type) == "bam_stat" + #set $pattern = "Proper-paired reads map to different chrom:" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "gene_body_coverage" + #for $k, $file in enumerate($repeat2.type.input) + ln -s '$file' '$repeat_dir/file_${k}.geneBodyCoverage.txt' && + #end for + #elif str($repeat2.type.type) == "inner_distance" + #for $k, $file in enumerate($repeat2.type.input) + ln -s '${file}' '$repeat_dir/file_${k}.inner_distance_freq.txt' && + #end for + #elif str($repeat2.type.type) == "junction_annotation" + #set $pattern = "Partial Novel Splicing Junctions:" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "read_gc" + #for $k, $file in enumerate($repeat2.type.input) + ln -s '$file' '$repeat_dir/file_${k}.GC.xls' && + #end for + #elif str($repeat2.type.type) == "junction_annotation" + #set $pattern = "Group Total_bases Tag_count Tags/Kb" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "read_duplication_pos" + #for $k, $file in enumerate($repeat2.type.input) + ln -s '$file' '$repeat_dir/file_${k}.pos.DupRate.xls' && + #end for + #elif str($repeat2.type.type) == "infer_experiment" + #set $pattern = "Fraction of reads explained by" + #for $k, $file in enumerate($repeat2.type.input) + grep -q "$pattern" $file || die "'$pattern' not found in the file" && + ln -s '$file' '$repeat_dir/$file_${k}_infer_experiment.txt' && + #end for + #end if + #end for + #elif str($repeat.software_cond.software) == "salmon" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) + mkdir '$repeat_dir' && + #if str($repeat2.type.type) == "meta" + #for $k, $file in enumerate($repeat2.type.input) + #set file_dir = $repeat_dir + '/file_' + str($k) + mkdir '$file_dir' && + ln -s '$file' '$file_dir/meta_info.json' && + #end for + #elif str($repeat2.type.type) == "fld" + #for $k, $file in enumerate($repeat2.type.input) + #set file_dir = $repeat_dir + '/file_' + str($k) + mkdir '$file_dir' && + ln -s '$file' '$file_dir/flenDist.txt' && + #end for + #end if + #end for + #elif str($repeat.software_cond.software) == "samblaster" + #set $pattern = "samblaster: Version" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "samtools" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) + mkdir '$repeat_dir' && + #if str($repeat2.type.type) == "stats" + #set $pattern = "This file was produced by samtools stats" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "flagstat" + #set $pattern = "in total (QC-passed reads + QC-failed reads)" + @LN_3_FILES@ + #elif str($repeat2.type.type) == "idxstats" + #for $file in $repeat2.type.input + ln -s '$file' '$repeat_dir/${file.element_identifier}_idxstat' && + #end for + #elif str($repeat2.type.type) == "rmdup" + #set $pattern = "[bam_rmdup" + @LN_3_FILES@ + #end if + #end for + #elif str($repeat.software_cond.software) == "snpeff" + #set $pattern = "SnpEff_version" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "sortmerna" + #set $pattern = "Minimal SW score based on E-value" + @LN_FILES@ + #else if str($repeat.software_cond.software) == "star": + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #set repeat_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) + mkdir $repeat_dir && + #if str($repeat2.type.type) == "log" + #for $file in $repeat2.type.input + ln -s '$file' '${repeat_dir}/{$file.element_identifier}_Log.final.out' && + #end for + #elif str($repeat2.type.type) == "genecounts" + #for $file in $repeat2.type.input + ln -s '$file' '${repeat_dir}/{$file.element_identifier}_ReadsPerGene.out.tab' && + #end for + #end if + #end for + #elif str($repeat.software_cond.software) == "tophat" + #for $file in $repeat.software_cond.input + ln -s '$file' '$software_dir/${file.element_identifier}align_summary.txt' && + #end for + #elif str($repeat.software_cond.software) == "trimmomatic" + #set $pattern = "Trimmomatic" + @LN_FILES@ + #elif str($repeat.software_cond.software) == "vcftools" + #for $j, $repeat2 in enumerate( $repeat.software_cond.output ) + #set file_dir = $software_dir + '/' + str($repeat2.type.type) + '_' + str($j) + mkdir $file_dir && + #if str($repeat2.type.type) == "relatedness2" + #for $file in $repeat2.type.input + ln -s '$file' '${repeat_dir}/{$file.element_identifier}.relatedness2' && + #end for + #elif str($repeat2.type) == "tstv_by_count" + #for $file in $repeat2.type.input + ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.count' && + #end for + #elif str($repeat2.type) == "tstv_by_qual" + #for $file in $repeat2.type.input + ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.qual' && + #end for + #elif str($repeat2.type) == "tstv_summary" + #for $file in $repeat2.type.input + ln -s '$file' '${repeat_dir}/{$file.element_identifier}.TsTv.summary' && + #end for + #end if + #end for + #else if str($repeat.software_cond.software) == "custom_content": + #set $configfile = "T" + #for $j, $file in enumerate( $repeat.software_cond.input ) + ln -s '$file' '${software_dir}/file_${i}_${j}' && + more $file && + #end for + #end if +#end for + +multiqc multiqc_WDir + +#if $configfile == "T" + -c '$multiqc_config' +#end if + ]]> + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + saveLog + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_ aggregates results from bioinformatics analyses across many samples into a single report. It takes results of multiple analyses and creates a report that can be viewed as a single beautiful web-page. It's a general use tool, perfect for summarizing the output from numerous bioinformatics tools. + +**Inputs** + +MultiQC takes software output summaries/logs and creates a single report from them. You need to tell the tool which software was used to generate the report. This is done using the **Software name** dropdown. At present only the Galaxy tools found in the ToolShed produce logs that can used with MultiQC + +---- + +The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`EnginesOn `_ and Rennes GenOuest Bio-informatics Core Facility). + ]]> + + 10.1093/bioinformatics/btw354 + + diff -r 000000000000 -r 3bad335ccea9 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,21 @@ +Galaxy MultiQC wrapper +======================== + +Aggregate results from bioinformatics analyses across many samples into a single report + +MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + + +Prevent displaying MultiQC webpage as gibberish +----------------------------------------------- + +For Galaxy to display MultiQC's HTML output properly, you need to either: + +1. Deactivate the sanitize_all_html option in galaxy.ini (sanitize_all_html = False), or +2. Whitelist the tool in "Manage Display Whitelist" after installing + +Support new modules +------------------- + +Currently, the wrapper supports the modules for tools found on the MTS. +To add new ones, you can look at the patterns at https://github.com/ewels/MultiQC/blob/master/multiqc/utils/search_patterns.yaml diff -r 000000000000 -r 3bad335ccea9 test-data/aligner_soft_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/aligner_soft_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,14 @@ +Sample Cutadapt_percent_trimmed Kallisto_fragment_length Kallisto_percent_aligned Kallisto_pseudoaligned_reads Bismark_aligned_reads Bismark_percent_aligned Bowtie 2_overall_alignment_rate HISAT2_overall_alignment_rate STAR_uniquely_mapped_percent STAR_uniquely_mapped Tophat_overall_aligned_percent Tophat_aligned_not_multimapped_discordant +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1 5.880883098970165 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.65114569077758 48531088.0 +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2 31.038195169381073 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1 7.7267901650356645 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.50278473550448 59280920.0 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2 32.18485266309055 +bismark_SE_report 220558.0 69.71079996207212 +bowtie2_1 98.33 +bowtie2_2 98.31 +hisat2_1 96.15 +hisat2_2 96.15 +star_log 89.0 89.0 +tophat_align 99.5 307733.0 diff -r 000000000000 -r 3bad335ccea9 test-data/bamtools.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,16 @@ +********************************************** +Stats for BAM file(s): +********************************************** + +Total reads: 339957930 +Mapped reads: 316585701 (93.125%) +Forward strand: 181666967 (53.4381%) +Reverse strand: 158290963 (46.5619%) +Failed QC: 0 (0%) +Duplicates: 0 (0%) +Paired-end reads: 339957930 (100%) +'Proper-pairs': 312895116 (92.0394%) +Both pairs mapped: 314020716 (92.3705%) +Read 1: 169978965 +Read 2: 169978965 +Singletons: 2564985 (0.754501%) diff -r 000000000000 -r 3bad335ccea9 test-data/bamtools_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bamtools_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample mapped_reads mapped_reads_pct forward_strand_pct read_2 read_1 duplicates both_mapped reverse_strand_pct duplicates_pct reverse_strand forward_strand failed_qc_pct both_mapped_pct failed_qc singletons total_reads singletons_pct paired_end paired_end_pct +bamtools 316585701.0 93.125 53.4381 169978965.0 169978965.0 0.0 314020716.0 46.5619 0.0 158290963.0 181666967.0 0.0 92.3705 0.0 2564985.0 339957930.0 0.754501 339957930.0 100.0 diff -r 000000000000 -r 3bad335ccea9 test-data/bcftools.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bcftools.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,1177 @@ +# This file was produced by bcftools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-vcfstats. +# The command line was: bcftools stats Test1.vcf.gz +# +# Definition of sets: +# ID [2]id [3]tab-separated file names +ID 0 Test1.vcf.gz +# SN, Summary numbers: +# SN [2]id [3]key [4]value +SN 0 number of samples: 1 +SN 0 number of records: 5522770 +SN 0 number of no-ALTs: 0 +SN 0 number of SNPs: 4474244 +SN 0 number of MNPs: 72330 +SN 0 number of indels: 902934 +SN 0 number of others: 73262 +SN 0 number of multiallelic sites: 0 +SN 0 number of multiallelic SNP sites: 0 +# TSTV, transitions/transversions: +# TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT) +TSTV 0 2968539 1505704 1.97 2968539 1505704 1.97 +# SiS, Singleton stats: +# SiS [2]id [3]allele count [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable +SiS 0 1 4474243 2968539 1505704 902934 0 0 902934 +# AF, Stats by non-reference allele frequency: +# AF [2]id [3]allele frequency [4]number of SNPs [5]number of transitions [6]number of transversions [7]number of indels [8]repeat-consistent [9]repeat-inconsistent [10]not applicable +AF 0 0.000000 4474243 2968539 1505704 902934 0 0 902934 +# QUAL, Stats by quality: +# QUAL [2]id [3]Quality [4]number of SNPs [5]number of transitions (1st ALT) [6]number of transversions (1st ALT) [7]number of indels +QUAL 0 25 0 0 0 2 +QUAL 0 26 0 0 0 14 +QUAL 0 27 330 117 213 52 +QUAL 0 28 0 0 0 36 +QUAL 0 29 698 273 425 136 +QUAL 0 30 0 0 0 70 +QUAL 0 31 0 0 0 70 +QUAL 0 32 1071 538 533 242 +QUAL 0 33 0 0 0 134 +QUAL 0 34 2006 1108 898 483 +QUAL 0 35 0 0 0 169 +QUAL 0 36 0 0 0 114 +QUAL 0 37 3117 1822 1295 717 +QUAL 0 38 0 0 0 203 +QUAL 0 39 4890 2607 2283 794 +QUAL 0 40 475 251 224 194 +QUAL 0 41 0 0 0 100 +QUAL 0 42 9823 5611 4212 1577 +QUAL 0 43 0 0 0 44 +QUAL 0 44 1294 671 623 107 +QUAL 0 45 575 308 267 113 +QUAL 0 46 0 0 0 53 +QUAL 0 47 1220 724 496 137 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+QUAL 0 406 57 34 23 6 +QUAL 0 407 51 33 18 8 +QUAL 0 408 55 33 22 1 +QUAL 0 409 48 34 14 4 +QUAL 0 410 42 24 18 7 +QUAL 0 411 45 22 23 6 +QUAL 0 412 56 26 30 5 +QUAL 0 413 41 26 15 4 +QUAL 0 414 59 36 23 5 +QUAL 0 415 40 21 19 6 +QUAL 0 416 27 15 12 1 +QUAL 0 417 37 24 13 2 +QUAL 0 418 25 17 8 2 +QUAL 0 419 24 15 9 3 +QUAL 0 420 26 15 11 1 +QUAL 0 421 21 9 12 1 +QUAL 0 422 24 16 8 1 +QUAL 0 423 25 18 7 3 +QUAL 0 424 16 11 5 0 +QUAL 0 425 9 5 4 2 +QUAL 0 426 18 14 4 2 +QUAL 0 427 15 10 5 1 +QUAL 0 428 12 9 3 1 +QUAL 0 429 12 9 3 2 +QUAL 0 430 11 6 5 2 +QUAL 0 431 12 4 8 0 +QUAL 0 432 10 5 5 1 +QUAL 0 433 10 6 4 0 +QUAL 0 434 12 8 4 0 +QUAL 0 435 8 4 4 3 +QUAL 0 436 4 1 3 3 +QUAL 0 437 13 6 7 0 +QUAL 0 438 9 6 3 0 +QUAL 0 439 5 3 2 1 +QUAL 0 440 5 4 1 0 +QUAL 0 441 6 4 2 3 +QUAL 0 442 2 0 2 0 +QUAL 0 443 3 3 0 1 +QUAL 0 444 5 1 4 4 +QUAL 0 445 4 3 1 0 +QUAL 0 446 5 3 2 0 +QUAL 0 447 4 2 2 0 +QUAL 0 448 6 2 4 0 +QUAL 0 449 1 1 0 2 +QUAL 0 450 1 1 0 1 +QUAL 0 451 4 1 3 0 +QUAL 0 452 0 0 0 1 +QUAL 0 453 4 4 0 3 +QUAL 0 455 2 0 2 0 +QUAL 0 456 4 2 2 1 +QUAL 0 458 0 0 0 1 +QUAL 0 459 1 0 1 0 +QUAL 0 460 4 3 1 0 +QUAL 0 462 2 1 1 0 +QUAL 0 463 2 1 1 0 +QUAL 0 464 1 1 0 0 +QUAL 0 465 4 2 2 0 +QUAL 0 466 2 1 1 0 +QUAL 0 467 0 0 0 1 +QUAL 0 468 2 1 1 0 +QUAL 0 469 0 0 0 1 +QUAL 0 470 1 0 1 0 +QUAL 0 471 2 1 1 1 +QUAL 0 472 2 0 2 2 +QUAL 0 473 1 1 0 0 +QUAL 0 474 1 0 1 0 +QUAL 0 476 1 1 0 0 +QUAL 0 477 0 0 0 1 +QUAL 0 478 0 0 0 1 +QUAL 0 479 2 1 1 0 +QUAL 0 480 1 0 1 0 +QUAL 0 481 1 1 0 1 +QUAL 0 482 1 1 0 0 +QUAL 0 484 3 2 1 2 +QUAL 0 485 1 1 0 0 +QUAL 0 486 2 1 1 0 +QUAL 0 489 0 0 0 1 +QUAL 0 490 0 0 0 1 +QUAL 0 491 1 0 1 0 +QUAL 0 492 2 1 1 1 +QUAL 0 494 2 1 1 0 +QUAL 0 496 1 0 1 0 +QUAL 0 497 1 0 1 0 +QUAL 0 499 2 2 0 0 +QUAL 0 500 0 0 0 2 +QUAL 0 501 2 0 2 1 +QUAL 0 502 0 0 0 1 +QUAL 0 503 0 0 0 2 +QUAL 0 504 0 0 0 1 +QUAL 0 506 1 0 1 0 +QUAL 0 508 1 1 0 0 +QUAL 0 509 1 1 0 0 +QUAL 0 510 1 1 0 0 +QUAL 0 512 2 1 1 0 +QUAL 0 517 0 0 0 1 +QUAL 0 518 0 0 0 1 +QUAL 0 519 1 0 1 0 +QUAL 0 520 1 1 0 0 +QUAL 0 521 2 1 1 2 +QUAL 0 524 2 1 1 0 +QUAL 0 526 2 0 2 0 +QUAL 0 527 2 1 1 0 +QUAL 0 533 1 1 0 0 +QUAL 0 537 0 0 0 1 +QUAL 0 550 1 1 0 0 +QUAL 0 554 1 1 0 0 +QUAL 0 558 1 1 0 0 +QUAL 0 560 1 0 1 1 +QUAL 0 562 1 1 0 0 +QUAL 0 565 1 0 1 0 +QUAL 0 567 1 0 1 1 +QUAL 0 575 1 1 0 0 +QUAL 0 577 1 0 1 0 +QUAL 0 578 2 0 2 0 +QUAL 0 579 1 1 0 0 +QUAL 0 580 2 0 2 0 +QUAL 0 583 1 0 1 0 +QUAL 0 585 1 0 1 0 +QUAL 0 588 1 1 0 0 +QUAL 0 594 2 0 2 0 +QUAL 0 595 0 0 0 1 +QUAL 0 598 0 0 0 2 +QUAL 0 604 1 1 0 0 +QUAL 0 608 1 0 1 0 +QUAL 0 612 0 0 0 1 +QUAL 0 624 1 0 1 0 +QUAL 0 627 1 0 1 0 +QUAL 0 664 0 0 0 1 +QUAL 0 684 0 0 0 1 +# IDD, InDel distribution: +# IDD [2]id [3]length (deletions negative) [4]count +IDD 0 -60 2761 +IDD 0 -59 60 +IDD 0 -58 89 +IDD 0 -57 65 +IDD 0 -56 141 +IDD 0 -55 85 +IDD 0 -54 150 +IDD 0 -53 68 +IDD 0 -52 146 +IDD 0 -51 96 +IDD 0 -50 196 +IDD 0 -49 143 +IDD 0 -48 251 +IDD 0 -47 109 +IDD 0 -46 167 +IDD 0 -45 126 +IDD 0 -44 219 +IDD 0 -43 116 +IDD 0 -42 274 +IDD 0 -41 151 +IDD 0 -40 452 +IDD 0 -39 204 +IDD 0 -38 324 +IDD 0 -37 228 +IDD 0 -36 476 +IDD 0 -35 269 +IDD 0 -34 417 +IDD 0 -33 275 +IDD 0 -32 682 +IDD 0 -31 332 +IDD 0 -30 748 +IDD 0 -29 374 +IDD 0 -28 983 +IDD 0 -27 513 +IDD 0 -26 914 +IDD 0 -25 632 +IDD 0 -24 1487 +IDD 0 -23 627 +IDD 0 -22 1253 +IDD 0 -21 778 +IDD 0 -20 2355 +IDD 0 -19 935 +IDD 0 -18 2258 +IDD 0 -17 1134 +IDD 0 -16 3574 +IDD 0 -15 2161 +IDD 0 -14 3343 +IDD 0 -13 1954 +IDD 0 -12 7196 +IDD 0 -11 2464 +IDD 0 -10 6677 +IDD 0 -9 4123 +IDD 0 -8 12639 +IDD 0 -7 4880 +IDD 0 -6 15111 +IDD 0 -5 13607 +IDD 0 -4 50873 +IDD 0 -3 31879 +IDD 0 -2 84831 +IDD 0 -1 211446 +IDD 0 1 204974 +IDD 0 2 71798 +IDD 0 3 24987 +IDD 0 4 41760 +IDD 0 5 10916 +IDD 0 6 12286 +IDD 0 7 3696 +IDD 0 8 10221 +IDD 0 9 3013 +IDD 0 10 5210 +IDD 0 11 1711 +IDD 0 12 5375 +IDD 0 13 1275 +IDD 0 14 2243 +IDD 0 15 1482 +IDD 0 16 2442 +IDD 0 17 731 +IDD 0 18 1359 +IDD 0 19 598 +IDD 0 20 1581 +IDD 0 21 552 +IDD 0 22 716 +IDD 0 23 418 +IDD 0 24 1022 +IDD 0 25 430 +IDD 0 26 503 +IDD 0 27 310 +IDD 0 28 550 +IDD 0 29 230 +IDD 0 30 407 +IDD 0 31 200 +IDD 0 32 361 +IDD 0 33 154 +IDD 0 34 253 +IDD 0 35 164 +IDD 0 36 250 +IDD 0 37 118 +IDD 0 38 168 +IDD 0 39 123 +IDD 0 40 190 +IDD 0 41 106 +IDD 0 42 128 +IDD 0 43 122 +IDD 0 44 128 +IDD 0 45 99 +IDD 0 46 116 +IDD 0 47 82 +IDD 0 48 133 +IDD 0 49 88 +IDD 0 50 98 +IDD 0 51 81 +IDD 0 52 96 +IDD 0 53 70 +IDD 0 54 73 +IDD 0 55 74 +IDD 0 56 78 +IDD 0 57 92 +IDD 0 58 96 +IDD 0 59 79 +IDD 0 60 5497 +# ST, Substitution types: +# ST [2]id [3]type [4]count +ST 0 A>C 190164 +ST 0 A>G 721395 +ST 0 A>T 166827 +ST 0 C>A 196831 +ST 0 C>G 197211 +ST 0 C>T 762114 +ST 0 G>A 763594 +ST 0 G>C 197866 +ST 0 G>T 201005 +ST 0 T>A 166222 +ST 0 T>C 721436 +ST 0 T>G 189578 +# DP, Depth distribution +# DP [2]id [3]bin [4]number of genotypes [5]fraction of genotypes (%) [6]number of sites [7]fraction of sites (%) +DP 0 1 0 0.000000 4 0.000072 +DP 0 2 0 0.000000 1655 0.029967 +DP 0 3 0 0.000000 2091 0.037861 +DP 0 4 0 0.000000 2126 0.038495 +DP 0 5 0 0.000000 2259 0.040903 +DP 0 6 0 0.000000 2114 0.038278 +DP 0 7 0 0.000000 2132 0.038604 +DP 0 8 0 0.000000 2030 0.036757 +DP 0 9 0 0.000000 2118 0.038350 +DP 0 10 0 0.000000 2085 0.037753 +DP 0 11 0 0.000000 2033 0.036811 +DP 0 12 0 0.000000 2014 0.036467 +DP 0 13 0 0.000000 1995 0.036123 +DP 0 14 0 0.000000 1981 0.035870 +DP 0 15 0 0.000000 2018 0.036540 +DP 0 16 0 0.000000 2015 0.036485 +DP 0 17 0 0.000000 2070 0.037481 +DP 0 18 0 0.000000 1976 0.035779 +DP 0 19 0 0.000000 1962 0.035526 +DP 0 20 0 0.000000 1961 0.035508 +DP 0 21 0 0.000000 1925 0.034856 +DP 0 22 0 0.000000 1902 0.034439 +DP 0 23 0 0.000000 2069 0.037463 +DP 0 24 0 0.000000 2021 0.036594 +DP 0 25 0 0.000000 2005 0.036304 +DP 0 26 0 0.000000 2072 0.037517 +DP 0 27 0 0.000000 2029 0.036739 +DP 0 28 0 0.000000 1986 0.035960 +DP 0 29 0 0.000000 2063 0.037354 +DP 0 30 0 0.000000 2083 0.037717 +DP 0 31 0 0.000000 2097 0.037970 +DP 0 32 0 0.000000 2062 0.037336 +DP 0 33 0 0.000000 2050 0.037119 +DP 0 34 0 0.000000 2047 0.037065 +DP 0 35 0 0.000000 2069 0.037463 +DP 0 36 0 0.000000 2097 0.037970 +DP 0 37 0 0.000000 2047 0.037065 +DP 0 38 0 0.000000 2123 0.038441 +DP 0 39 0 0.000000 2097 0.037970 +DP 0 40 0 0.000000 2052 0.037155 +DP 0 41 0 0.000000 2123 0.038441 +DP 0 42 0 0.000000 2107 0.038151 +DP 0 43 0 0.000000 2106 0.038133 +DP 0 44 0 0.000000 2134 0.038640 +DP 0 45 0 0.000000 2198 0.039799 +DP 0 46 0 0.000000 2085 0.037753 +DP 0 47 0 0.000000 2220 0.040197 +DP 0 48 0 0.000000 2187 0.039600 +DP 0 49 0 0.000000 2262 0.040958 +DP 0 50 0 0.000000 2217 0.040143 +DP 0 51 0 0.000000 2280 0.041284 +DP 0 52 0 0.000000 2278 0.041247 +DP 0 53 0 0.000000 2362 0.042768 +DP 0 54 0 0.000000 2307 0.041773 +DP 0 55 0 0.000000 2317 0.041954 +DP 0 56 0 0.000000 2359 0.042714 +DP 0 57 0 0.000000 2423 0.043873 +DP 0 58 0 0.000000 2346 0.042479 +DP 0 59 0 0.000000 2399 0.043438 +DP 0 60 0 0.000000 2421 0.043837 +DP 0 61 0 0.000000 2478 0.044869 +DP 0 62 0 0.000000 2449 0.044344 +DP 0 63 0 0.000000 2485 0.044996 +DP 0 64 0 0.000000 2586 0.046824 +DP 0 65 0 0.000000 2556 0.046281 +DP 0 66 0 0.000000 2628 0.047585 +DP 0 67 0 0.000000 2146 0.038857 +DP 0 68 0 0.000000 2174 0.039364 +DP 0 69 0 0.000000 2149 0.038912 +DP 0 70 0 0.000000 2209 0.039998 +DP 0 71 0 0.000000 2208 0.039980 +DP 0 72 0 0.000000 2232 0.040415 +DP 0 73 0 0.000000 2263 0.040976 +DP 0 74 0 0.000000 2309 0.041809 +DP 0 75 0 0.000000 2357 0.042678 +DP 0 76 0 0.000000 2334 0.042261 +DP 0 77 0 0.000000 2419 0.043800 +DP 0 78 0 0.000000 2363 0.042787 +DP 0 79 0 0.000000 2425 0.043909 +DP 0 80 0 0.000000 2561 0.046372 +DP 0 81 0 0.000000 2473 0.044778 +DP 0 82 0 0.000000 2574 0.046607 +DP 0 83 0 0.000000 2520 0.045629 +DP 0 84 0 0.000000 2628 0.047585 +DP 0 85 0 0.000000 2620 0.047440 +DP 0 86 0 0.000000 2542 0.046028 +DP 0 87 0 0.000000 2637 0.047748 +DP 0 88 0 0.000000 2722 0.049287 +DP 0 89 0 0.000000 2793 0.050572 +DP 0 90 0 0.000000 2772 0.050192 +DP 0 91 0 0.000000 2936 0.053162 +DP 0 92 0 0.000000 2938 0.053198 +DP 0 93 0 0.000000 3030 0.054864 +DP 0 94 0 0.000000 3013 0.054556 +DP 0 95 0 0.000000 3186 0.057688 +DP 0 96 0 0.000000 3222 0.058340 +DP 0 97 0 0.000000 3346 0.060586 +DP 0 98 0 0.000000 3364 0.060911 +DP 0 99 0 0.000000 3508 0.063519 +DP 0 100 0 0.000000 3051 0.055244 +DP 0 101 0 0.000000 3079 0.055751 +DP 0 102 0 0.000000 3152 0.057073 +DP 0 103 0 0.000000 3274 0.059282 +DP 0 104 0 0.000000 3413 0.061799 +DP 0 105 0 0.000000 3516 0.063664 +DP 0 106 0 0.000000 3599 0.065167 +DP 0 107 0 0.000000 3755 0.067991 +DP 0 108 0 0.000000 3784 0.068516 +DP 0 109 0 0.000000 4059 0.073496 +DP 0 110 0 0.000000 4161 0.075343 +DP 0 111 0 0.000000 4169 0.075487 +DP 0 112 0 0.000000 4331 0.078421 +DP 0 113 0 0.000000 4481 0.081137 +DP 0 114 0 0.000000 4730 0.085645 +DP 0 115 0 0.000000 4812 0.087130 +DP 0 116 0 0.000000 4893 0.088597 +DP 0 117 0 0.000000 5201 0.094174 +DP 0 118 0 0.000000 5163 0.093486 +DP 0 119 0 0.000000 5441 0.098519 +DP 0 120 0 0.000000 5466 0.098972 +DP 0 121 0 0.000000 5615 0.101670 +DP 0 122 0 0.000000 5715 0.103481 +DP 0 123 0 0.000000 5622 0.101797 +DP 0 124 0 0.000000 5809 0.105183 +DP 0 125 0 0.000000 5909 0.106993 +DP 0 126 0 0.000000 6031 0.109202 +DP 0 127 0 0.000000 5938 0.107519 +DP 0 128 0 0.000000 6364 0.115232 +DP 0 129 0 0.000000 6360 0.115160 +DP 0 130 0 0.000000 6337 0.114743 +DP 0 131 0 0.000000 6466 0.117079 +DP 0 132 0 0.000000 6417 0.116192 +DP 0 133 0 0.000000 6370 0.115341 +DP 0 134 0 0.000000 5913 0.107066 +DP 0 135 0 0.000000 5925 0.107283 +DP 0 136 0 0.000000 5875 0.106378 +DP 0 137 0 0.000000 5826 0.105491 +DP 0 138 0 0.000000 5878 0.106432 +DP 0 139 0 0.000000 5896 0.106758 +DP 0 140 0 0.000000 5948 0.107700 +DP 0 141 0 0.000000 5828 0.105527 +DP 0 142 0 0.000000 5818 0.105346 +DP 0 143 0 0.000000 5884 0.106541 +DP 0 144 0 0.000000 5917 0.107138 +DP 0 145 0 0.000000 5704 0.103282 +DP 0 146 0 0.000000 5716 0.103499 +DP 0 147 0 0.000000 5647 0.102249 +DP 0 148 0 0.000000 5604 0.101471 +DP 0 149 0 0.000000 5564 0.100747 +DP 0 150 0 0.000000 5460 0.098863 +DP 0 151 0 0.000000 5408 0.097922 +DP 0 152 0 0.000000 5345 0.096781 +DP 0 153 0 0.000000 5558 0.100638 +DP 0 154 0 0.000000 5520 0.099950 +DP 0 155 0 0.000000 5471 0.099063 +DP 0 156 0 0.000000 5520 0.099950 +DP 0 157 0 0.000000 5419 0.098121 +DP 0 158 0 0.000000 5363 0.097107 +DP 0 159 0 0.000000 5545 0.100403 +DP 0 160 0 0.000000 5617 0.101706 +DP 0 161 0 0.000000 5468 0.099008 +DP 0 162 0 0.000000 5549 0.100475 +DP 0 163 0 0.000000 5800 0.105020 +DP 0 164 0 0.000000 5643 0.102177 +DP 0 165 0 0.000000 5647 0.102249 +DP 0 166 0 0.000000 5934 0.107446 +DP 0 167 0 0.000000 5648 0.102268 +DP 0 168 0 0.000000 5689 0.103010 +DP 0 169 0 0.000000 5801 0.105038 +DP 0 170 0 0.000000 5746 0.104042 +DP 0 171 0 0.000000 6010 0.108822 +DP 0 172 0 0.000000 6004 0.108714 +DP 0 173 0 0.000000 6278 0.113675 +DP 0 174 0 0.000000 6318 0.114399 +DP 0 175 0 0.000000 6293 0.113946 +DP 0 176 0 0.000000 6652 0.120447 +DP 0 177 0 0.000000 6587 0.119270 +DP 0 178 0 0.000000 6757 0.122348 +DP 0 179 0 0.000000 7102 0.128595 +DP 0 180 0 0.000000 7319 0.132524 +DP 0 181 0 0.000000 7421 0.134371 +DP 0 182 0 0.000000 7483 0.135494 +DP 0 183 0 0.000000 7869 0.142483 +DP 0 184 0 0.000000 8043 0.145633 +DP 0 185 0 0.000000 8261 0.149581 +DP 0 186 0 0.000000 8269 0.149726 +DP 0 187 0 0.000000 8604 0.155791 +DP 0 188 0 0.000000 9081 0.164428 +DP 0 189 0 0.000000 9347 0.169245 +DP 0 190 0 0.000000 9356 0.169408 +DP 0 191 0 0.000000 9715 0.175908 +DP 0 192 0 0.000000 10073 0.182390 +DP 0 193 0 0.000000 10355 0.187496 +DP 0 194 0 0.000000 10598 0.191896 +DP 0 195 0 0.000000 11034 0.199791 +DP 0 196 0 0.000000 11434 0.207034 +DP 0 197 0 0.000000 11976 0.216848 +DP 0 198 0 0.000000 12072 0.218586 +DP 0 199 0 0.000000 12483 0.226028 +DP 0 200 0 0.000000 13036 0.236041 +DP 0 201 0 0.000000 13068 0.236620 +DP 0 202 0 0.000000 13615 0.246525 +DP 0 203 0 0.000000 14229 0.257642 +DP 0 204 0 0.000000 14600 0.264360 +DP 0 205 0 0.000000 15263 0.276365 +DP 0 206 0 0.000000 15943 0.288678 +DP 0 207 0 0.000000 16299 0.295124 +DP 0 208 0 0.000000 16955 0.307002 +DP 0 209 0 0.000000 17954 0.325090 +DP 0 210 0 0.000000 18509 0.335140 +DP 0 211 0 0.000000 18976 0.343596 +DP 0 212 0 0.000000 19896 0.360254 +DP 0 213 0 0.000000 20655 0.373997 +DP 0 214 0 0.000000 21541 0.390040 +DP 0 215 0 0.000000 22162 0.401284 +DP 0 216 0 0.000000 23167 0.419482 +DP 0 217 0 0.000000 23767 0.430346 +DP 0 218 0 0.000000 24771 0.448525 +DP 0 219 0 0.000000 25688 0.465129 +DP 0 220 0 0.000000 26530 0.480375 +DP 0 221 0 0.000000 27901 0.505199 +DP 0 222 0 0.000000 28700 0.519667 +DP 0 223 0 0.000000 29733 0.538371 +DP 0 224 0 0.000000 30892 0.559357 +DP 0 225 0 0.000000 32034 0.580035 +DP 0 226 0 0.000000 33290 0.602777 +DP 0 227 0 0.000000 33864 0.613171 +DP 0 228 0 0.000000 34934 0.632545 +DP 0 229 0 0.000000 36299 0.657261 +DP 0 230 0 0.000000 37461 0.678301 +DP 0 231 0 0.000000 38376 0.694869 +DP 0 232 0 0.000000 39929 0.722989 +DP 0 233 0 0.000000 40516 0.733617 +DP 0 234 0 0.000000 41541 0.752177 +DP 0 235 0 0.000000 42484 0.769252 +DP 0 236 0 0.000000 43413 0.786073 +DP 0 237 0 0.000000 44933 0.813595 +DP 0 238 0 0.000000 45953 0.832064 +DP 0 239 0 0.000000 47384 0.857975 +DP 0 240 0 0.000000 48232 0.873330 +DP 0 241 0 0.000000 49304 0.892740 +DP 0 242 0 0.000000 50259 0.910032 +DP 0 243 0 0.000000 51622 0.934712 +DP 0 244 0 0.000000 52045 0.942371 +DP 0 245 0 0.000000 52847 0.956893 +DP 0 246 0 0.000000 53834 0.974764 +DP 0 247 0 0.000000 55117 0.997996 +DP 0 248 0 0.000000 55895 1.012083 +DP 0 249 0 0.000000 56403 1.021281 +DP 0 250 0 0.000000 56933 1.030878 +DP 0 251 0 0.000000 57468 1.040565 +DP 0 252 0 0.000000 58118 1.052334 +DP 0 253 0 0.000000 58615 1.061333 +DP 0 254 0 0.000000 58878 1.066095 +DP 0 255 0 0.000000 59705 1.081070 +DP 0 256 0 0.000000 59921 1.084981 +DP 0 257 0 0.000000 60721 1.099466 +DP 0 258 0 0.000000 61119 1.106673 +DP 0 259 0 0.000000 60475 1.095012 +DP 0 260 0 0.000000 60882 1.102382 +DP 0 261 0 0.000000 60936 1.103359 +DP 0 262 0 0.000000 60609 1.097438 +DP 0 263 0 0.000000 60550 1.096370 +DP 0 264 0 0.000000 60495 1.095374 +DP 0 265 0 0.000000 60120 1.088584 +DP 0 266 0 0.000000 59574 1.078698 +DP 0 267 0 0.000000 58923 1.066910 +DP 0 268 0 0.000000 58438 1.058128 +DP 0 269 0 0.000000 57705 1.044856 +DP 0 270 0 0.000000 57009 1.032254 +DP 0 271 0 0.000000 56288 1.019199 +DP 0 272 0 0.000000 55623 1.007158 +DP 0 273 0 0.000000 54941 0.994809 +DP 0 274 0 0.000000 53526 0.969188 +DP 0 275 0 0.000000 52953 0.958812 +DP 0 276 0 0.000000 51562 0.933626 +DP 0 277 0 0.000000 51132 0.925840 +DP 0 278 0 0.000000 49778 0.901323 +DP 0 279 0 0.000000 48100 0.870940 +DP 0 280 0 0.000000 47727 0.864186 +DP 0 281 0 0.000000 46148 0.835595 +DP 0 282 0 0.000000 45250 0.819335 +DP 0 283 0 0.000000 43822 0.793479 +DP 0 284 0 0.000000 42706 0.773271 +DP 0 285 0 0.000000 41109 0.744355 +DP 0 286 0 0.000000 40082 0.725759 +DP 0 287 0 0.000000 38740 0.701460 +DP 0 288 0 0.000000 37148 0.672633 +DP 0 289 0 0.000000 36144 0.654454 +DP 0 290 0 0.000000 34453 0.623836 +DP 0 291 0 0.000000 33420 0.605131 +DP 0 292 0 0.000000 32105 0.581321 +DP 0 293 0 0.000000 30976 0.560878 +DP 0 294 0 0.000000 29376 0.531907 +DP 0 295 0 0.000000 28300 0.512424 +DP 0 296 0 0.000000 26766 0.484648 +DP 0 297 0 0.000000 25614 0.463789 +DP 0 298 0 0.000000 24692 0.447094 +DP 0 299 0 0.000000 23658 0.428372 +DP 0 300 0 0.000000 22395 0.405503 +DP 0 301 0 0.000000 20737 0.375482 +DP 0 302 0 0.000000 19933 0.360924 +DP 0 303 0 0.000000 18911 0.342419 +DP 0 304 0 0.000000 18054 0.326901 +DP 0 305 0 0.000000 17007 0.307943 +DP 0 306 0 0.000000 16003 0.289764 +DP 0 307 0 0.000000 15047 0.272454 +DP 0 308 0 0.000000 14344 0.259725 +DP 0 309 0 0.000000 13408 0.242777 +DP 0 310 0 0.000000 12482 0.226010 +DP 0 311 0 0.000000 11760 0.212937 +DP 0 312 0 0.000000 11352 0.205549 +DP 0 313 0 0.000000 10511 0.190321 +DP 0 314 0 0.000000 10010 0.181250 +DP 0 315 0 0.000000 9353 0.169353 +DP 0 316 0 0.000000 8598 0.155683 +DP 0 317 0 0.000000 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0.008601 +DP 0 493 0 0.000000 466 0.008438 +DP 0 494 0 0.000000 471 0.008528 +DP 0 495 0 0.000000 480 0.008691 +DP 0 496 0 0.000000 500 0.009053 +DP 0 497 0 0.000000 471 0.008528 +DP 0 498 0 0.000000 496 0.008981 +DP 0 499 0 0.000000 440 0.007967 +DP 0 500 0 0.000000 455 0.008239 +DP 0 >500 0 0.000000 144729 2.620587 diff -r 000000000000 -r 3bad335ccea9 test-data/bcftools_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bcftools_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample substitution_type_G>T number_of_samples substitution_type_G>C substitution_type_G>A tstv tv_1st_ALT number_of_others number_of_multiallelic_SNP_sites number_of_no-ALTs ts_1st_ALT number_of_MNPs ts number_of_multiallelic_sites number_of_SNPs number_of_indels substitution_type_C>A substitution_type_C>G substitution_type_A>T substitution_type_A>C number_of_records substitution_type_A>G substitution_type_C>T substitution_type_T>A substitution_type_T>C tstv_1st_ALT substitution_type_T>G tv +Test1 201005.0 1.0 197866.0 763594.0 1.97 1505704.0 73262.0 0.0 0.0 2968539.0 72330.0 2968539.0 0.0 4474244.0 902934.0 196831.0 197211.0 166827.0 190164.0 5522770.0 721395.0 762114.0 166222.0 721436.0 1.97 189578.0 1505704.0 diff -r 000000000000 -r 3bad335ccea9 test-data/bismark.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bismark.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,39 @@ +Bismark report for: /omaha-beach/cloud_26/files/000/dataset_33.dat (version: v0.10.0) +Option '--directional' specified: alignments to complementary strands will be ignored (i.e. not performed!) +Bowtie was run against the bisulfite genome of /root/galaxy/database/tmp/tmpvNBPSF/ with the specified options: -q -L 20 -D 15 -R 2 --score-min L,0,-0.2 --ignore-quals --quiet + +Final Alignment report +====================== +Sequences analysed in total: 316390 +Number of alignments with a unique best hit from the different alignments: 220558 +Mapping efficiency: 69.7% +Sequences with no alignments under any condition: 93928 +Sequences did not map uniquely: 1904 +Sequences which were discarded because genomic sequence could not be extracted: 0 + +Number of sequences with unique best (first) alignment came from the bowtie output: +CT/CT: 108352 ((converted) top strand) +CT/GA: 112206 ((converted) bottom strand) +GA/CT: 0 (complementary to (converted) top strand) +GA/GA: 0 (complementary to (converted) bottom strand) + +Number of alignments to (merely theoretical) complementary strands being rejected in total: 0 + +Final Cytosine Methylation Report +================================= +Total number of C's analysed: 5291918 + +Total methylated C's in CpG context: 465068 +Total methylated C's in CHG context: 1358074 +Total methylated C's in CHH context: 3449120 +Total methylated C's in Unknown context: 1499 + +Total unmethylated C's in CpG context: 6399 +Total unmethylated C's in CHG context: 2988 +Total unmethylated C's in CHH context: 10269 +Total unmethylated C's in Unknown context: 454 + +C methylated in CpG context: 98.6% +C methylated in CHG context: 99.8% +C methylated in CHH context: 99.7% +C methylated in Unknown context (CN or CHN): 76.8% diff -r 000000000000 -r 3bad335ccea9 test-data/bismark_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bismark_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample aligned_reads ambig_reads discarded_reads meth_chg meth_chh meth_cpg no_alignments percent_aligned percent_chg_meth percent_chh_meth percent_cpg_meth strand_ctob strand_ctot strand_ob strand_ot total_c total_reads unmeth_chg unmeth_chh unmeth_cpg +bismark_SE_report 220558.0 1904.0 0.0 1358074.0 3449120.0 465068.0 93928.0 69.7107999621 99.8 99.7 98.6 0.0 0.0 112206.0 108352.0 5291918.0 316390.0 2988.0 10269.0 6399.0 diff -r 000000000000 -r 3bad335ccea9 test-data/bowtie2_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2_1.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,6 @@ +21040602 reads; of these: + 21040602 (100.00%) were unpaired; of these: + 351563 (1.67%) aligned 0 times + 13299463 (63.21%) aligned exactly 1 time + 7389576 (35.12%) aligned >1 times +98.33% overall alignment rate diff -r 000000000000 -r 3bad335ccea9 test-data/bowtie2_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2_2.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,6 @@ +16199126 reads; of these: + 16199126 (100.00%) were unpaired; of these: + 274008 (1.69%) aligned 0 times + 10087714 (62.27%) aligned exactly 1 time + 5837404 (36.04%) aligned >1 times +98.31% overall alignment rate diff -r 000000000000 -r 3bad335ccea9 test-data/bowtie2_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bowtie2_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,3 @@ +Sample overall_alignment_rate unpaired_total unpaired_aligned_one unpaired_aligned_none unpaired_aligned_multi total_reads +bowtie2_1 98.33 21040602 13299463 351563 7389576 21040602 +bowtie2_2 98.31 16199126 10087714 274008 5837404 16199126 diff -r 000000000000 -r 3bad335ccea9 test-data/busco.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busco.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,15 @@ +# BUSCO version is: 2.0 +# The lineage dataset is: fungi_odb9 (Creation date: 2016-02-13, number of species: 85, number of BUSCOs: 290) +# To reproduce this run: python /home/remi/opt/busco/BUSCO.py -i /assemblies/BUSCO_v2_test.scf.fasta -o BUSCO_v2_test -l fungi_odb9/ -m genome -c 4 -sp aspergillus_nidulans +# +# Summarized benchmarking in BUSCO notation for file /assemblies/BUSCO_v2_test.scf.fasta +# BUSCO was run in mode: genome + + C:88.6%[S:87.9%,D:0.7%],F:1.7%,M:9.7%,n:290 + + 257 Complete BUSCOs (C) + 255 Complete and single-copy BUSCOs (S) + 2 Complete and duplicated BUSCOs (D) + 5 Fragmented BUSCOs (F) + 28 Missing BUSCOs (M) + 290 Total BUSCO groups searched \ No newline at end of file diff -r 000000000000 -r 3bad335ccea9 test-data/busco_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busco_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample fragmented complete missing complete_single_copy total lineage_dataset complete_duplicated +short 5.0 257.0 28.0 255.0 290.0 fungi_odb9 2.0 diff -r 000000000000 -r 3bad335ccea9 test-data/cc_ko15.bpc.embedded.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cc_ko15.bpc.embedded.tab Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,1289 @@ +# file_format: 'tsv' +# section_name: 'BPC' +# title: 'Base peak chromatogram' +# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' +# plot_type: 'linegraph' +# pconfig: +# id: 'bpc_lineplot' +# title: 'Base peak chromatogram' +# ylab: 'Base Peak Intensity' +# xlab: 'Retention Time' +Retention Time Base Peak Intensity +2502.98928676082 43888 +2504.55428676082 43960 +2506.11928676082 43392 +2507.68428676082 42632 +2509.24928676082 42200 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+4504.39222276304 565 +4505.95722276304 722 diff -r 000000000000 -r 3bad335ccea9 test-data/cc_wt15.bpc.embedded.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cc_wt15.bpc.embedded.tab Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,1289 @@ +# file_format: 'tsv' +# section_name: 'BPC' +# title: 'Base peak chromatogram' +# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)' +# plot_type: 'linegraph' +# pconfig: +# id: 'bpc_lineplot' +# title: 'Base peak chromatogram' +# ylab: 'Base Peak Intensity' +# xlab: 'Retention Time' +Retention Time Base Peak Intensity +2503.69308488001 44464 +2505.25808488001 44632 +2506.82308488001 45232 +2508.38808488001 46200 +2509.95308488001 46592 +2511.51808488001 46376 +2513.08308488001 45760 +2514.64808488001 45632 +2516.21308488001 45152 +2517.77808488001 44280 +2519.34308488001 43360 +2520.90708488001 43768 +2522.47208488001 44536 +2524.03708488001 45072 +2525.60208488001 44528 +2527.16708488001 43632 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3969 +4461.35215089905 4055 +4462.91715089905 4262 +4464.48215089905 4494 +4466.04715089905 4501 +4467.61215089905 4404 +4469.17715089905 4316 +4470.74215089905 4290 +4472.30715089905 4232 +4473.87215089905 4215 +4475.43715089905 4443 +4477.00115089905 4838 +4478.56615089905 4920 +4480.13115089905 4294 +4481.69615089905 3437 +4483.26115089905 3096 +4484.82615089905 3312 +4486.39115089905 3426 +4487.95615089905 3085 +4489.52115089905 2750 +4491.08615089905 2696 +4492.65115089905 2920 +4494.21615089905 3119 +4495.78115089905 3322 +4497.34615089905 3463 +4498.91115089905 3313 +4500.47615089905 3184 +4502.04115089905 3217 +4503.60615089905 3240 +4505.17115089905 3288 +4506.73615089905 3582 +4508.30115089905 3963 diff -r 000000000000 -r 3bad335ccea9 test-data/cutadapt.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,129 @@ +You are running cutadapt 1.6 with Python 2.7.3 +Command line parameters: --format=fastq --anywhere=fakadaptater=CACG --error-rate=0.1 --times=1 --overlap=3 --output=/omaha-beach/cloud_26/files/000/dataset_82.dat /omaha-beach/cloud_26/files/000/dataset_33.dat +Maximum error rate: 10.00% + No. of adapters: 1 + Processed reads: 316390 + Processed bases: 31955390 bp (32.0 Mbp) + Trimmed reads: 68795 (21.7%) + Trimmed bases: 3443775 bp (3.4 Mbp) (10.78% of total) + Too short reads: 0 (0.0% of processed reads) + Too long reads: 0 (0.0% of processed reads) + Total time: 5.28 s + Time per read: 0.017 ms + +=== Adapter 'fakadaptater' === + +Sequence: CACG; Length: 4; Trimmed: 68795 times. +2162 times, it overlapped the 5' end of a read +66633 times, it overlapped the 3' end or was within the read + +No. of allowed errors: +0-4 bp: 0 + +Overview of removed sequences (5') +length count expect max.err error counts +3 357 4943.6 0 357 +4 1805 1235.9 0 1805 + + +Overview of removed sequences (3' or within) +length count expect max.err error counts +3 4175 4943.6 0 4175 +4 520 1235.9 0 520 +5 442 1235.9 0 442 +6 522 1235.9 0 522 +7 538 1235.9 0 538 +8 526 1235.9 0 526 +9 482 1235.9 0 482 +10 547 1235.9 0 547 +11 502 1235.9 0 502 +12 539 1235.9 0 539 +13 571 1235.9 0 571 +14 601 1235.9 0 601 +15 537 1235.9 0 537 +16 592 1235.9 0 592 +17 604 1235.9 0 604 +18 617 1235.9 0 617 +19 594 1235.9 0 594 +20 493 1235.9 0 493 +21 558 1235.9 0 558 +22 503 1235.9 0 503 +23 573 1235.9 0 573 +24 609 1235.9 0 609 +25 653 1235.9 0 653 +26 625 1235.9 0 625 +27 541 1235.9 0 541 +28 501 1235.9 0 501 +29 618 1235.9 0 618 +30 539 1235.9 0 539 +31 614 1235.9 0 614 +32 594 1235.9 0 594 +33 627 1235.9 0 627 +34 572 1235.9 0 572 +35 690 1235.9 0 690 +36 615 1235.9 0 615 +37 654 1235.9 0 654 +38 681 1235.9 0 681 +39 530 1235.9 0 530 +40 731 1235.9 0 731 +41 622 1235.9 0 622 +42 611 1235.9 0 611 +43 722 1235.9 0 722 +44 664 1235.9 0 664 +45 659 1235.9 0 659 +46 651 1235.9 0 651 +47 591 1235.9 0 591 +48 642 1235.9 0 642 +49 545 1235.9 0 545 +50 573 1235.9 0 573 +51 591 1235.9 0 591 +52 567 1235.9 0 567 +53 749 1235.9 0 749 +54 647 1235.9 0 647 +55 753 1235.9 0 753 +56 696 1235.9 0 696 +57 780 1235.9 0 780 +58 607 1235.9 0 607 +59 758 1235.9 0 758 +60 643 1235.9 0 643 +61 578 1235.9 0 578 +62 670 1235.9 0 670 +63 652 1235.9 0 652 +64 816 1235.9 0 816 +65 732 1235.9 0 732 +66 640 1235.9 0 640 +67 644 1235.9 0 644 +68 818 1235.9 0 818 +69 658 1235.9 0 658 +70 587 1235.9 0 587 +71 672 1235.9 0 672 +72 588 1235.9 0 588 +73 645 1235.9 0 645 +74 668 1235.9 0 668 +75 725 1235.9 0 725 +76 651 1235.9 0 651 +77 701 1235.9 0 701 +78 662 1235.9 0 662 +79 655 1235.9 0 655 +80 760 1235.9 0 760 +81 746 1235.9 0 746 +82 705 1235.9 0 705 +83 704 1235.9 0 704 +84 726 1235.9 0 726 +85 692 1235.9 0 692 +86 700 1235.9 0 700 +87 758 1235.9 0 758 +88 640 1235.9 0 640 +89 665 1235.9 0 665 +90 848 1235.9 0 848 +91 693 1235.9 0 693 +92 775 1235.9 0 775 +93 1237 1235.9 0 1237 +94 629 1235.9 0 629 +95 574 1235.9 0 574 +96 525 1235.9 0 525 +97 586 1235.9 0 586 +98 696 1235.9 0 696 +99 860 1235.9 0 860 +100 851 1235.9 0 851 + diff -r 000000000000 -r 3bad335ccea9 test-data/cutadapt_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cutadapt_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample r_trimmed bp_trimmed bp_processed too_short r_processed too_long percent_trimmed +dataset_33 68795 3443775 31955390 0 316390 0 10.7768204362 diff -r 000000000000 -r 3bad335ccea9 test-data/fastqc_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_1.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2181 @@ +##FastQC 0.11.4 +>>Basic Statistics pass +#Measure Value +Filename poulet5_1 +File type Conventional base calls +Encoding Sanger / Illumina 1.9 +Total Sequences 267849 +Sequences flagged as poor quality 0 +Sequence length 101 +%GC 48 +>>END_MODULE +>>Per base sequence quality warn +#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile +1 20.91988023102569 21.0 21.0 21.0 21.0 21.0 +2 20.71684045861661 21.0 20.0 22.0 19.0 23.0 +3 20.351574954545285 21.0 20.0 21.0 18.0 22.0 +4 22.531542025544244 23.0 22.0 24.0 20.0 24.0 +5 24.673566076408722 25.0 24.0 26.0 24.0 26.0 +6 25.813099918237516 26.0 25.0 27.0 25.0 27.0 +7 27.587864804423386 28.0 27.0 29.0 26.0 29.0 +8 27.598941941168345 28.0 27.0 29.0 26.0 29.0 +9 27.07115949658203 28.0 26.0 28.0 26.0 28.0 +10-11 27.129873548155864 28.0 26.0 28.0 25.5 28.0 +12-13 27.009298149330405 27.5 26.0 28.0 25.5 28.0 +14-15 27.123565889736383 28.0 26.5 28.0 26.0 28.0 +16-17 27.086309823818645 28.0 26.0 28.0 26.0 28.0 +18-19 27.07924614241606 28.0 26.0 28.0 25.5 28.0 +20-21 27.082520375286073 28.0 26.0 28.0 26.0 28.0 +22-23 27.054301117420636 28.0 26.0 28.0 25.0 28.0 +24-25 27.06350966402712 28.0 26.0 28.0 25.0 28.0 +26-27 27.082996389756914 28.0 26.0 28.0 26.0 28.0 +28-29 27.065495857740743 28.0 26.0 28.0 25.5 28.0 +30-31 27.09608772106672 28.0 26.0 28.0 26.0 28.0 +32-33 27.087097581099798 28.0 26.0 28.0 26.0 28.0 +34-35 27.098251253504774 28.0 26.5 28.0 26.0 28.0 +36-37 27.05184077595959 28.0 26.0 28.0 25.5 28.0 +38-39 27.06521958267531 28.0 26.0 28.0 26.0 28.0 +40-41 27.072148859992012 28.0 26.0 28.0 26.0 28.0 +42-43 27.065725464720796 28.0 26.0 28.0 25.5 28.0 +44-45 27.07168031241483 28.0 26.5 28.0 25.5 28.0 +46-47 27.048083061725073 28.0 26.0 28.0 25.5 28.0 +48-49 27.04642354460909 28.0 26.0 28.0 25.5 28.0 +50-51 27.062865644448927 28.0 26.0 28.0 25.5 28.0 +52-53 27.01859629866081 28.0 26.0 28.0 25.0 28.0 +54-55 26.994157155710866 27.5 26.0 28.0 25.0 28.0 +56-57 27.110127347871376 28.0 27.0 28.0 26.0 28.0 +58-59 26.995846540401494 27.5 26.0 28.0 25.0 28.0 +60-61 27.00461640700544 27.5 26.0 28.0 25.0 28.0 +62-63 26.981614641085088 27.5 26.5 28.0 25.5 28.5 +64-65 26.98900313236189 28.0 26.0 28.0 25.0 28.0 +66-67 27.001189102815392 28.0 26.0 28.0 25.0 28.0 +68-69 26.917739099268616 27.5 26.0 28.0 25.0 28.5 +70-71 26.98481793846533 28.0 27.0 28.0 25.0 29.0 +72-73 26.89518908041471 27.5 26.5 28.0 25.0 28.5 +74-75 26.93677034448514 28.0 27.0 28.0 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23.648025566643895 +88-89 24.194788854914524 25.881373460419866 25.988710056785724 23.935127627879886 +90-91 24.30641891513502 25.716915127553207 25.838438821873517 24.13822713543825 +92-93 23.89331302338258 26.09231320632147 26.2431444582582 23.771229312037754 +94-95 24.343006694070166 25.78803728966694 25.850945868754412 24.018010147508484 +96-97 24.293351851229612 25.853745953877 25.936815145847103 23.916087049046293 +98-99 24.295965264010693 25.91702787764748 26.050311929482657 23.73669492885917 +100-101 24.65138940223783 25.744542634096078 25.755742974586425 23.848324989079668 +>>END_MODULE +>>Per sequence GC content pass +#GC Content Count +0 0.0 +1 0.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +10 0.0 +11 0.0 +12 0.0 +13 0.0 +14 0.5 +15 2.0 +16 5.0 +17 7.5 +18 10.5 +19 15.5 +20 20.0 +21 28.5 +22 42.5 +23 63.0 +24 126.5 +25 228.0 +26 385.0 +27 545.0 +28 720.0 +29 1080.5 +30 1474.5 +31 1743.5 +32 2015.0 +33 2324.0 +34 2747.0 +35 3375.5 +36 3996.5 +37 4590.5 +38 5365.0 +39 6219.5 +40 7284.0 +41 8648.0 +42 9680.5 +43 10325.5 +44 10906.0 +45 11123.5 +46 11325.5 +47 12122.5 +48 12960.5 +49 13030.0 +50 12518.5 +51 11744.0 +52 10781.0 +53 10248.5 +54 10433.5 +55 9922.0 +56 8785.5 +57 7997.0 +58 6901.0 +59 5796.0 +60 4967.0 +61 4072.5 +62 3639.5 +63 3267.0 +64 2561.5 +65 2002.5 +66 1561.5 +67 1355.5 +68 1222.0 +69 1019.0 +70 803.0 +71 568.5 +72 371.5 +73 235.0 +74 164.5 +75 110.5 +76 70.5 +77 56.0 +78 39.5 +79 27.0 +80 18.0 +81 17.0 +82 15.5 +83 12.5 +84 6.5 +85 1.5 +86 0.0 +87 0.0 +88 0.0 +89 0.0 +90 0.0 +91 0.0 +92 0.0 +93 0.0 +94 0.0 +95 0.0 +96 0.0 +97 0.0 +98 0.0 +99 0.0 +100 0.0 +>>END_MODULE +>>Per base N content pass +#Base N-Count +1 0.029867574640935753 +2 0.0 +3 0.003733446830116969 +4 0.0 +5 3.733446830116969E-4 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +10-11 0.0 +12-13 0.0 +14-15 0.0 +16-17 0.0 +18-19 0.0 +20-21 0.0 +22-23 0.0 +24-25 0.0 +26-27 0.0 +28-29 0.0 +30-31 0.0 +32-33 0.0 +34-35 0.0 +36-37 0.0 +38-39 0.0 +40-41 0.0 +42-43 0.0 +44-45 0.0 +46-47 0.0 +48-49 0.0 +50-51 0.0 +52-53 0.0 +54-55 0.0 +56-57 0.0 +58-59 0.0 +60-61 0.0 +62-63 0.0 +64-65 0.0 +66-67 0.0 +68-69 0.0 +70-71 0.0 +72-73 0.0 +74-75 0.0 +76-77 0.0 +78-79 0.0 +80-81 0.0 +82-83 0.0 +84-85 0.0 +86-87 0.0 +88-89 0.0 +90-91 0.0 +92-93 0.0 +94-95 0.0 +96-97 0.0 +98-99 0.0 +100-101 0.0 +>>END_MODULE +>>Sequence Length Distribution pass +#Length Count +101 267849.0 +>>END_MODULE +>>Sequence Duplication Levels warn +#Total Deduplicated Percentage 63.69408840068983 +#Duplication Level Percentage of deduplicated Percentage of total +1 81.5623716290639 51.950409087115126 +2 9.995611185249079 12.733226849043577 +3 3.1947144335386772 6.104532706343167 +4 1.4905270052149588 3.797510353351082 +5 0.8725392208870194 2.778779513412342 +6 0.55360835935223 2.115694786796508 +7 0.38537193434967776 1.718213983752925 +8 0.314619574221819 1.603152557845755 +9 0.2033036957962869 1.1654319215012086 +>10 1.4223398099582591 15.850860027094066 +>50 0.0049931523680946535 0.18218821374420768 +>100 0.0 0.0 +>500 0.0 0.0 +>1k 0.0 0.0 +>5k 0.0 0.0 +>10k+ 0.0 0.0 +>>END_MODULE +>>Overrepresented sequences pass +>>END_MODULE +>>Adapter Content pass +#Position Illumina Universal Adapter Illumina Small RNA Adapter Nextera Transposase Sequence SOLID Small RNA Adapter +1 0.0 0.0 0.0 0.0 +2 0.0 0.0 0.0 0.0 +3 0.0 0.0 0.0 0.0 +4 0.0 0.0 0.0 0.0 +5 0.0 0.0 0.0 0.0 +6 0.0 0.0 0.0 0.0 +7 0.0 0.0 0.0 0.0 +8 0.0 0.0 0.0 0.0 +9 0.0 0.0 0.0 0.0 +10-11 0.0 0.0 0.0 0.0 +12-13 0.0 0.0 0.0 0.0 +14-15 0.0 0.0 0.0 0.0 +16-17 0.0 0.0 0.0 0.0 +18-19 0.0 0.0 0.0 0.0 +20-21 0.0 0.0 0.0 0.0 +22-23 0.0 0.0 0.0 0.0 +24-25 0.0 0.0 0.0 0.0 +26-27 0.0 0.0 0.0 0.0 +28-29 0.0 0.0 0.0 0.0 +30-31 0.0 0.0 0.0 0.0 +32-33 0.0 0.0 0.0 0.0 +34-35 0.0 0.0 0.0 0.0 +36-37 0.0 0.0 0.0 0.0 +38-39 0.0 0.0 0.0 0.0 +40-41 0.0 0.0 0.0 0.0 +42-43 0.0 0.0 0.0 0.0 +44-45 0.0 0.0 0.0 0.0 +46-47 0.0 0.0 0.0 0.0 +48-49 0.0 0.0 0.0 0.0 +50-51 0.0 0.0 0.0 0.0 +52-53 0.0 0.0 0.0 0.0 +54-55 0.0 0.0 0.0 0.0 +56-57 0.0 0.0 0.0 0.0 +58-59 0.0 0.0 0.0 0.0 +60-61 0.0 0.0 0.0 0.0 +62-63 0.0 0.0 0.0 0.0 +64-65 0.0 0.0 0.0 0.0 +66-67 0.0 0.0 0.0 0.0 +68-69 0.0 0.0 0.0 0.0 +70-71 0.0 0.0 0.0 0.0 +72-73 0.0 0.0 0.0 0.0 +74-75 0.0 0.0 0.0 0.0 +76-77 0.0 0.0 0.0 0.0 +78-79 0.0 0.0 0.0 0.0 +80-81 0.0 0.0 0.0 0.0 +82-83 0.0 0.0 0.0 0.0 +84-85 0.0 0.0 0.0 0.0 +86-87 0.0 0.0 0.0 0.0 +88-89 0.0 0.0 0.0 0.0 +>>END_MODULE +>>Kmer Content warn +#Sequence Count PValue Obs/Exp Max Max Obs/Exp Position +TTAGTGG 50 0.0016122013 38.00672 3 +CCGGGAA 65 0.0058204937 29.246862 1 +CTCGCCA 65 0.0058204937 29.246862 1 +CCCGCTT 70 0.008357804 27.157803 1 +AACAATT 125 0.006013185 19.00336 2 +CTGGGAT 205 3.3062082E-4 16.228443 1 +AGTTCAA 195 0.0044498937 14.615241 5 +GAGTAGT 125 0.0014974214 13.29987 30-31 +AAGTTCA 220 0.009890434 12.954418 4 +CTGAAAT 275 0.003044474 12.097567 1 +CCCAGCT 405 3.2130985E-5 11.734852 1 +AGGGTGT 145 0.0045575905 11.465405 66-67 +CTGAATT 335 0.001024679 11.349529 1 +CTTGAAT 295 0.0051441877 11.277392 1 +GAATGTC 425 6.555659E-4 10.058724 4 +GGTAGTA 190 0.002949709 9.999902 52-53 +CTCTGCC 390 0.0036302158 9.748955 1 +CTCCTTT 535 5.356131E-4 8.883393 1 +CTTTGCT 500 0.0028739348 8.5547085 1 +>>END_MODULE diff -r 000000000000 -r 3bad335ccea9 test-data/fastqc_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_2.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2170 @@ +##FastQC 0.11.4 +>>Basic Statistics pass +#Measure Value +Filename poulet5_2 +File type Conventional base calls +Encoding Sanger / Illumina 1.9 +Total Sequences 267849 +Sequences flagged as poor quality 0 +Sequence length 101 +%GC 48 +>>END_MODULE +>>Per base sequence quality warn +#Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile +1 20.590586487162543 21.0 21.0 21.0 20.0 21.0 +2 20.458478471078855 21.0 19.0 22.0 19.0 22.0 +3 20.178608096352797 21.0 20.0 21.0 18.0 22.0 +4 22.495204387546714 23.0 22.0 24.0 20.0 24.0 +5 24.59397272343746 25.0 24.0 26.0 24.0 26.0 +6 25.77560491172265 26.0 25.0 27.0 25.0 27.0 +7 26.651378201897337 27.0 26.0 28.0 26.0 28.0 +8 27.54968284369178 28.0 27.0 29.0 26.0 29.0 +9 27.089005372429988 28.0 26.0 28.0 26.0 28.0 +10-11 27.058984726469017 28.0 26.0 28.0 25.5 28.0 +12-13 26.954911162632676 27.5 26.0 28.0 25.5 28.0 +14-15 27.066410552214123 28.0 26.0 28.0 26.0 28.0 +16-17 27.04552938409328 28.0 26.0 28.0 25.5 28.0 +18-19 27.025118630273028 28.0 26.0 28.0 25.0 28.0 +20-21 27.019042445557012 28.0 26.0 28.0 25.0 28.0 +22-23 27.010315513591614 28.0 26.0 28.0 25.0 28.0 +24-25 27.03931879529138 28.0 26.0 28.0 25.5 28.0 +26-27 26.978450544896567 28.0 26.0 28.0 25.0 28.0 +28-29 27.003714779595967 28.0 26.0 28.0 25.0 28.0 +30-31 27.025971722873706 28.0 26.0 28.0 25.0 28.0 +32-33 27.017791740868923 28.0 26.0 28.0 25.0 28.0 +34-35 27.00628899118533 28.0 26.0 28.0 25.0 28.0 +36-37 27.00906294218011 28.0 26.0 28.0 25.0 28.0 +38-39 27.034922661648913 28.0 26.0 28.0 25.5 28.0 +40-41 27.005346295860726 28.0 26.0 28.0 25.0 28.0 +42-43 27.000909094303132 28.0 26.0 28.0 25.0 28.0 +44-45 27.004913216028434 28.0 26.0 28.0 25.0 28.0 +46-47 26.979999925331065 28.0 26.0 28.0 25.0 28.0 +48-49 26.941037674211962 27.5 26.0 28.0 25.0 28.0 +50-51 26.99995146519121 27.5 26.0 28.0 25.5 28.0 +52-53 26.95084543903468 27.5 26.0 28.0 25.0 28.0 +54-55 26.97609847339359 28.0 26.0 28.0 25.0 28.0 +56-57 26.99262270906369 27.5 26.0 28.0 25.0 28.0 +58-59 26.942271578389317 27.0 26.0 28.0 25.0 28.0 +60-61 26.88024222603034 27.0 26.0 28.0 25.0 28.0 +62-63 26.866450873439888 27.0 26.0 28.0 25.0 28.0 +64-65 26.947610407356386 28.0 26.0 28.0 25.0 28.0 +66-67 26.975012040366025 28.0 26.5 28.0 25.0 28.5 +68-69 26.966286975124042 28.0 26.5 28.0 25.0 29.0 +70-71 26.917634562757375 28.0 26.0 28.0 25.0 29.0 +72-73 26.885127441207544 28.0 26.0 28.0 25.0 29.0 +74-75 26.846286527110426 28.0 26.5 28.0 25.0 29.0 +76-77 26.769134848366058 28.0 26.0 28.0 25.0 29.0 +78-79 26.709703975000842 28.0 26.5 28.0 25.0 29.0 +80-81 26.551336760637525 27.5 26.0 28.0 25.0 28.5 +82-83 26.42626069165836 27.5 26.0 28.0 25.0 28.5 +84-85 26.309463541024982 27.5 26.0 28.0 25.0 29.0 +86-87 26.127226534353312 27.5 26.0 28.0 25.0 29.0 +88-89 25.91885539987082 27.5 26.0 28.0 24.0 29.0 +90-91 25.674260497519125 27.0 26.0 28.0 23.5 29.0 +92-93 25.371903572535274 27.0 26.0 28.0 22.0 29.0 +94-95 24.758753999454918 27.0 26.0 28.0 20.5 28.5 +96-97 23.84710415196622 26.5 25.0 27.5 7.0 28.0 +98-99 22.40618968149965 25.5 24.0 26.5 2.0 27.0 +100-101 23.009550156991438 27.0 25.0 28.0 2.0 29.0 +>>END_MODULE +>>Per tile sequence quality pass +#Tile Base Mean +1101 1 -0.1408369887985721 +1101 2 -0.019030947201084558 +1101 3 -0.060059442415557385 +1101 4 0.004085939732711097 +1101 5 -0.018429270835582656 +1101 6 -0.10404524639907464 +1101 7 0.05541229462318498 +1101 8 0.06703529503928962 +1101 9 0.0644374620344621 +1101 10-11 0.06977859906234585 +1101 12-13 0.048103685880093394 +1101 14-15 0.0848396420659725 +1101 16-17 0.030233298636137107 +1101 18-19 0.05253119669850648 +1101 20-21 0.08961672433820667 +1101 22-23 0.014190195653434046 +1101 24-25 -0.013817302849609803 +1101 26-27 0.046003756870838686 +1101 28-29 0.04599618351544166 +1101 30-31 0.04851104267937956 +1101 32-33 0.04656194043190354 +1101 34-35 0.057517795385400916 +1101 36-37 -0.00326392946157128 +1101 38-39 0.0753296536157606 +1101 40-41 0.005995075411309614 +1101 42-43 -0.013913414669129764 +1101 44-45 -0.03438241660346364 +1101 46-47 -0.028176852907705552 +1101 48-49 0.024338955929199102 +1101 50-51 0.028402595301869837 +1101 52-53 -0.014925605805846232 +1101 54-55 -0.039593664804112194 +1101 56-57 -0.02319294555917395 +1101 58-59 -0.05831481380350212 +1101 60-61 -0.007231705782142939 +1101 62-63 0.1346543703300931 +1101 64-65 0.019757339374642413 +1101 66-67 0.032473131921936016 +1101 68-69 0.06580901615117085 +1101 70-71 -5.192806625906599E-4 +1101 72-73 0.007598890765713406 +1101 74-75 0.018862762851210135 +1101 76-77 0.032333821260792206 +1101 78-79 0.012622327563921232 +1101 80-81 0.07758176267470418 +1101 82-83 0.0989714754431752 +1101 84-85 0.0737115932200112 +1101 86-87 0.1197152444492886 +1101 88-89 0.2945766871252822 +1101 90-91 0.39366183935213783 +1101 92-93 0.38892187749654283 +1101 94-95 0.4587836546800368 +1101 96-97 0.2815282150812948 +1101 98-99 0.27882391282161123 +1101 100-101 0.2642351714779956 +1102 1 -0.07975744334402535 +1102 2 -0.03332450286213273 +1102 3 -0.06284472012740139 +1102 4 0.0368379869674591 +1102 5 0.022244684777994905 +1102 6 0.04829943079057486 +1102 7 0.0964534173385907 +1102 8 0.12806291787337543 +1102 9 0.017503121896794482 +1102 10-11 0.09683028432225882 +1102 12-13 0.0801659040144358 +1102 14-15 0.09997323155090498 +1102 16-17 0.06881366001757883 +1102 18-19 0.10386227016159566 +1102 20-21 0.034994127613781956 +1102 22-23 0.08425050006833601 +1102 24-25 0.08546060185013005 +1102 26-27 0.1378511637068236 +1102 28-29 0.10893752578935434 +1102 30-31 0.10323748464472615 +1102 32-33 0.009366800389180696 +1102 34-35 0.06916329740296234 +1102 36-37 0.07905938527851575 +1102 38-39 0.0742726574135304 +1102 40-41 0.05207269231138412 +1102 42-43 0.08908437491074395 +1102 44-45 0.14235105716819518 +1102 46-47 0.04198358798952029 +1102 48-49 0.10279588982428223 +1102 50-51 0.12128845454706294 +1102 52-53 0.10804941199619833 +1102 54-55 0.0783485675718687 +1102 56-57 0.06077705800123567 +1102 58-59 0.12424141097693919 +1102 60-61 0.18279210444809735 +1102 62-63 0.061083725896200036 +1102 64-65 0.1318323156385901 +1102 66-67 0.1546303684517234 +1102 68-69 0.06580901615117085 +1102 70-71 -0.014914827185258162 +1102 72-73 0.020401525467825365 +1102 74-75 0.10567182112322726 +1102 76-77 0.3096377021057961 +1102 78-79 0.12471399324158483 +1102 80-81 0.06436931014681235 +1102 82-83 0.158391351422285 +1102 84-85 0.09494238185043713 +1102 86-87 0.14155983262873306 +1102 88-89 0.19229839671464788 +1102 90-91 0.0736534575576897 +1102 92-93 0.2624179758824887 +1102 94-95 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0.16223498728917818 +2208 84-85 0.29698166748188015 +2208 86-87 0.34962135142227524 +2208 88-89 0.4342264392117947 +2208 90-91 0.3797608757426971 +2208 92-93 0.4508154149191341 +2208 94-95 0.48645938159379654 +2208 96-97 0.5017912165171694 +2208 98-99 0.6138457594966518 +2208 100-101 0.5558034486475201 +>>END_MODULE +>>Per sequence quality scores warn +#Quality Count +2 308.0 +3 0.0 +4 0.0 +5 2.0 +6 2.0 +7 5.0 +8 11.0 +9 19.0 +10 24.0 +11 37.0 +12 67.0 +13 75.0 +14 135.0 +15 215.0 +16 364.0 +17 551.0 +18 904.0 +19 1284.0 +20 1843.0 +21 2574.0 +22 3707.0 +23 5673.0 +24 9154.0 +25 18567.0 +26 152994.0 +27 69334.0 +>>END_MODULE +>>Per base sequence content fail +#Base G A T C +1 24.259742395586485 12.979270544437881 10.183447832489852 52.57753922748578 +2 18.617901052497956 21.439745518763136 40.641206097693015 19.30114733104589 +3 24.37754107724875 22.73930460819342 24.34692681324179 28.53622750131604 +4 24.41562223491594 30.088221348595663 20.10050438866675 25.395652027821647 +5 26.98610037745147 30.530261453281515 22.40926790841108 20.074370260855932 +6 21.71820690015643 32.48808097099485 23.803336954776757 21.990375174071957 +7 20.013888422208034 18.00865412975221 38.0975848332456 23.879872614794156 +8 20.609746536294704 21.85895784565184 29.885495185720313 27.645800432333147 +9 20.915142486998274 20.74116386471482 31.829127605479208 26.5145660428077 +10-11 24.97414588070144 29.204327811565474 22.19142128587376 23.630105021859332 +12-13 22.91160317940332 24.228949893410093 27.574118253194897 25.285328673991692 +14-15 23.741361737396815 25.36261102337511 26.722705703586726 24.17332153564135 +16-17 24.579147206075064 25.610138548211864 25.582884386352013 24.22782985936106 +18-19 24.019316853899024 25.60957853118735 25.727182106336034 24.643922508577596 +20-21 23.88827287016192 25.856546038999582 26.02679121445292 24.228389876385574 +22-23 23.961261755690707 26.122927470328435 25.75256954478083 24.163241229200032 +24-25 23.863818793424656 26.03985827835833 25.928974907503854 24.167348020713163 +26-27 23.84141811244395 26.16418205780122 26.033138074064116 23.961261755690707 +28-29 23.890326265918485 25.823318362211545 25.908814294621223 24.37754107724875 +30-31 23.84515155927407 25.788223962008445 25.969856150293637 24.39676832842385 +32-33 23.917393755436834 26.149621615163767 26.046018465628023 23.88696616377138 +34-35 24.097159220306963 26.049191895433623 25.611445254602405 24.24220362965701 +36-37 23.718027694708585 25.954922362973164 25.862706226269278 24.464343716048965 +38-39 23.9228072533405 25.979376439710432 26.10724699364194 23.990569313307127 +40-41 23.882672699916743 25.983296558882056 26.044338414554467 24.08969232664673 +42-43 23.787283133407257 26.000097069617585 25.91497448189092 24.297645315084246 +44-45 23.768055882232154 26.142154721503534 26.11620726603422 23.973582130230092 +46-47 23.956034930128542 26.0038305164477 25.79867761313277 24.241456940290984 +48-49 23.8716590317679 25.95436234594865 25.834892047384905 24.339086574898545 +50-51 23.940727798125064 26.11900735115681 25.965562686439004 23.974702164279126 +52-53 23.85952532957002 26.227277309230203 25.698807910427146 24.214389450772636 +54-55 23.936621006611936 25.95342898424112 25.899480677545935 24.210469331601015 +56-57 24.102199373527622 25.939801903311192 26.084286295636723 23.873712427524463 +58-59 24.02267695604613 26.216823658105877 25.769370055516355 23.991129330331642 +60-61 23.884726095673308 26.040978312407365 25.961455894925873 24.112839696993454 +62-63 23.794563354725984 26.08801974246684 26.275252100997204 23.842164801809975 +64-65 23.963688496130285 26.01055072074191 25.83302532396985 24.19273545915796 +66-67 23.792323286627916 25.963135945999426 25.901534073302496 24.343006694070166 +68-69 23.88509944035632 26.06225895933903 26.086713036076297 23.965928564228353 +70-71 23.78392303126015 26.232877479475373 25.739315808533913 24.243883680730562 +72-73 23.80445698882579 26.11751397242476 25.980869818442482 24.097159220306963 +74-75 23.956781619494567 26.278238858461293 26.054418720995788 23.710560801048352 +76-77 23.885659457380836 26.073085955146368 25.85971946880519 24.181535118667608 +78-79 23.94035445344205 26.194236304783665 25.794384149278137 24.071025092496146 +80-81 23.81640401868217 26.158021870531527 26.12890098525662 23.896673125529684 +82-83 23.995467587087475 25.704269391092353 26.116256017860845 24.18400700395933 +84-85 23.760588988571918 25.9592158268278 26.086339691393285 24.193855493206993 +86-87 23.802261352966323 26.35799715137475 26.019186219075337 23.82055527658359 +88-89 24.123840280759396 26.200414418786984 25.7484739308182 23.927271369635424 +90-91 24.09603918625793 25.911801052085316 25.786170566251883 24.20598919540487 +92-93 23.827497890578915 26.454007153364245 25.948866139498072 23.769628816558768 +94-95 24.156707697247327 25.997670329178007 25.765076591661717 24.080545381912945 +96-97 24.214576123114142 26.079246142416064 25.670433714518254 24.03574401995154 +98-99 24.170334778177256 26.024551146354852 25.918147911696515 23.88696616377138 +100-101 24.662260557858183 25.864978902953588 25.310294611851685 24.162465927336545 +>>END_MODULE +>>Per sequence GC content pass +#GC Content Count +0 0.0 +1 0.0 +2 0.0 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +10 0.0 +11 0.0 +12 0.0 +13 0.0 +14 0.5 +15 2.5 +16 5.0 +17 6.0 +18 9.5 +19 18.0 +20 26.0 +21 35.5 +22 46.0 +23 71.0 +24 130.0 +25 233.5 +26 389.5 +27 542.5 +28 724.5 +29 1063.0 +30 1433.0 +31 1683.5 +32 1996.0 +33 2367.5 +34 2840.5 +35 3318.0 +36 3924.5 +37 4721.0 +38 5510.0 +39 6259.0 +40 7364.0 +41 8736.0 +42 9608.5 +43 10256.0 +44 10928.5 +45 11153.5 +46 11271.5 +47 12042.0 +48 12804.5 +49 12874.0 +50 12482.5 +51 11758.0 +52 10827.0 +53 10433.0 +54 10615.0 +55 9955.0 +56 8760.0 +57 7986.5 +58 6982.5 +59 5802.5 +60 4913.5 +61 4177.5 +62 3751.5 +63 3282.0 +64 2533.0 +65 1954.0 +66 1513.0 +67 1247.5 +68 1102.0 +69 957.0 +70 777.0 +71 535.5 +72 361.5 +73 253.0 +74 157.0 +75 99.0 +76 60.0 +77 46.5 +78 37.0 +79 21.5 +80 13.5 +81 16.5 +82 19.5 +83 14.0 +84 6.5 +85 3.0 +86 0.5 +87 0.0 +88 0.0 +89 0.0 +90 0.0 +91 0.0 +92 0.0 +93 0.0 +94 0.0 +95 0.0 +96 0.0 +97 0.0 +98 0.0 +99 0.0 +100 0.0 +>>END_MODULE +>>Per base N content pass +#Base N-Count +1 0.11461681768459094 +2 0.003733446830116969 +3 0.0 +4 0.0 +5 0.0 +6 0.0 +7 0.0 +8 0.0 +9 0.0 +10-11 0.0 +12-13 0.0 +14-15 0.0 +16-17 0.0 +18-19 0.0 +20-21 0.0 +22-23 0.0 +24-25 0.0 +26-27 0.0 +28-29 0.0 +30-31 0.0 +32-33 0.0 +34-35 0.0 +36-37 0.0 +38-39 0.0 +40-41 0.0 +42-43 0.0 +44-45 0.0 +46-47 0.0 +48-49 0.0 +50-51 0.0 +52-53 0.0 +54-55 0.0 +56-57 0.0 +58-59 0.0 +60-61 0.0 +62-63 0.0 +64-65 0.0 +66-67 0.0 +68-69 0.0 +70-71 0.0 +72-73 0.0 +74-75 0.0 +76-77 0.0 +78-79 0.0 +80-81 0.0 +82-83 1.8667234150584845E-4 +84-85 0.0 +86-87 1.8667234150584845E-4 +88-89 0.0014933787320467876 +90-91 0.0 +92-93 0.0011200340490350907 +94-95 0.0 +96-97 0.0 +98-99 0.0 +100-101 0.01456044263745618 +>>END_MODULE +>>Sequence Length Distribution pass +#Length Count +101 267849.0 +>>END_MODULE +>>Sequence Duplication Levels warn +#Total Deduplicated Percentage 63.826611251945884 +#Duplication Level Percentage of deduplicated Percentage of total +1 81.66283073871745 52.122617512935754 +2 9.894108596885154 12.630148461958491 +3 3.18062640137576 6.090258145748586 +4 1.5566170090070461 3.974143548082379 +5 0.8538567368205473 2.7249391002950074 +6 0.5533319107768025 2.119038045746843 +7 0.3960736941041749 1.7696029190496514 +8 0.2698969625036296 1.3781286803040145 +9 0.23212846037984958 1.3334375701059644 +>10 1.3969694370078172 15.730893862039416 +>50 0.0035600524217624095 0.12679215373389083 +>100 0.0 0.0 +>500 0.0 0.0 +>1k 0.0 0.0 +>5k 0.0 0.0 +>10k+ 0.0 0.0 +>>END_MODULE +>>Overrepresented sequences pass +>>END_MODULE +>>Adapter Content pass +#Position Illumina Universal Adapter Illumina Small RNA Adapter Nextera Transposase Sequence SOLID Small RNA Adapter +1 0.0 0.0 0.0 0.0 +2 0.0 0.0 0.0 0.0 +3 0.0 0.0 0.0 0.0 +4 0.0 0.0 0.0 0.0 +5 0.0 0.0 0.0 0.0 +6 0.0 0.0 0.0 0.0 +7 0.0 0.0 0.0 0.0 +8 0.0 0.0 0.0 0.0 +9 0.0 0.0 0.0 0.0 +10-11 0.0 0.0 0.0 0.0 +12-13 0.0 0.0 0.0 0.0 +14-15 0.0 0.0 0.0 0.0 +16-17 0.0 0.0 0.0 0.0 +18-19 0.0 0.0 0.0 0.0 +20-21 0.0 0.0 0.0 0.0 +22-23 0.0 0.0 0.0 0.0 +24-25 0.0 0.0 0.0 0.0 +26-27 0.0 0.0 0.0 0.0 +28-29 0.0 0.0 0.0 0.0 +30-31 0.0 0.0 0.0 0.0 +32-33 0.0 0.0 0.0 0.0 +34-35 0.0 0.0 0.0 0.0 +36-37 0.0 0.0 0.0 0.0 +38-39 0.0 0.0 0.0 0.0 +40-41 0.0 0.0 0.0 0.0 +42-43 0.0 0.0 0.0 0.0 +44-45 0.0 0.0 0.0 0.0 +46-47 0.0 0.0 0.0 0.0 +48-49 0.0 0.0 0.0 0.0 +50-51 0.0 0.0 0.0 0.0 +52-53 0.0 0.0 0.0 0.0 +54-55 0.0 0.0 0.0 0.0 +56-57 0.0 0.0 0.0 0.0 +58-59 0.0 0.0 0.0 0.0 +60-61 0.0 0.0 0.0 0.0 +62-63 0.0 0.0 0.0 0.0 +64-65 0.0 0.0 0.0 0.0 +66-67 0.0 0.0 0.0 0.0 +68-69 0.0 0.0 0.0 0.0 +70-71 0.0 0.0 0.0 0.0 +72-73 0.0 0.0 0.0 0.0 +74-75 0.0 0.0 0.0 0.0 +76-77 0.0 0.0 0.0 0.0 +78-79 0.0 0.0 0.0 0.0 +80-81 0.0 0.0 0.0 0.0 +82-83 0.0 0.0 0.0 0.0 +84-85 0.0 0.0 0.0 0.0 +86-87 0.0 0.0 0.0 0.0 +88-89 0.0 0.0 0.0 0.0 +>>END_MODULE +>>Kmer Content warn +#Sequence Count PValue Obs/Exp Max Max Obs/Exp Position +TACGAGG 60 0.0039460836 31.665857 9 +CCCAGAT 105 6.861368E-5 27.157375 1 +AATCAAC 70 0.008381328 27.142164 5 +CTTGTAT 120 0.004739449 19.802252 1 +TCGCTCA 130 0.007549489 18.268764 2 +CCCCACT 195 0.0044338168 14.623201 1 +TTCAACA 295 0.005166332 11.270898 2 +CTTGAAG 305 0.006593838 10.90747 1 +>>END_MODULE diff -r 000000000000 -r 3bad335ccea9 test-data/fastqc_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fastqc_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,3 @@ +Sample adapter_content Sequences flagged as poor quality sequence_duplication_levels avg_sequence_length Encoding kmer_content per_base_sequence_quality sequence_length_distribution Sequence length File type basic_statistics per_sequence_gc_content Total Sequences per_base_n_content per_base_sequence_content overrepresented_sequences %GC total_deduplicated_percentage Filename per_tile_sequence_quality per_sequence_quality_scores +poulet5_1 pass 0.0 warn 101.0 Sanger / Illumina 1.9 warn warn pass 101.0 Conventional base calls pass pass 267849.0 pass fail pass 48.0 63.6940884007 poulet5_1 pass warn +poulet5_2 pass 0.0 warn 101.0 Sanger / Illumina 1.9 warn warn pass 101.0 Conventional base calls pass pass 267849.0 pass fail pass 48.0 63.8266112519 poulet5_2 pass warn diff -r 000000000000 -r 3bad335ccea9 test-data/featureCounts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featureCounts.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,12 @@ +Status 70: TopHat on data 1, data 4, and data 3: accepted_hits 75: TopHat on data 1, data 6, and data 5: accepted_hits 80: TopHat on data 1, data 8, and data 7: accepted_hits 85: TopHat on data 1, data 10, and data 9: accepted_hits 90: TopHat on data 1, data 12, and data 11: accepted_hits 95: TopHat on data 1, data 14, and data 13: accepted_hits +Assigned 321797 445012 394981 437485 388170 453929 +Unassigned_Ambiguity 2333 3424 3121 3692 2782 3554 +Unassigned_MultiMapping 19123 25293 22580 19907 21164 23533 +Unassigned_NoFeatures 111117 165786 129664 146327 132063 160805 +Unassigned_Unmapped 0 0 0 0 0 0 +Unassigned_MappingQuality 0 0 0 0 0 0 +Unassigned_FragmentLength 0 0 0 0 0 0 +Unassigned_Chimera 0 0 0 0 0 0 +Unassigned_Secondary 0 0 0 0 0 0 +Unassigned_Nonjunction 0 0 0 0 0 0 +Unassigned_Duplicate 0 0 0 0 0 0 diff -r 000000000000 -r 3bad335ccea9 test-data/featureCounts_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/featureCounts_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,7 @@ +Sample Unassigned_Ambiguity Unassigned_MappingQuality percent_assigned Unassigned_Nonjunction Unassigned_Duplicate Unassigned_Chimera Unassigned_Unmapped Assigned Unassigned_MultiMapping Unassigned_Secondary Unassigned_NoFeatures Unassigned_FragmentLength Total +70: TopHat on data 1, data 4, and data 3: accepted_hits 2333 0 70.8226775535 0 0 0 0 321797 19123 0 111117 0 454370 +75: TopHat on data 1, data 6, and data 5: accepted_hits 3424 0 69.585858033 0 0 0 0 445012 25293 0 165786 0 639515 +80: TopHat on data 1, data 8, and data 7: accepted_hits 3121 0 71.7695776839 0 0 0 0 394981 22580 0 129664 0 550346 +85: TopHat on data 1, data 10, and data 9: accepted_hits 3692 0 72.0245435134 0 0 0 0 437485 19907 0 146327 0 607411 +90: TopHat on data 1, data 12, and data 11: accepted_hits 2782 0 71.3313082644 0 0 0 0 388170 21164 0 132063 0 544179 +95: TopHat on data 1, data 14, and data 13: accepted_hits 3554 0 70.7251710368 0 0 0 0 453929 23533 0 160805 0 641821 diff -r 000000000000 -r 3bad335ccea9 test-data/flexbar.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flexbar.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,71 @@ + + ________ __ + / ____/ /__ _ __/ /_ ____ ______ + / /_ / / _ \| |/ / __ \/ __ `/ ___/ + / __/ / / __/> 10kbp_of_uniques Trans_of_uniques +Sample-1.A007.C8DRAANXX.s_2.r_1_2.filt.bam 7029431 6978457 876396 4591811 1510250 +Sample-1.A002.C8DRAANXX.s_2.r_1_2.filt.bam 8935388 8864466 1159324 5742469 1962673 +Sample-1.A005.C8DRAANXX.s_2.r_1_2.filt.bam 11314841 11219537 1495237 7243835 2480465 +Sample-1.A019.C8DRAANXX.s_2.r_1_2.filt.bam 11766363 11658185 1811982 7779338 2066865 +Sample-1.A012.C8DRAANXX.s_2.r_1_2.filt.bam 11705308 11609411 1261011 7003201 3345199 +Sample-1.A006.C8DRAANXX.s_2.r_1_2.filt.bam 13106391 12998003 2043926 8107586 2846491 diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_filter.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_filter.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,7 @@ +File Total_pairs Valid_pairs Cis_<10kbp Cis_>10kbp Trans Invalid_pairs Same_circularised Same_dangling_ends Same_internal Re-ligation Contiguous_sequence Wrong_size +Sample-1.A002.C8DRAANXX.s_2.r_1_2.pair.bam 14383198 8935388 1169666 5787588 1978134 5447810 136087 530246 2442480 834795 48328 1455874 +Sample-1.A007.C8DRAANXX.s_2.r_1_2.pair.bam 14621513 7029431 882929 4625450 1521052 7592082 157241 452563 4031859 771757 37367 2141295 +Sample-1.A005.C8DRAANXX.s_2.r_1_2.pair.bam 15245021 11314841 1509270 7304795 2500776 3930180 187236 298334 1580105 924315 59919 880271 +Sample-1.A019.C8DRAANXX.s_2.r_1_2.pair.bam 16053923 11766363 1830414 7850293 2085656 4287560 223187 305385 1541376 1070842 72067 1074703 +Sample-1.A006.C8DRAANXX.s_2.r_1_2.pair.bam 18473566 13106391 2063334 8173491 2869566 5367175 220527 408217 2075370 961388 65086 1636587 +Sample-1.A012.C8DRAANXX.s_2.r_1_2.pair.bam 19070455 11705308 1272882 7060212 3372214 7365147 163868 663463 3810160 976378 55368 1695910 diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_mapper.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_mapper.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,13 @@ +File Total_reads_processed Reads_too_short_to_map %Reads_too_short_to_map Unique_alignments %Unique_alignments Multiple_alignments %Multiple_alignments Failed_to_align %failed_to_align Paired %Paired +Sample-1.A006.C8DRAANXX.s_2.r_1.trunc.fastq.gz 34760244 579570 1.7 25926210 74.6 5230796 15.0 3023668 8.7 18473566 53.1 +Sample-1.A006.C8DRAANXX.s_2.r_2.trunc.fastq.gz 34760244 539500 1.6 25637256 73.8 5121683 14.7 3461805 10.0 18473566 53.1 +Sample-1.A005.C8DRAANXX.s_2.r_1.trunc.fastq.gz 26780491 431302 1.6 20379141 76.1 4263954 15.9 1706094 6.4 15245021 56.9 +Sample-1.A005.C8DRAANXX.s_2.r_2.trunc.fastq.gz 26780491 407260 1.5 20071745 74.9 4167422 15.6 2134064 8.0 15245021 56.9 +Sample-1.A012.C8DRAANXX.s_2.r_1.trunc.fastq.gz 35472550 526747 1.5 26504291 74.7 5362349 15.1 3079163 8.7 19070455 53.8 +Sample-1.A012.C8DRAANXX.s_2.r_2.trunc.fastq.gz 35472550 494718 1.4 26142222 73.7 5264577 14.8 3571033 10.1 19070455 53.8 +Sample-1.A002.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28754600 751623 2.6 21072845 73.3 4475271 15.6 2454861 8.5 14383198 50.0 +Sample-1.A002.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28754600 698375 2.4 20505141 71.3 4336149 15.1 3214935 11.2 14383198 50.0 +Sample-1.A007.C8DRAANXX.s_2.r_1.trunc.fastq.gz 31000250 368533 1.2 22327487 72.0 4263821 13.8 4040409 13.0 14621513 47.2 +Sample-1.A007.C8DRAANXX.s_2.r_2.trunc.fastq.gz 31000250 338254 1.1 21828226 70.4 4140992 13.4 4692778 15.1 14621513 47.2 +Sample-1.A019.C8DRAANXX.s_2.r_1.trunc.fastq.gz 28583413 519100 1.8 21667602 75.8 4404215 15.4 1992496 7.0 16053923 56.2 +Sample-1.A019.C8DRAANXX.s_2.r_2.trunc.fastq.gz 28583413 488517 1.7 21491634 75.2 4342639 15.2 2260623 7.9 16053923 56.2 diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_truncater.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_truncater.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,13 @@ +File Total_Reads_Processed Truncated %Truncated Not_truncated %Not_truncated Average_length_truncated_sequence +Sample-1.A002.C8DRAANXX.s_2.r_1.fq 28754600 7548969 26.25 21205631 73.75 58.69 +Sample-1.A002.C8DRAANXX.s_2.r_2.fq 28754600 7446167 25.90 21308433 74.10 59.65 +Sample-1.A006.C8DRAANXX.s_2.r_2.fq 34760244 10523907 30.28 24236337 69.72 66.68 +Sample-1.A012.C8DRAANXX.s_2.r_2.fq 35472550 9050477 25.51 26422073 74.49 66.30 +Sample-1.A006.C8DRAANXX.s_2.r_1.fq 34760244 10420308 29.98 24339936 70.02 65.67 +Sample-1.A012.C8DRAANXX.s_2.r_1.fq 35472550 8999621 25.37 26472929 74.63 65.39 +Sample-1.A005.C8DRAANXX.s_2.r_2.fq 26780491 8436781 31.50 18343710 68.50 67.02 +Sample-1.A005.C8DRAANXX.s_2.r_1.fq 26780491 8361813 31.22 18418678 68.78 66.22 +Sample-1.A019.C8DRAANXX.s_2.r_2.fq 28583413 9321837 32.61 19261576 67.39 66.38 +Sample-1.A019.C8DRAANXX.s_2.r_1.fq 28583413 9151107 32.02 19432306 67.98 65.11 +Sample-1.A007.C8DRAANXX.s_2.r_1.fq 31000250 6212988 20.04 24787262 79.96 65.01 +Sample-1.A007.C8DRAANXX.s_2.r_2.fq 31000250 6187239 19.96 24813011 80.04 65.94 diff -r 000000000000 -r 3bad335ccea9 test-data/hisat2_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat2_1.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,6 @@ +HISAT2 summary stats: + Total reads: 99978 + Aligned 0 time: 3849 (3.85%) + Aligned 1 time: 86176 (86.19%) + Aligned >1 times: 9953 (9.96%) + Overall alignment rate: 96.15% diff -r 000000000000 -r 3bad335ccea9 test-data/hisat2_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat2_2.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,6 @@ +HISAT2 summary stats: + Total reads: 99978 + Aligned 0 time: 3849 (3.85%) + Aligned 1 time: 86176 (86.19%) + Aligned >1 times: 9953 (9.96%) + Overall alignment rate: 96.15% diff -r 000000000000 -r 3bad335ccea9 test-data/hisat2_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hisat2_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,3 @@ +Sample overall_alignment_rate unpaired_aligned_none unpaired_aligned_multi unpaired_total unpaired_aligned_one +hisat2_1 96.15 3849 9953 99978 86176 +hisat2_2 96.15 3849 9953 99978 86176 diff -r 000000000000 -r 3bad335ccea9 test-data/htseq.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,5 @@ +__no_feature 19 +__ambiguous 0 +__too_low_aQual 0 +__not_aligned 1336 +__alignment_not_unique 0 diff -r 000000000000 -r 3bad335ccea9 test-data/htseq_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/htseq_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample ambiguous percent_assigned too_low_aQual total_count no_feature alignment_not_unique assigned not_aligned +htseq 0 0.0 0 1355 19 0 0 1336 diff -r 000000000000 -r 3bad335ccea9 test-data/kallisto_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_1.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,489 @@ + +-------------------------------------------------------------------------------- +Module: fastqc +Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run +Job ID: cf_fastq_kallisto_1463255307_fastqc_732 +Previous Job ID: start_000 +Date & Time: 20:48, 14-05-2016 +-------------------------------------------------------------------------------- + +---------- FastQC version information ---------- +FastQC v0.11.5 + +------- End of FastQC version information ------ + +###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz + +###CF FastQC successfully ran, took 12 minutes + +###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz + +###CF FastQC successfully ran, took 11 minutes, 16 seconds + + + + +-------------------------------------------------------------------------------- +Module: trim_galore +Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run +Job ID: cf_fastq_kallisto_1463255307_trim_galore_659 +Previous Job ID: start_000 +Date & Time: 20:48, 14-05-2016 +-------------------------------------------------------------------------------- + +---------- Cutadapt version information ---------- +1.8.1 + +------- End of Cutadapt version information ------ +---------- Trim Galore! version information ---------- + + Quality-/Adapter-/RRBS-Trimming + (powered by Cutadapt) + version 0.4.1 + + Last update: 20 07 2015 + + +------- End of Trim Galore! version information ------ + +###CFCMD trim_galore --paired --gzip --phred33 --fastqc HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz + +Path to Cutadapt set as: 'cutadapt' (default) +1.8.1 +Cutadapt seems to be working fine (tested command 'cutadapt --version') + + +AUTO-DETECTING ADAPTER TYPE +=========================== +Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz <<) + +Found perfect matches for the following adapter sequences: +Adapter type Count Sequence Sequences analysed Percentage +Illumina 4591 AGATCGGAAGAGC 1000000 0.46 +Nextera 4 CTGTCTCTTATA 1000000 0.00 +smallRNA 2 TGGAATTCTCGG 1000000 0.00 +Using Illumina adapter for trimming (count: 4591). Second best hit was Nextera (count: 4) + +Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_trimming_report.txt' + +SUMMARISING RUN PARAMETERS +========================== +Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.8.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file(s) will be GZIP compressed + +Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz + + + >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz <<< +10000000 sequences processed +20000000 sequences processed +30000000 sequences processed +40000000 sequences processed +50000000 sequences processed +60000000 sequences processed +This is cutadapt 1.8.1 with Python 2.7.5 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1129.68 s (19 us/read; 3.20 M reads/minute). + +=== Summary === + +Total reads processed: 60,339,006 +Reads with adapters: 19,773,783 (32.8%) +Reads written (passing filters): 60,339,006 (100.0%) + +Total basepairs processed: 6,094,239,606 bp +Quality-trimmed: 318,558,927 bp (5.2%) +Total written (filtered): 5,735,844,499 bp (94.1%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19773783 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 29.4% + C: 32.6% + G: 21.6% + T: 16.2% + none/other: 0.2% + +Overview of removed sequences +length count expect max.err error counts +1 13107583 15084751.5 0 13107583 +2 4517008 3771187.9 0 4517008 +3 1168959 942797.0 0 1168959 +4 281663 235699.2 0 281663 +5 104792 58924.8 0 104792 +6 69263 14731.2 0 69263 +7 51851 3682.8 0 51851 +8 51844 920.7 0 51844 +9 41855 230.2 0 41073 782 +10 36637 57.5 1 35344 1293 +11 29587 14.4 1 28680 907 +12 28042 3.6 1 27586 456 +13 22536 0.9 1 22227 309 +14 19927 0.9 1 19661 266 +15 17329 0.9 1 17095 234 +16 15643 0.9 1 15353 290 +17 13807 0.9 1 13539 268 +18 11603 0.9 1 11389 214 +19 8338 0.9 1 8198 140 +20 8131 0.9 1 8001 130 +21 6942 0.9 1 6778 164 +22 5839 0.9 1 5731 108 +23 5474 0.9 1 5341 133 +24 4736 0.9 1 4599 137 +25 4504 0.9 1 4393 111 +26 3852 0.9 1 3728 124 +27 4425 0.9 1 4203 222 +28 3575 0.9 1 3433 142 +29 3316 0.9 1 3165 151 +30 3370 0.9 1 3209 161 +31 2266 0.9 1 2167 99 +32 2158 0.9 1 2035 123 +33 2462 0.9 1 2308 154 +34 2879 0.9 1 2595 284 +35 3667 0.9 1 3330 337 +36 4027 0.9 1 3697 330 +37 2582 0.9 1 2341 241 +38 2056 0.9 1 1830 226 +39 2926 0.9 1 2733 193 +40 1401 0.9 1 1278 123 +41 1847 0.9 1 1733 114 +42 1508 0.9 1 1413 95 +43 1211 0.9 1 1130 81 +44 1112 0.9 1 975 137 +45 1507 0.9 1 1329 178 +46 1640 0.9 1 1514 126 +47 1116 0.9 1 1028 88 +48 1158 0.9 1 1060 98 +49 1375 0.9 1 1274 101 +50 1121 0.9 1 1020 101 +51 1703 0.9 1 1474 229 +52 1994 0.9 1 1755 239 +53 2141 0.9 1 1984 157 +54 919 0.9 1 835 84 +55 822 0.9 1 721 101 +56 1428 0.9 1 1252 176 +57 1649 0.9 1 1438 211 +58 1372 0.9 1 1179 193 +59 1835 0.9 1 1664 171 +60 1510 0.9 1 1296 214 +61 1538 0.9 1 1240 298 +62 2471 0.9 1 1928 543 +63 3805 0.9 1 3104 701 +64 4243 0.9 1 3806 437 +65 2208 0.9 1 1851 357 +66 2382 0.9 1 1899 483 +67 3595 0.9 1 2610 985 +68 6338 0.9 1 4553 1785 +69 10826 0.9 1 7037 3789 +70 15641 0.9 1 13860 1781 +71 6064 0.9 1 5031 1033 +72 2588 0.9 1 2271 317 +73 1010 0.9 1 855 155 +74 466 0.9 1 379 87 +75 232 0.9 1 169 63 +76 133 0.9 1 87 46 +77 123 0.9 1 83 40 +78 109 0.9 1 73 36 +79 67 0.9 1 38 29 +80 62 0.9 1 33 29 +81 63 0.9 1 21 42 +82 77 0.9 1 33 44 +83 59 0.9 1 22 37 +84 67 0.9 1 23 44 +85 62 0.9 1 23 39 +86 72 0.9 1 33 39 +87 73 0.9 1 22 51 +88 79 0.9 1 24 55 +89 54 0.9 1 22 32 +90 66 0.9 1 31 35 +91 62 0.9 1 30 32 +92 85 0.9 1 32 53 +93 70 0.9 1 27 43 +94 61 0.9 1 27 34 +95 56 0.9 1 25 31 +96 79 0.9 1 35 44 +97 78 0.9 1 39 39 +98 125 0.9 1 50 75 +99 87 0.9 1 43 44 +100 137 0.9 1 79 58 +101 547 0.9 1 329 218 + + +RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz +============================================= +60339006 sequences processed in total +The length threshold of paired-end sequences gets evaluated later on (in the validation step) + +Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz_trimming_report.txt' + +SUMMARISING RUN PARAMETERS +========================== +Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.8.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file(s) will be GZIP compressed + +Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz + + + >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz <<< +10000000 sequences processed +20000000 sequences processed +30000000 sequences processed +40000000 sequences processed +50000000 sequences processed +60000000 sequences processed +This is cutadapt 1.8.1 with Python 2.7.5 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1357.49 s (22 us/read; 2.67 M reads/minute). + +=== Summary === + +Total reads processed: 60,339,006 +Reads with adapters: 17,101,385 (28.3%) +Reads written (passing filters): 60,339,006 (100.0%) + +Total basepairs processed: 6,094,239,606 bp +Quality-trimmed: 1,861,214,185 bp (30.5%) +Total written (filtered): 4,202,697,623 bp (69.0%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17101385 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 30.1% + C: 33.1% + G: 21.0% + T: 15.6% + none/other: 0.2% + +Overview of removed sequences +length count expect max.err error counts +1 10224232 15084751.5 0 10224232 +2 5630139 3771187.9 0 5630139 +3 824951 942797.0 0 824951 +4 237457 235699.2 0 237457 +5 42614 58924.8 0 42614 +6 8620 14731.2 0 8620 +7 4051 3682.8 0 4051 +8 2491 920.7 0 2491 +9 2860 230.2 0 1848 1012 +10 4289 57.5 1 2932 1357 +11 1923 14.4 1 1196 727 +12 3234 3.6 1 2884 350 +13 1974 0.9 1 1769 205 +14 3402 0.9 1 3193 209 +15 1303 0.9 1 1215 88 +16 1677 0.9 1 1563 114 +17 3501 0.9 1 3304 197 +18 753 0.9 1 662 91 +19 1959 0.9 1 1820 139 +20 1348 0.9 1 1256 92 +21 807 0.9 1 745 62 +22 1343 0.9 1 1262 81 +23 1485 0.9 1 1358 127 +24 3748 0.9 1 3541 207 +25 1313 0.9 1 1219 94 +26 1605 0.9 1 1405 200 +27 1260 0.9 1 1122 138 +28 2828 0.9 1 2673 155 +29 1187 0.9 1 1064 123 +30 4440 0.9 1 4243 197 +31 383 0.9 1 326 57 +32 1491 0.9 1 1382 109 +33 753 0.9 1 683 70 +34 736 0.9 1 649 87 +35 1840 0.9 1 1717 123 +36 923 0.9 1 835 88 +37 1792 0.9 1 1685 107 +38 875 0.9 1 795 80 +39 2158 0.9 1 2040 118 +40 1496 0.9 1 1370 126 +41 2113 0.9 1 1958 155 +42 4026 0.9 1 3801 225 +43 837 0.9 1 761 76 +44 2041 0.9 1 1906 135 +45 3100 0.9 1 2934 166 +46 687 0.9 1 630 57 +47 1082 0.9 1 1003 79 +48 1398 0.9 1 1297 101 +49 1470 0.9 1 1380 90 +50 2185 0.9 1 2046 139 +51 3600 0.9 1 3427 173 +52 786 0.9 1 712 74 +53 343 0.9 1 290 53 +54 1810 0.9 1 1687 123 +55 1581 0.9 1 1462 119 +56 662 0.9 1 605 57 +57 1454 0.9 1 1336 118 +58 2899 0.9 1 2636 263 +59 1818 0.9 1 1633 185 +60 1593 0.9 1 1376 217 +61 1968 0.9 1 1722 246 +62 2449 0.9 1 2062 387 +63 4233 0.9 1 3609 624 +64 5813 0.9 1 4609 1204 +65 9498 0.9 1 7807 1691 +66 5265 0.9 1 4540 725 +67 755 0.9 1 565 190 +68 303 0.9 1 257 46 +69 106 0.9 1 84 22 +70 86 0.9 1 55 31 +71 51 0.9 1 26 25 +72 40 0.9 1 20 20 +73 54 0.9 1 38 16 +74 32 0.9 1 21 11 +76 1 0.9 1 0 1 +77 2 0.9 1 1 1 +79 3 0.9 1 2 1 + + +RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz +============================================= +60339006 sequences processed in total +The length threshold of paired-end sequences gets evaluated later on (in the validation step) + +Validate paired-end files HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz +file_1: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz, file_2: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz + + +>>>>> Now validing the length of the 2 paired-end infiles: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz <<<<< +Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz + +Total number of sequences analysed: 60339006 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2322959 (3.85%) + + + >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz<<< + +Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz +Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz + + >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz<<< + +Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +Deleting both intermediate output files HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_trimmed.fq.gz + +==================================================================================================== + +###CF Trim galore (PE mode) successfully exited, took 1 hours, 45 minutes, 38 seconds.. + + + + +-------------------------------------------------------------------------------- +Module: kallisto +Run File: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run +Job ID: cf_fastq_kallisto_1463255307_kallisto_017 +Previous Job ID: cf_fastq_kallisto_1463255307_trim_galore_659 +Date & Time: 22:34, 14-05-2016 +-------------------------------------------------------------------------------- + + +Pseudoaligning against /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx + +---------- Kallisto version information ---------- +kallisto 0.42.5 + +------- End of Kallisto version information ------ + +###CFCMD kallisto quant -t 1 --pseudobam -i /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx -o HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz_kallisto_output -b 100 HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz | samtools view -Sb - > HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz_kallisto.bam + + +[quant] fragment length distribution will be estimated from the data +[index] k-mer length: 31 +[index] number of targets: 176,241 +[index] number of k-mers: 104,600,239 +[index] number of equivalence classes: 702,950 +[quant] running in paired-end mode +[quant] will process pair 1: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1.fq.gz + HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2_val_2.fq.gz +[quant] finding pseudoalignments for the reads ... done +[quant] processed 58,016,047 reads, 48,531,088 reads pseudoaligned +[quant] estimated average fragment length: 167.866 +[ em] quantifying the abundances ... done +[ em] the Expectation-Maximization algorithm ran for 1,210 rounds +[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM for the bootstrap: 14 [bstrp] running EM for the bootstrap: 15 [bstrp] running EM for the bootstrap: 16 [bstrp] running EM for the bootstrap: 17 [bstrp] running EM for the bootstrap: 18 [bstrp] running EM for the bootstrap: 19 [bstrp] running EM for the bootstrap: 20 [bstrp] running EM for the bootstrap: 21 [bstrp] running EM 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[bstrp] running EM for the bootstrap: 71 [bstrp] running EM for the bootstrap: 72 [bstrp] running EM for the bootstrap: 73 [bstrp] running EM for the bootstrap: 74 [bstrp] running EM for the bootstrap: 75 [bstrp] running EM for the bootstrap: 76 [bstrp] running EM for the bootstrap: 77 [bstrp] running EM for the bootstrap: 78 [bstrp] running EM for the bootstrap: 79 [bstrp] running EM for the bootstrap: 80 [bstrp] running EM for the bootstrap: 81 [bstrp] running EM for the bootstrap: 82 [bstrp] running EM for the bootstrap: 83 [bstrp] running EM for the bootstrap: 84 [bstrp] running EM for the bootstrap: 85 [bstrp] running EM for the bootstrap: 86 [bstrp] running EM for the bootstrap: 87 [bstrp] running EM for the bootstrap: 88 [bstrp] running EM for the bootstrap: 89 [bstrp] running EM for the bootstrap: 90 [bstrp] running EM for the bootstrap: 91 [bstrp] running EM for the bootstrap: 92 [bstrp] running EM for the bootstrap: 93 [bstrp] running EM for the bootstrap: 94 [bstrp] running EM for the bootstrap: 95 [bstrp] running EM for the bootstrap: 96 [bstrp] running EM for the bootstrap: 97 [bstrp] running EM for the bootstrap: 98 [bstrp] running EM for the bootstrap: 99 [bstrp] running EM for the bootstrap: 100 + +###CF kallisto (PE mode) successfully exited, took 2 hours, 30 minutes, 54 seconds.. + + + + +================================================================================ + + + + + +###CF Run finished at 01:06 15-05-2016 diff -r 000000000000 -r 3bad335ccea9 test-data/kallisto_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_2.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,496 @@ + +-------------------------------------------------------------------------------- +Module: fastqc +Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run +Job ID: cf_fastq_kallisto_1463255307_fastqc_792 +Previous Job ID: start_000 +Date & Time: 20:48, 14-05-2016 +-------------------------------------------------------------------------------- + +---------- FastQC version information ---------- +FastQC v0.11.5 + +------- End of FastQC version information ------ + +###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz + +###CF FastQC successfully ran, took 13 minutes, 29 seconds + +###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz + +###CF FastQC successfully ran, took 12 minutes, 27 seconds + + + + +-------------------------------------------------------------------------------- +Module: trim_galore +Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run +Job ID: cf_fastq_kallisto_1463255307_trim_galore_160 +Previous Job ID: start_000 +Date & Time: 20:48, 14-05-2016 +-------------------------------------------------------------------------------- + +---------- Cutadapt version information ---------- +1.8.1 + +------- End of Cutadapt version information ------ +---------- Trim Galore! version information ---------- + + Quality-/Adapter-/RRBS-Trimming + (powered by Cutadapt) + version 0.4.1 + + Last update: 20 07 2015 + + +------- End of Trim Galore! version information ------ + +###CFCMD trim_galore --paired --gzip --phred33 --fastqc HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz + +Path to Cutadapt set as: 'cutadapt' (default) +1.8.1 +Cutadapt seems to be working fine (tested command 'cutadapt --version') + + +AUTO-DETECTING ADAPTER TYPE +=========================== +Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz <<) + +Found perfect matches for the following adapter sequences: +Adapter type Count Sequence Sequences analysed Percentage +Illumina 7610 AGATCGGAAGAGC 1000000 0.76 +Nextera 8 CTGTCTCTTATA 1000000 0.00 +smallRNA 3 TGGAATTCTCGG 1000000 0.00 +Using Illumina adapter for trimming (count: 7610). Second best hit was Nextera (count: 8) + +Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_trimming_report.txt' + +SUMMARISING RUN PARAMETERS +========================== +Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.8.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file(s) will be GZIP compressed + +Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz + + + >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz <<< +10000000 sequences processed +20000000 sequences processed +30000000 sequences processed +40000000 sequences processed +50000000 sequences processed +60000000 sequences processed +70000000 sequences processed +This is cutadapt 1.8.1 with Python 2.7.5 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1418.14 s (19 us/read; 3.14 M reads/minute). + +=== Summary === + +Total reads processed: 74,203,167 +Reads with adapters: 24,438,848 (32.9%) +Reads written (passing filters): 74,203,167 (100.0%) + +Total basepairs processed: 7,494,519,867 bp +Quality-trimmed: 512,942,133 bp (6.8%) +Total written (filtered): 6,915,434,043 bp (92.3%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24438848 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 29.1% + C: 32.5% + G: 21.5% + T: 15.6% + none/other: 1.2% + +Overview of removed sequences +length count expect max.err error counts +1 15780739 18550791.8 0 15780739 +2 5577733 4637697.9 0 5577733 +3 1416646 1159424.5 0 1416646 +4 357832 289856.1 0 357832 +5 146943 72464.0 0 146943 +6 108165 18116.0 0 108165 +7 80461 4529.0 0 80461 +8 82845 1132.3 0 82845 +9 70563 283.1 0 69432 1131 +10 60090 70.8 1 58009 2081 +11 47646 17.7 1 46210 1436 +12 46325 4.4 1 45426 899 +13 36297 1.1 1 35620 677 +14 33206 1.1 1 32517 689 +15 30200 1.1 1 29537 663 +16 26650 1.1 1 25941 709 +17 23883 1.1 1 23175 708 +18 22814 1.1 1 22206 608 +19 15317 1.1 1 14942 375 +20 14734 1.1 1 14316 418 +21 12981 1.1 1 12572 409 +22 10726 1.1 1 10386 340 +23 10585 1.1 1 10145 440 +24 8211 1.1 1 7813 398 +25 7776 1.1 1 7401 375 +26 6577 1.1 1 6226 351 +27 7824 1.1 1 7188 636 +28 6995 1.1 1 6562 433 +29 5964 1.1 1 5450 514 +30 6235 1.1 1 5759 476 +31 4001 1.1 1 3651 350 +32 4002 1.1 1 3591 411 +33 3627 1.1 1 3171 456 +34 4898 1.1 1 3703 1195 +35 5262 1.1 1 4277 985 +36 5078 1.1 1 3913 1165 +37 5358 1.1 1 4348 1010 +38 4700 1.1 1 3853 847 +39 4403 1.1 1 3314 1089 +40 5420 1.1 1 3916 1504 +41 6469 1.1 1 5586 883 +42 3392 1.1 1 2865 527 +43 2475 1.1 1 2072 403 +44 2456 1.1 1 1563 893 +45 4035 1.1 1 2956 1079 +46 3992 1.1 1 3345 647 +47 2424 1.1 1 1858 566 +48 2639 1.1 1 1947 692 +49 2945 1.1 1 2271 674 +50 2427 1.1 1 1771 656 +51 3773 1.1 1 2342 1431 +52 5065 1.1 1 3343 1722 +53 4906 1.1 1 4300 606 +54 1870 1.1 1 1307 563 +55 1999 1.1 1 1388 611 +56 2968 1.1 1 1945 1023 +57 3724 1.1 1 2617 1107 +58 3918 1.1 1 2489 1429 +59 4730 1.1 1 3582 1148 +60 4028 1.1 1 2633 1395 +61 4988 1.1 1 3106 1882 +62 8736 1.1 1 4240 4496 +63 14165 1.1 1 8720 5445 +64 12661 1.1 1 10106 2555 +65 6864 1.1 1 4432 2432 +66 8136 1.1 1 4501 3635 +67 13203 1.1 1 6497 6706 +68 25197 1.1 1 12465 12732 +69 50150 1.1 1 22596 27554 +70 57190 1.1 1 45540 11650 +71 24203 1.1 1 17833 6370 +72 10860 1.1 1 7925 2935 +73 4677 1.1 1 3765 912 +74 1417 1.1 1 1054 363 +75 588 1.1 1 413 175 +76 488 1.1 1 343 145 +77 560 1.1 1 379 181 +78 531 1.1 1 361 170 +79 280 1.1 1 172 108 +80 252 1.1 1 156 96 +81 202 1.1 1 123 79 +82 186 1.1 1 100 86 +83 165 1.1 1 93 72 +84 176 1.1 1 81 95 +85 196 1.1 1 110 86 +86 217 1.1 1 116 101 +87 235 1.1 1 119 116 +88 256 1.1 1 137 119 +89 249 1.1 1 132 117 +90 276 1.1 1 140 136 +91 278 1.1 1 138 140 +92 347 1.1 1 176 171 +93 314 1.1 1 171 143 +94 333 1.1 1 205 128 +95 361 1.1 1 228 133 +96 461 1.1 1 237 224 +97 505 1.1 1 250 255 +98 640 1.1 1 312 328 +99 628 1.1 1 330 298 +100 1356 1.1 1 726 630 +101 6374 1.1 1 3751 2623 + + +RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz +============================================= +74203167 sequences processed in total +The length threshold of paired-end sequences gets evaluated later on (in the validation step) + +Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz_trimming_report.txt' + +SUMMARISING RUN PARAMETERS +========================== +Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.1 +Cutadapt version: 1.8.1 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Running FastQC on the data once trimming has completed +Output file(s) will be GZIP compressed + +Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz + + + >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz <<< +10000000 sequences processed +20000000 sequences processed +30000000 sequences processed +40000000 sequences processed +50000000 sequences processed +60000000 sequences processed +70000000 sequences processed +This is cutadapt 1.8.1 with Python 2.7.5 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 1721.22 s (23 us/read; 2.59 M reads/minute). + +=== Summary === + +Total reads processed: 74,203,167 +Reads with adapters: 21,064,160 (28.4%) +Reads written (passing filters): 74,203,167 (100.0%) + +Total basepairs processed: 7,494,519,867 bp +Quality-trimmed: 2,366,541,609 bp (31.6%) +Total written (filtered): 5,082,419,690 bp (67.8%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21064160 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 30.1% + C: 33.0% + G: 20.7% + T: 15.2% + none/other: 0.9% + +Overview of removed sequences +length count expect max.err error counts +1 12550241 18550791.8 0 12550241 +2 6853426 4637697.9 0 6853426 +3 1004381 1159424.5 0 1004381 +4 288343 289856.1 0 288343 +5 51798 72464.0 0 51798 +6 12267 18116.0 0 12267 +7 5590 4529.0 0 5590 +8 3548 1132.3 0 3548 +9 4029 283.1 0 2533 1496 +10 5830 70.8 1 4021 1809 +11 2853 17.7 1 1580 1273 +12 4735 4.4 1 4249 486 +13 2911 1.1 1 2430 481 +14 4856 1.1 1 4434 422 +15 1804 1.1 1 1593 211 +16 2368 1.1 1 2059 309 +17 4669 1.1 1 4321 348 +18 1030 1.1 1 866 164 +19 2547 1.1 1 2321 226 +20 1754 1.1 1 1600 154 +21 950 1.1 1 868 82 +22 1594 1.1 1 1455 139 +23 1951 1.1 1 1677 274 +24 4690 1.1 1 4305 385 +25 1690 1.1 1 1476 214 +26 2584 1.1 1 1543 1041 +27 1859 1.1 1 1414 445 +28 3527 1.1 1 3194 333 +29 1791 1.1 1 1440 351 +30 5381 1.1 1 4997 384 +31 567 1.1 1 440 127 +32 1756 1.1 1 1597 159 +33 999 1.1 1 858 141 +34 1029 1.1 1 911 118 +35 2074 1.1 1 1899 175 +36 1288 1.1 1 1109 179 +37 2081 1.1 1 1892 189 +38 1339 1.1 1 1197 142 +39 2811 1.1 1 2570 241 +40 2661 1.1 1 2354 307 +41 3432 1.1 1 3016 416 +42 6993 1.1 1 6439 554 +43 1468 1.1 1 1286 182 +44 2728 1.1 1 2432 296 +45 4923 1.1 1 4561 362 +46 1119 1.1 1 989 130 +47 1665 1.1 1 1489 176 +48 1946 1.1 1 1791 155 +49 1932 1.1 1 1752 180 +50 4384 1.1 1 4019 365 +51 3873 1.1 1 3633 240 +52 1010 1.1 1 918 92 +53 506 1.1 1 432 74 +54 2117 1.1 1 1959 158 +55 2453 1.1 1 2286 167 +56 1117 1.1 1 995 122 +57 2284 1.1 1 2007 277 +58 5593 1.1 1 5183 410 +59 3875 1.1 1 3516 359 +60 4107 1.1 1 3667 440 +61 5724 1.1 1 5107 617 +62 8646 1.1 1 7513 1133 +63 18293 1.1 1 16357 1936 +64 29353 1.1 1 24721 4632 +65 54668 1.1 1 47835 6833 +66 30607 1.1 1 28229 2378 +67 4181 1.1 1 3499 682 +68 1785 1.1 1 1607 178 +69 649 1.1 1 581 68 +70 386 1.1 1 331 55 +71 201 1.1 1 149 52 +72 181 1.1 1 161 20 +73 238 1.1 1 203 35 +74 116 1.1 1 100 16 +75 1 1.1 1 0 1 +79 2 1.1 1 1 1 +80 2 1.1 1 1 1 + + +RUN STATISTICS FOR INPUT FILE: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz +============================================= +74203167 sequences processed in total +The length threshold of paired-end sequences gets evaluated later on (in the validation step) + +Validate paired-end files HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz +file_1: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz, file_2: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz + + +>>>>> Now validing the length of the 2 paired-end infiles: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz <<<<< +Writing validated paired-end read 1 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Writing validated paired-end read 2 reads to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz + +Total number of sequences analysed: 74203167 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4050544 (5.46%) + + + >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz<<< + +Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz +Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz + + >>> Now running FastQC on the validated data HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz<<< + +Started analysis of HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 5% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 10% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 15% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 20% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 25% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 30% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 35% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 40% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 45% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 50% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 55% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 60% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 65% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 70% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 75% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 80% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 85% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 90% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Approx 95% complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Analysis complete for HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +Deleting both intermediate output files HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz and HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_trimmed.fq.gz + +==================================================================================================== + +###CF Trim galore (PE mode) successfully exited, took 2 hours, 14 minutes, 51 seconds.. + + + + +-------------------------------------------------------------------------------- +Module: kallisto +Run File: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run +Job ID: cf_fastq_kallisto_1463255307_kallisto_460 +Previous Job ID: cf_fastq_kallisto_1463255307_trim_galore_160 +Date & Time: 23:03, 14-05-2016 +-------------------------------------------------------------------------------- + + +Pseudoaligning against /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx + +---------- Kallisto version information ---------- +kallisto 0.42.5 + +------- End of Kallisto version information ------ + +###CFCMD kallisto quant -t 1 --pseudobam -i /home/rsh46/scratch/Genomes/Homo_sapiens/GRCh38/Homo_sapiens.GRCh38.cdna.all.idx -o HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz_kallisto_output -b 100 HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz | samtools view -Sb - > HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz_kallisto.bam + + +[quant] fragment length distribution will be estimated from the data +[index] k-mer length: 31 +[index] number of targets: 176,241 +[index] number of k-mers: 104,600,239 +[index] number of equivalence classes: 702,950 +[quant] running in paired-end mode +[quant] will process pair 1: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1.fq.gz + HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2_val_2.fq.gz +[quant] finding pseudoalignments for the reads ... done +[quant] processed 70,152,623 reads, 59,280,920 reads pseudoaligned +[quant] estimated average fragment length: 169.418 +[ em] quantifying the abundances ... done +[ em] the Expectation-Maximization algorithm ran for 1,380 rounds +[bstrp] running EM for the bootstrap: 1 [bstrp] running EM for the bootstrap: 2 [bstrp] running EM for the bootstrap: 3 [bstrp] running EM for the bootstrap: 4 [bstrp] running EM for the bootstrap: 5 [bstrp] running EM for the bootstrap: 6 [bstrp] running EM for the bootstrap: 7 [bstrp] running EM for the bootstrap: 8 [bstrp] running EM for the bootstrap: 9 [bstrp] running EM for the bootstrap: 10 [bstrp] running EM for the bootstrap: 11 [bstrp] running EM for the bootstrap: 12 [bstrp] running EM for the bootstrap: 13 [bstrp] running EM 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EM for the bootstrap: 87 [bstrp] running EM for the bootstrap: 88 [bstrp] running EM for the bootstrap: 89 [bstrp] running EM for the bootstrap: 90 [bstrp] running EM for the bootstrap: 91 [bstrp] running EM for the bootstrap: 92 [bstrp] running EM for the bootstrap: 93 [bstrp] running EM for the bootstrap: 94 [bstrp] running EM for the bootstrap: 95 [bstrp] running EM for the bootstrap: 96 [bstrp] running EM for the bootstrap: 97 [bstrp] running EM for the bootstrap: 98 [bstrp] running EM for the bootstrap: 99 [bstrp] running EM for the bootstrap: 100 + +###CF kallisto (PE mode) successfully exited, took 2 hours, 44 minutes, 36 seconds.. + + + +================================================================================ + + + + + +###CF Run finished at 01:48 15-05-2016 + + +###CF Pipeline fastq_kallisto finished at 01:59 15-05-2016 + +Sending HTML e-mail with sendmail.. +Sent a pipeline e-mail notification to rsh46@cam.ac.uk diff -r 000000000000 -r 3bad335ccea9 test-data/kallisto_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,3 @@ +Sample fragment_length percent_aligned total_reads not_pseudoaligned_reads pseudoaligned_reads +HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_val_1 167.866 83.6511456908 58016047.0 9484959.0 48531088.0 +HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_val_1 169.418 84.5027847355 70152623.0 10871703.0 59280920.0 diff -r 000000000000 -r 3bad335ccea9 test-data/picard_AlignmentSummaryMetrics_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_AlignmentSummaryMetrics_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample PF_HQ_ALIGNED_READS READS_ALIGNED_IN_PAIRS MEAN_READ_LENGTH BAD_CYCLES PF_INDEL_RATE PCT_READS_ALIGNED_IN_PAIRS TOTAL_READS PCT_CHIMERAS PF_HQ_ERROR_RATE PF_ALIGNED_BASES PCT_PF_READS LIBRARY PF_READS PCT_ADAPTER PCT_PF_READS_ALIGNED READ_GROUP SAMPLE PF_NOISE_READS STRAND_BALANCE PF_HQ_ALIGNED_Q20_BASES CATEGORY PF_HQ_MEDIAN_MISMATCHES PF_HQ_ALIGNED_BASES PF_MISMATCH_RATE PF_READS_ALIGNED +D11_H4K16ac_Rep1_R1_fastq_gz 11288718.0 0.0 74.733459 0.0 0.000848 0.0 16199126.0 0.0 0.006165 1189439864.0 1.0 16199126.0 1.4e-05 0.983085 112.0 0.494061 802235299.0 UNPAIRED 0.0 843872901.0 0.011597 15925118.0 diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectAlignmentSummaryMetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectAlignmentSummaryMetrics.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,10 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false REFERENCE_SEQUENCE=/data/repository/organisms/GRCm38_ensembl/genome_fasta/genome.fa INPUT=D11_H4K16ac_Rep1_R1_fastq_gz OUTPUT=/data/galaxy2/files/000/163/dataset_163662.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Fri Apr 21 14:00:55 CEST 2017 + +## METRICS CLASS picard.analysis.AlignmentSummaryMetrics +CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP +UNPAIRED 16199126 16199126 1 112 15925118 0.983085 1189439864 11288718 843872901 802235299 0 0.011597 0.006165 0.000848 74.733459 0 0 0 0.494061 0 0.000014 + + diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectBaseDistributionByCycle.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectBaseDistributionByCycle.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,84 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectBaseDistributionByCycle CHART_OUTPUT=/data/galaxy2/files/000/163/dataset_163657.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=D11_H4K16ac_Rep1_R1_fastq_gz OUTPUT=/data/galaxy2/files/000/163/dataset_163656.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=/data/repository/organisms/GRCm38_ensembl/genome_fasta/genome.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Fri Apr 21 13:59:56 CEST 2017 + +## METRICS CLASS picard.analysis.BaseDistributionByCycleMetrics +READ_END CYCLE PCT_A PCT_C PCT_G PCT_T PCT_N +1 1 45.534532 6.100294 6.278409 41.942176 0.144589 +1 2 18.642016 31.079914 32.291905 17.974837 0.011328 +1 3 25.118841 24.321879 26.15791 24.401106 0.000264 +1 4 22.612561 27.464826 27.30928 22.606024 0.007309 +1 5 27.970543 22.96859 21.970694 27.090173 0 +1 6 28.405874 22.976144 21.741647 26.875952 0.000383 +1 7 31.150444 19.648545 20.094438 29.10656 0.000013 +1 8 31.215988 19.341113 20.496087 28.946812 0 +1 9 31.733121 18.755302 20.342562 29.169015 0 +1 10 31.51068 19.338274 20.26157 28.889475 0 +1 11 31.155932 19.344704 20.729096 28.770267 0 +1 12 28.641307 21.681095 22.115748 27.561843 0.000006 +1 13 28.644403 21.190688 21.233551 28.931359 0 +1 14 27.912176 22.509522 21.398893 28.179408 0 +1 15 29.987269 20.65125 20.583967 28.777514 0 +1 16 30.695446 20.751024 19.720664 28.832866 0 +1 17 32.301494 19.466964 19.056719 29.174754 0.000069 +1 18 31.991424 19.465319 19.428886 29.114371 0 +1 19 31.223398 19.283091 20.843846 28.649665 0 +1 20 30.001159 20.431045 21.682439 27.885357 0 +1 21 30.268972 20.128608 21.518529 28.08389 0 +1 22 29.507609 20.991486 21.551678 27.949227 0 +1 23 29.228924 20.961638 22.202396 27.607042 0 +1 24 28.895271 21.140428 22.773371 27.190931 0 +1 25 30.220087 20.183506 21.007244 28.589163 0 +1 26 30.747733 19.55149 20.989765 28.711005 0.000006 +1 27 30.618992 19.162575 20.686703 29.531698 0.000031 +1 28 31.561628 19.651299 20.291748 28.495305 0.000019 +1 29 31.889741 19.244628 20.387671 28.477401 0.000559 +1 30 30.01585 20.370968 21.669604 27.943339 0.000239 +1 31 29.948939 20.187892 21.74697 28.116198 0 +1 32 29.83526 20.721207 21.226889 28.216644 0 +1 33 28.951574 21.118594 21.807089 28.122743 0 +1 34 29.250508 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+1 53 28.876831 20.985166 22.109191 28.028328 0.000484 +1 54 28.25128 21.263287 22.617006 27.868106 0.000321 +1 55 29.677859 20.048159 21.516525 28.756368 0.001089 +1 56 31.025964 19.638994 21.162354 28.1717 0.000988 +1 57 32.3089 19.022943 19.727314 28.939987 0.000856 +1 58 33.069967 18.780516 19.315424 28.832859 0.001234 +1 59 32.5634 19.018873 19.681712 28.735624 0.000391 +1 60 31.033388 19.63991 20.28236 29.043106 0.001235 +1 61 28.877884 21.063797 22.54864 27.508242 0.001437 +1 62 28.206236 21.933072 21.756687 28.103248 0.000757 +1 63 28.076144 21.765468 22.13245 28.025345 0.000593 +1 64 28.444021 21.930975 21.519278 28.105031 0.000694 +1 65 30.427586 20.515343 21.251214 27.804511 0.001345 +1 66 30.96119 20.454946 20.819432 27.764078 0.000354 +1 67 31.55559 19.752271 19.98091 28.7104 0.000829 +1 68 30.884355 19.787006 21.169721 28.158438 0.000481 +1 69 29.915794 19.951388 21.827419 28.302832 0.002566 +1 70 29.720163 20.878848 21.185973 28.214947 0.00007 +1 71 28.563014 21.296438 21.558676 28.580233 0.001639 +1 72 27.775812 22.725309 21.897851 27.599987 0.001041 +1 73 28.801882 22.042398 21.835818 27.319535 0.000367 +1 74 29.842933 21.375107 20.192959 28.587638 0.001363 +1 75 28.875221 21.990286 22.042923 27.09157 0 + + diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectInsertSizeMetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectInsertSizeMetrics.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,737 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/omaha-beach/cloud_26/files/000/dataset_199.dat DEVIATIONS=10.0 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_198.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:33:00 UTC 2016 + +## METRICS CLASS picard.analysis.InsertSizeMetrics +MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP +194 63 100 5331452 271.809759 196.076488 311788 FR 25 47 69 91 127 343 941 1515 2585 16663 + +## HISTOGRAM java.lang.Integer +insert_size All_Reads.fr_count +100 2 +101 117 +102 424 +103 390 +104 376 +105 335 +106 360 +107 343 +108 353 +109 386 +110 349 +111 368 +112 445 +113 459 +114 470 +115 512 +116 478 +117 520 +118 558 +119 599 +120 603 +121 600 +122 696 +123 703 +124 657 +125 747 +126 734 +127 753 +128 820 +129 880 +130 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+697 106 +698 92 +699 90 +700 97 +701 102 +702 105 +703 109 +704 122 +705 101 +706 123 +707 126 +708 115 +709 114 +710 99 +711 136 +712 102 +713 114 +714 114 +715 119 +716 105 +717 121 +718 140 +719 113 +720 124 +721 140 +722 102 +723 146 +724 118 +725 145 +726 133 +727 155 +728 149 +729 129 +730 146 +731 153 +732 155 +733 164 +734 162 +735 179 +736 162 +737 158 +738 161 +739 171 +740 171 +741 168 +742 161 +743 198 +744 185 +745 146 +746 161 +747 178 +748 184 +749 185 +750 179 +751 189 +752 187 +753 166 +754 179 +755 170 +756 181 +757 193 +758 185 +759 201 +760 202 +761 195 +762 176 +763 204 +764 201 +765 182 +766 183 +767 180 +768 161 +769 174 +770 173 +771 185 +772 160 +773 180 +774 170 +775 167 +776 187 +777 167 +778 179 +779 187 +780 157 +781 176 +782 162 +783 158 +784 161 +785 160 +786 177 +787 161 +788 174 +789 145 +790 143 +791 148 +792 162 +793 170 +794 145 +795 157 +796 132 +797 150 +798 149 +799 131 +800 158 +801 132 +802 128 +803 118 +804 107 +805 120 +806 132 +807 122 +808 108 +809 116 +810 133 +811 112 +812 125 +813 93 +814 94 +815 94 +816 101 +817 91 +818 94 +819 98 +820 82 +821 73 +822 87 +823 69 +824 84 + diff -r 000000000000 -r 3bad335ccea9 test-data/picard_CollectRnaSeqMetrics.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,113 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/tmp/tmpRJquSu/files/000/dataset_14.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=picard_CollectRnaSeqMetrics_bam OUTPUT=/tmp/tmpRJquSu/files/000/dataset_15.dat ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Thu Dec 08 10:55:06 CET 2016 + +## METRICS CLASS picard.analysis.RnaSeqMetrics +PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP +48870 48712 0 38786 0 9926 0 0 0 0 0.796231 0 0.203769 0.796231 0.793657 0 0.91593 0.430026 0.235755 1.402829 + +## HISTOGRAM java.lang.Integer +normalized_position All_Reads.normalized_coverage +0 0.313906 +1 0.333933 +2 0.365536 +3 0.344525 +4 0.371353 +5 0.378606 +6 0.518015 +7 0.51266 +8 0.500497 +9 0.690539 +10 0.829611 +11 0.784227 +12 0.825037 +13 0.730533 +14 0.73133 +15 0.693057 +16 0.873759 +17 0.774195 +18 0.721989 +19 0.791727 +20 0.697702 +21 0.698451 +22 0.568885 +23 0.689955 +24 0.580475 +25 0.602348 +26 0.657286 +27 0.600594 +28 0.48185 +29 0.478605 +30 0.646053 +31 0.689366 +32 0.740073 +33 0.695415 +34 0.708419 +35 0.714707 +36 0.707421 +37 0.793703 +38 0.84384 +39 0.819497 +40 0.982412 +41 1.172387 +42 1.28116 +43 1.379184 +44 1.416285 +45 1.32892 +46 1.248258 +47 1.308676 +48 1.085518 +49 1.006687 +50 0.851309 +51 0.693805 +52 0.672921 +53 0.684999 +54 0.62579 +55 0.529832 +56 0.546564 +57 0.566014 +58 0.615824 +59 0.565042 +60 0.547677 +61 0.642067 +62 0.83636 +63 0.937071 +64 1.057465 +65 1.168829 +66 1.375228 +67 1.489487 +68 1.530099 +69 1.287542 +70 1.442585 +71 1.347823 +72 1.424913 +73 1.468345 +74 1.796846 +75 1.79639 +76 1.747908 +77 1.76867 +78 1.773528 +79 1.670178 +80 1.740083 +81 1.809632 +82 2.019967 +83 2.201517 +84 2.150455 +85 2.327367 +86 2.261259 +87 1.929731 +88 1.936627 +89 1.80697 +90 1.789004 +91 1.642341 +92 1.408203 +93 1.159737 +94 0.990047 +95 0.697842 +96 0.377809 +97 0.243433 +98 0.218816 +99 0.223665 +100 0.225079 + diff -r 000000000000 -r 3bad335ccea9 test-data/picard_MarkDuplicates.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MarkDuplicates.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,112 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.sam.markduplicates.MarkDuplicates INPUT=[/omaha-beach/cloud_26/files/000/dataset_114.dat] OUTPUT=/omaha-beach/cloud_26/files/000/dataset_197.dat METRICS_FILE=/omaha-beach/cloud_26/files/000/dataset_196.dat REMOVE_DUPLICATES=false ASSUME_SORTED=true DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:32:41 UTC 2016 + +## METRICS CLASS picard.sam.DuplicationMetrics +LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE +Unknown Library 2900 313405 0 2257 629 0 0.005582 77973949 + +## HISTOGRAM java.lang.Double +BIN VALUE +1.0 1 +2.0 1.995989 +3.0 2.987982 +4.0 3.975997 +5.0 4.960048 +6.0 5.940152 +7.0 6.916324 +8.0 7.88858 +9.0 8.856937 +10.0 9.821409 +11.0 10.782013 +12.0 11.738763 +13.0 12.691676 +14.0 13.640766 +15.0 14.586049 +16.0 15.52754 +17.0 16.465254 +18.0 17.399207 +19.0 18.329414 +20.0 19.25589 +21.0 20.178649 +22.0 21.097706 +23.0 22.013077 +24.0 22.924776 +25.0 23.832819 +26.0 24.737218 +27.0 25.63799 +28.0 26.535149 +29.0 27.428709 +30.0 28.318684 +31.0 29.20509 +32.0 30.08794 +33.0 30.967248 +34.0 31.84303 +35.0 32.715298 +36.0 33.584068 +37.0 34.449352 +38.0 35.311166 +39.0 36.169523 +40.0 37.024436 +41.0 37.875921 +42.0 38.723989 +43.0 39.568656 +44.0 40.409935 +45.0 41.247839 +46.0 42.082382 +47.0 42.913578 +48.0 43.741439 +49.0 44.565979 +50.0 45.387212 +51.0 46.205151 +52.0 47.019809 +53.0 47.831199 +54.0 48.639334 +55.0 49.444228 +56.0 50.245893 +57.0 51.044342 +58.0 51.839588 +59.0 52.631645 +60.0 53.420524 +61.0 54.206239 +62.0 54.988802 +63.0 55.768226 +64.0 56.544524 +65.0 57.317707 +66.0 58.087789 +67.0 58.854783 +68.0 59.618699 +69.0 60.379551 +70.0 61.137352 +71.0 61.892112 +72.0 62.643845 +73.0 63.392562 +74.0 64.138276 +75.0 64.880999 +76.0 65.620743 +77.0 66.357519 +78.0 67.09134 +79.0 67.822217 +80.0 68.550163 +81.0 69.275188 +82.0 69.997306 +83.0 70.716526 +84.0 71.432862 +85.0 72.146324 +86.0 72.856924 +87.0 73.564674 +88.0 74.269585 +89.0 74.971668 +90.0 75.670935 +91.0 76.367397 +92.0 77.061066 +93.0 77.751952 +94.0 78.440066 +95.0 79.12542 +96.0 79.808025 +97.0 80.487892 +98.0 81.165032 +99.0 81.839456 +100.0 82.511174 + diff -r 000000000000 -r 3bad335ccea9 test-data/picard_RnaSeqMetrics_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_RnaSeqMetrics_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample PCT_CODING_BASES RIBOSOMAL_BASES PF_NOT_ALIGNED_BASES PCT_MRNA_BASES CORRECT_STRAND_READS MEDIAN_CV_COVERAGE PCT_RIBOSOMAL_BASES PCT_INTRONIC_BASES MEDIAN_3PRIME_BIAS PF_ALIGNED_BASES LIBRARY MEDIAN_5PRIME_BIAS PCT_USABLE_BASES PF_BASES READ_GROUP IGNORED_READS SAMPLE INTERGENIC_BASES INTRONIC_BASES MEDIAN_5PRIME_TO_3PRIME_BIAS PCT_INTERGENIC_BASES PCT_CORRECT_STRAND_READS INCORRECT_STRAND_READS CODING_BASES UTR_BASES PCT_UTR_BASES +picard_CollectRnaSeqMetrics_bam 0.0 158.0 79.6231 0.0 0.91593 0.0 0.235755 48712.0 0.430026 79.3657 48870.0 0.0 9926.0 0.0 1.402829 20.3769 0.0 0.0 0.0 38786.0 79.6231 diff -r 000000000000 -r 3bad335ccea9 test-data/picard_baseContent_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_baseContent_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample sum_pct_n mean_pct_t sum_pct_g sum_pct_a sum_pct_c mean_pct_a sum_pct_t mean_pct_c cycle_count mean_pct_g +D11_H4K16ac_Rep1_R1_fastq_gz 0.499258 28.1544206133 1590.390797 2251.590365 1545.938026 30.0212048667 2111.581546 20.6125070133 75 21.2052106267 diff -r 000000000000 -r 3bad335ccea9 test-data/picard_collectGcBias.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_collectGcBias.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,110 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_195.dat SUMMARY_OUTPUT=/omaha-beach/cloud_26/files/000/dataset_193.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 IS_BISULFITE_SEQUENCED=true INPUT=/omaha-beach/cloud_26/files/000/dataset_114.dat OUTPUT=/omaha-beach/cloud_26/files/000/dataset_194.dat ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT REFERENCE_SEQUENCE=localref.fa METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon May 23 09:32:30 UTC 2016 + +## METRICS CLASS picard.analysis.GcBiasDetailMetrics +ACCUMULATION_LEVEL GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH SAMPLE LIBRARY READ_GROUP +All Reads 0 0 0 0 0 0 +All Reads 1 0 0 0 0 0 +All Reads 2 0 0 0 0 0 +All Reads 3 10 0 0 0 0 +All Reads 4 7 0 0 0 0 +All Reads 5 6 0 0 0 0 +All Reads 6 4 0 0 0 0 +All Reads 7 9 0 0 0 0 +All Reads 8 22 0 0 0 0 +All Reads 9 15 0 0 0 0 +All Reads 10 20 0 0 0 0 +All Reads 11 18 0 0 0 0 +All Reads 12 101 0 0 0 0 +All Reads 13 118 0 0 0 0 +All Reads 14 137 1 20 0.110575 0.110575 +All Reads 15 243 4 19 0.249362 0.124681 +All Reads 16 366 10 21 0.4139 0.130887 +All Reads 17 468 9 24 0.291322 0.097107 +All Reads 18 689 25 24 0.549664 0.109933 +All Reads 19 1087 40 26 0.557451 0.088141 +All Reads 20 2152 95 25 0.668741 0.068611 +All Reads 21 3279 127 23 0.586731 0.052064 +All Reads 22 5106 178 23 0.528099 0.039583 +All Reads 23 7817 319 23 0.618197 0.034612 +All Reads 24 11933 630 24 0.799774 0.031864 +All Reads 25 17449 759 25 0.658943 0.023918 +All Reads 26 25272 1414 26 0.847591 0.02254 +All Reads 27 34926 1806 25 0.783331 0.018433 +All Reads 28 48489 2889 26 0.90257 0.016792 +All Reads 29 64950 4285 26 0.99942 0.015268 +All Reads 30 84452 5453 26 0.978142 0.013246 +All Reads 31 107535 6476 26 0.912291 0.011337 +All Reads 32 134982 7953 26 0.892548 0.010008 +All Reads 33 165941 9475 26 0.864972 0.008886 +All Reads 34 199087 11437 26 0.870253 0.008137 +All Reads 35 233144 12856 26 0.83533 0.007367 +All Reads 36 266049 14918 26 0.849426 0.006955 +All Reads 37 298999 17019 26 0.862265 0.00661 +All Reads 38 327958 20230 26 0.934446 0.00657 +All Reads 39 350801 22684 26 0.97957 0.006504 +All Reads 40 369841 23670 26 0.969527 0.006302 +All Reads 41 383262 25527 26 1.008975 0.006315 +All Reads 42 392470 26131 25 1.008617 0.006239 +All Reads 43 395234 25603 25 0.981326 0.006133 +All Reads 44 392428 26425 25 1.020074 0.006275 +All Reads 45 386569 25213 25 0.988039 0.006222 +All Reads 46 376763 25980 25 1.044594 0.006481 +All Reads 47 363422 24801 25 1.033795 0.006564 +All Reads 48 348339 24838 25 1.080167 0.006854 +All Reads 49 331960 24992 24 1.140491 0.007214 +All Reads 50 315781 23793 24 1.141405 0.0074 +All Reads 51 297249 22601 24 1.151818 0.007662 +All Reads 52 278159 19653 24 1.070317 0.007635 +All Reads 53 263713 19395 24 1.114127 0.008 +All Reads 54 247317 19047 24 1.166673 0.008453 +All Reads 55 230663 17922 23 1.177023 0.008792 +All Reads 56 215458 16244 23 1.142107 0.008961 +All Reads 57 198515 14904 23 1.137329 0.009316 +All Reads 58 180718 13720 23 1.150083 0.009819 +All Reads 59 165914 11940 23 1.090179 0.009977 +All Reads 60 152561 10775 23 1.069917 0.010307 +All Reads 61 138857 9746 23 1.063249 0.01077 +All Reads 62 125804 9067 22 1.091807 0.011466 +All Reads 63 112222 7148 22 0.964902 0.011413 +All Reads 64 99218 6056 23 0.924638 0.011882 +All Reads 65 85414 5612 24 0.995326 0.013286 +All Reads 66 72999 4286 23 0.88943 0.013586 +All Reads 67 61396 3631 23 0.895907 0.014868 +All Reads 68 52109 3341 22 0.971271 0.016804 +All Reads 69 45121 2735 21 0.918238 0.017558 +All Reads 70 38925 1675 21 0.651873 0.015928 +All Reads 71 32225 1053 22 0.495008 0.015254 +All Reads 72 27537 721 22 0.396639 0.014772 +All Reads 73 23481 483 22 0.311607 0.014179 +All Reads 74 20300 423 22 0.315661 0.015348 +All Reads 75 17785 245 22 0.208684 0.013332 +All Reads 76 15846 236 22 0.225615 0.014686 +All Reads 77 13683 230 22 0.254638 0.01679 +All Reads 78 11733 217 23 0.280174 0.019019 +All Reads 79 10547 188 22 0.270026 0.019694 +All Reads 80 9314 151 22 0.245594 0.019986 +All Reads 81 7659 149 23 0.294707 0.024143 +All Reads 82 5813 56 25 0.145937 0.019502 +All Reads 83 4687 46 23 0.148676 0.021921 +All Reads 84 3505 18 23 0.077797 0.018337 +All Reads 85 2385 8 23 0.050813 0.017965 +All Reads 86 1424 5 21 0.053191 0.023788 +All Reads 87 859 3 20 0.052906 0.030545 +All Reads 88 529 0 0 0 0 +All Reads 89 411 0 0 0 0 +All Reads 90 348 0 0 0 0 +All Reads 91 138 0 0 0 0 +All Reads 92 40 0 0 0 0 +All Reads 93 7 0 0 0 0 +All Reads 94 7 0 0 0 0 +All Reads 95 12 0 0 0 0 +All Reads 96 17 0 0 0 0 +All Reads 97 8 0 0 0 0 +All Reads 98 9 0 0 0 0 +All Reads 99 5 0 0 0 0 +All Reads 100 30 0 0 0 0 + + diff -r 000000000000 -r 3bad335ccea9 test-data/picard_dups_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_dups_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample UNMAPPED_READS ESTIMATED_LIBRARY_SIZE READ_PAIR_OPTICAL_DUPLICATES READ_PAIRS_EXAMINED UNPAIRED_READS_EXAMINED PERCENT_DUPLICATION LIBRARY READ_PAIR_DUPLICATES UNPAIRED_READ_DUPLICATES +dataset_114 0.0 77973949.0 0.0 313405.0 2900.0 0.005582 Unknown Library 629.0 2257.0 diff -r 000000000000 -r 3bad335ccea9 test-data/picard_insertSize_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_insertSize_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample SAMPLE_NAME MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT SAMPLE LIBRARY READ_GROUP +dataset_197_FR dataset_197 194.0 63.0 100.0 5331452.0 271.809759 196.076488 311788.0 FR 25.0 47.0 69.0 91.0 127.0 343.0 941.0 1515.0 2585.0 16663.0 diff -r 000000000000 -r 3bad335ccea9 test-data/post_aligner_soft_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/post_aligner_soft_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,21 @@ +Sample QUAST_N50 QUAST_Total_length featureCounts_percent_assigned featureCounts_Assigned Picard_PCT_PF_READS_ALIGNED Prokka_organism Prokka_contigs Prokka_bases Prokka_CDS Bcftools Stats_number_of_records Bcftools Stats_number_of_SNPs Bcftools Stats_number_of_indels Bcftools Stats_tstv Bcftools Stats_number_of_MNPs Bamtools_duplicates_pct Bamtools_mapped_reads_pct Picard_PERCENT_DUPLICATION Picard_summed_median Picard_summed_mean GATK VariantEval_known_titv GATK VariantEval_novel_titv HTSeq Count_percent_assigned HTSeq Count_assigned Picard_PCT_RIBOSOMAL_BASES Picard_PCT_MRNA_BASES Samtools Flagstat_mapped_passed Samtools Stats_error_rate Samtools Stats_non_primary_alignments Samtools Stats_reads_mapped Samtools Stats_reads_mapped_percent Samtools Stats_raw_total_sequences Samblaster_pct_dups +14892_1#15 115136.0 18435361.0 +70: TopHat on data 1, data 4, and data 3: accepted_hits 70.82267755353567 321797 +75: TopHat on data 1, data 6, and data 5: accepted_hits 69.58585803304067 445012 +80: TopHat on data 1, data 8, and data 7: accepted_hits 71.76957768385707 394981 +85: TopHat on data 1, data 10, and data 9: accepted_hits 72.02454351337069 437485 +90: TopHat on data 1, data 12, and data 11: accepted_hits 71.33130826437625 388170 +95: TopHat on data 1, data 14, and data 13: accepted_hits 70.72517103678439 453929 +D11_H4K16ac_Rep1_R1_fastq_gz 0.983085 +Sample1 Helicobacter pylori 30 1629978 1548 +Sample2 Escherichia coli 52 162997532523 1548 +Test1 5522770.0 4474244.0 902934.0 1.97 72330.0 +bamtools 0.0 93.125 +dataset_114 0.005582 +dataset_197 176 271.809759 +gatk_varianteval 0.0 2.2 +htseq 0.0 0 +picard_CollectRnaSeqMetrics_bam 79.62310000000001 +samtools_flagstat 20689039 +samtools_stats 0.004248509 12111.0 641821.0 100.0 641821.0 +virtual-normal 1.28 diff -r 000000000000 -r 3bad335ccea9 test-data/pre_alignment_soft_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pre_alignment_soft_log.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,75 @@ +[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/miniconda3/envs/multiqc2/lib/python2.7/site-packages/multiqc-1.2-py2.7.egg/multiqc_config.yaml +[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml +[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml +[2017-09-28 17:24:01,554] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir +[2017-09-28 17:24:02,209] multiqc [DEBUG ] Latest MultiQC version is v1.2 +[2017-09-28 17:24:02,210] multiqc [INFO ] This is MultiQC v1.2 +[2017-09-28 17:24:02,210] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir +[2017-09-28 17:24:02,210] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc +[2017-09-28 17:24:02,210] multiqc [INFO ] Template : default +[2017-09-28 17:24:02,210] multiqc [INFO ] Searching 'multiqc_WDir' +[2017-09-28 17:24:02,211] multiqc [DEBUG ] Analysing modules: afterqc, custom_content, conpair, peddy, methylQA, qualimap, preseq, quast, qorts, rna_seqc, rseqc, busco, goleft_indexcov, disambiguate, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, picard, prokka, samblaster, samtools, bamtools, jellyfish, vcftools, bismark, hicup, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, leehom, adapterRemoval, cutadapt, flexbar, trimmomatic, skewer, sortmerna, biobloomtools, fastq_screen, fastqc, clusterflow, bcl2fastq +[2017-09-28 17:24:02,249] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig +[2017-09-28 17:24:05,021] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,098] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found +[2017-09-28 17:24:05,144] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,235] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,259] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,306] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50 +[2017-09-28 17:24:05,306] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,315] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',) +[2017-09-28 17:24:05,329] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,347] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('multiqc_WDir',) +[2017-09-28 17:24:05,394] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('multiqc_WDir',) +[2017-09-28 17:24:05,424] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,430] multiqc.modules.busco.busco [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,469] multiqc.modules.goleft_indexcov.goleft_indexcov [DEBUG ] Did not find goleft indexcov outputs in ('multiqc_WDir',) +[2017-09-28 17:24:05,475] multiqc.modules.disambiguate.disambiguate [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2017-09-28 17:24:05,499] multiqc.modules.homer.homer [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,513] multiqc.modules.macs2.macs2 [DEBUG ] Could not find any MACS2 data in ('multiqc_WDir',) +[2017-09-28 17:24:05,552] multiqc.modules.theta2.theta2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,571] multiqc.modules.snpeff.snpeff [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2017-09-28 17:24:05,637] multiqc.modules.gatk.gatk [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,693] multiqc.modules.htseq.htseq [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,757] multiqc.modules.bcftools.bcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,787] multiqc.modules.featureCounts.feature_counts [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,868] multiqc.modules.picard.picard [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,874] multiqc.modules.prokka.prokka [DEBUG ] Could not find any Prokka data in ('multiqc_WDir',) +[2017-09-28 17:24:05,881] multiqc.modules.samblaster.samblaster [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2017-09-28 17:24:05,915] multiqc.modules.samtools.samtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,931] multiqc.modules.bamtools.bamtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:05,942] multiqc.modules.jellyfish.jellyfish [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2017-09-28 17:24:06,029] multiqc.modules.vcftools.vcftools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,064] multiqc.modules.bismark.bismark [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,083] multiqc.modules.hicup.hicup [DEBUG ] Could not find any HiCUP data in ('multiqc_WDir',) +[2017-09-28 17:24:06,107] multiqc.modules.salmon.salmon [DEBUG ] Could not find any Salmon data in ('multiqc_WDir',) +[2017-09-28 17:24:06,145] multiqc.modules.kallisto.kallisto [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,187] multiqc.modules.slamdunk.slamdunk [DEBUG ] No slamdunk reports found. +[2017-09-28 17:24:06,207] multiqc.modules.star.star [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,225] multiqc.modules.hisat2.hisat2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,238] multiqc.modules.tophat.tophat [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,245] multiqc.modules.bowtie2.bowtie2 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,250] multiqc.modules.bowtie1.bowtie1 [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,263] multiqc.modules.leehom.leehom [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,273] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,299] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports +[2017-09-28 17:24:06,351] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs +[2017-09-28 17:24:06,378] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs +[2017-09-28 17:24:06,403] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',) +[2017-09-28 17:24:06,421] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs +[2017-09-28 17:24:06,441] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,448] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,605] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports +[2017-09-28 17:24:06,908] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('multiqc_WDir',) +[2017-09-28 17:24:06,914] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('multiqc_WDir',) +[2017-09-28 17:24:06,923] multiqc [INFO ] Compressing plot data +[2017-09-28 17:24:07,121] multiqc [INFO ] Report : multiqc_report.html +[2017-09-28 17:24:07,121] multiqc [INFO ] Data : multiqc_data +[2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_cutadapt.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' +[2017-09-28 17:24:07,121] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_fastqc.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' +[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_flexbar.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' +[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_general_stats.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' +[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sortmerna.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' +[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_sources.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' +[2017-09-28 17:24:07,122] multiqc [DEBUG ] Moving data file from '/var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig/multiqc_data/multiqc_trimmomatic.txt' to '/Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc/multiqc_data' +[2017-09-28 17:24:07,952] multiqc [INFO ] MultiQC complete diff -r 000000000000 -r 3bad335ccea9 test-data/pre_alignment_soft_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pre_alignment_soft_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,7 @@ +Sample SortMeRNA_rRNA_pct Trimmomatic_dropped_pct Cutadapt_percent_trimmed FastQC_percent_duplicates FastQC_percent_gc FastQC_avg_sequence_length FastQC_total_sequences FastQC_percent_fails Flexbar_removed_bases_pct +25839_merged 1.09929975002 +C2 17.98 +dataset_33 10.7768204362 +poulet5_1 36.3059115993 48.0 101.0 267849.0 8.33333333333 +poulet5_2 36.1733887481 48.0 101.0 267849.0 8.33333333333 +result_right 45.2606635071 diff -r 000000000000 -r 3bad335ccea9 test-data/prokka_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prokka_1.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,9 @@ +organism: Helicobacter pylori Sample1 +contigs: 30 +bases: 1629978 +tmRNA: 1 +tRNA: 36 +repeat_region: 15 +sig_peptide: 88 +rRNA: 2 +CDS: 1548 diff -r 000000000000 -r 3bad335ccea9 test-data/prokka_2.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prokka_2.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,6 @@ +organism: Escherichia coli Sample2 +contigs: 52 +bases: 162997532523 +rRNA: 2 +CDS: 1548 +misc_RNA: 5152 diff -r 000000000000 -r 3bad335ccea9 test-data/prokka_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/prokka_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,3 @@ +Sample contigs tmRNA tRNA repeat_region sig_peptide bases rRNA CDS organism misc_RNA +Sample1 30 1 36 15 88 1629978 2 1548 Helicobacter pylori +Sample2 52 162997532523 2 1548 Escherichia coli 5152 diff -r 000000000000 -r 3bad335ccea9 test-data/quast.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quast.tsv Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,48 @@ +Assembly 14892_1#15 +# contigs (>= 0 bp) 545 +# contigs (>= 1000 bp) 376 +# contigs (>= 5000 bp) 242 +# contigs (>= 10000 bp) 215 +# contigs (>= 25000 bp) 181 +# contigs (>= 50000 bp) 123 +Total length (>= 0 bp) 18465341 +Total length (>= 1000 bp) 18373173 +Total length (>= 5000 bp) 18079934 +Total length (>= 10000 bp) 17893099 +Total length (>= 25000 bp) 17353907 +Total length (>= 50000 bp) 15112131 +# contigs 467 +Largest contig 435484 +Total length 18435361 +Reference length 18916112 +GC (%) 48.17 +Reference GC (%) 48.21 +N50 115136 +NG50 112874 +N75 62262 +NG75 56990 +L50 48 +LG50 50 +L75 100 +LG75 106 +# misassemblies 107 +# misassembled contigs 82 +Misassembled contigs length 4540800 +# local misassemblies 132 +# unaligned contigs 8 + 59 part +Unaligned length 88446 +Genome fraction (%) 95.482 +Duplication ratio 1.016 +# N's per 100 kbp 929.55 +# mismatches per 100 kbp 262.21 +# indels per 100 kbp 33.75 +# genes 7280 + 968 part +Largest alignment 356982 +NA50 102129 +NGA50 99244 +NA75 54365 +NGA75 51757 +LA50 56 +LGA50 59 +LA75 117 +LGA75 124 diff -r 000000000000 -r 3bad335ccea9 test-data/quast_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/quast_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample L50 Duplication ratio GC (%) LG75 # misassemblies # contigs (>= 25000 bp) L75 Total length (>= 10000 bp) # genes # mismatches per 100 kbp # indels per 100 kbp # contigs (>= 5000 bp) Unaligned length Total length # unaligned contigs # local misassemblies Reference GC (%) # N's per 100 kbp Total length (>= 25000 bp) # contigs (>= 0 bp) # genes_partial NGA50 NGA75 Largest contig # contigs # unaligned contigs_partial NG75 # contigs (>= 50000 bp) Total length (>= 0 bp) NG50 # contigs (>= 10000 bp) LGA50 NA75 Total length (>= 5000 bp) Genome fraction (%) LGA75 LG50 N75 Total length (>= 1000 bp) NA50 # contigs (>= 1000 bp) N50 Total length (>= 50000 bp) Largest alignment LA75 LA50 Misassembled contigs length Reference length # misassembled contigs +14892_1#15 48.0 1.016 48.17 106.0 107.0 181.0 100.0 17893099.0 7280.0 262.21 33.75 242.0 88446.0 18435361.0 8.0 132.0 48.21 929.55 17353907.0 545.0 968.0 99244.0 51757.0 435484.0 467.0 59.0 56990.0 123.0 18465341.0 112874.0 215.0 59.0 54365.0 18079934.0 95.482 124.0 50.0 62262.0 18373173.0 102129.0 376.0 115136.0 15112131.0 356982.0 117.0 56.0 4540800.0 18916112.0 82.0 diff -r 000000000000 -r 3bad335ccea9 test-data/report_manual_custom_content.html --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/report_manual_custom_content.html Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,4806 @@ + + + + + + + + + + + + + +MultiQC Report + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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        + MultiQC: Summarize analysis results for multiple tools and samples in a single report
        + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
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        + MultiQC: Summarize analysis results for multiple tools and samples in a single report
        + Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
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        + + +
        + + + + +
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2.52931e-05 1.89311e-05 1.31795e-05 1.42019e-05 2.08695e-05 2.32676e-05 1.8703e-05 1.41646e-05 1.21812e-05 1.75855e-05 3.22537e-05 3.79859e-05 2.58096e-05 1.50542e-05 1.67477e-05 2.13993e-05 2.12384e-05 1.96424e-05 2.3822e-05 2.70925e-05 2.03769e-05 1.48712e-05 1.72969e-05 1.78426e-05 1.65496e-05 2.31123e-05 3.28929e-05 3.18781e-05 2.35634e-05 1.86101e-05 1.68779e-05 1.7201e-05 1.67251e-05 1.42443e-05 1.60709e-05 2.0563e-05 1.8343e-05 1.07904e-05 6.50594e-06 6.90976e-06 9.51938e-06 1.37279e-05 1.99594e-05 2.63528e-05 2.62039e-05 1.9531e-05 1.40842e-05 1.0443e-05 6.19332e-06 3.15215e-06 1.9885e-06 2.66703e-06 6.713e-06 1.3677e-05 2.03104e-05 2.10663e-05 1.40711e-05 6.27583e-06 3.7427e-06 6.55367e-06 1.09452e-05 1.21797e-05 1.07195e-05 9.73698e-06 9.68352e-06 9.58964e-06 9.33026e-06 1.00018e-05 1.14061e-05 1.08428e-05 8.1754e-06 6.07466e-06 5.15208e-06 5.38196e-06 6.08604e-06 6.00756e-06 6.48509e-06 7.17523e-06 6.32834e-06 6.30781e-06 8.63972e-06 1.17246e-05 1.42171e-05 1.44737e-05 1.39417e-05 1.49739e-05 1.34774e-05 8.48393e-06 6.52076e-06 8.59729e-06 9.88876e-06 8.73588e-06 7.19017e-06 6.60393e-06 7.90853e-06 1.35146e-05 1.90635e-05 1.72624e-05 1.36599e-05 1.41403e-05 1.24135e-05 6.29769e-06 1.70231e-06 7.93462e-07 1.51668e-06 3.70154e-06 8.90089e-06 1.39394e-05 1.39214e-05 1.01037e-05 8.39903e-06 1.28578e-05 1.63268e-05 1.0656e-05 3.04466e-06 6.80488e-07 5.69187e-07 1.65732e-06 6.6409e-06 1.56287e-05 2.36638e-05 2.25498e-05 1.19664e-05 2.65332e-06 2.12142e-06 8.85763e-06 1.46954e-05 1.30284e-05 8.9613e-06 9.41787e-06 1.24864e-05 1.32299e-05 1.09039e-05 8.40077e-06 7.40911e-06 6.38258e-06 3.74339e-06 1.43927e-06 1.13906e-06 1.29372e-06 1.33564e-06 2.46596e-06 4.46963e-06 5.67218e-06 4.90606e-06 4.04313e-06 6.34515e-06 8.88379e-06 6.95433e-06 3.65637e-06 2.94153e-06 4.17195e-06 5.5028e-06 4.74869e-06 2.17937e-06 7.82578e-07 2.43841e-06 6.8549e-06 1.06683e-05 9.78123e-06 5.28579e-06 1.99386e-06 2.50526e-06 6.54417e-06 1.11548e-05 1.14234e-05 7.26258e-06 4.4539e-06 5.43921e-06 7.07614e-06 6.63592e-06 4.78539e-06 3.19464e-06 2.10155e-06 1.72895e-06 2.37028e-06 3.47349e-06 3.77081e-06 2.39965e-06 8.38368e-07 4.67798e-07 5.94779e-07 1.01159e-06 2.03373e-06 2.50506e-06 1.69265e-06 2.01259e-06 5.0072e-06 6.87755e-06 5.0568e-06 2.80961e-06 2.54084e-06 3.53985e-06 4.11274e-06 3.3652e-06 2.96116e-06 3.00754e-06 2.25854e-06 2.07636e-06 2.45488e-06 1.63659e-06 4.09147e-07 3.85885e-07 1.56387e-06 2.86285e-06 3.53111e-06 3.46887e-06 2.69838e-06 1.85779e-06 1.49693e-06 1.22314e-06 1.21479e-06 2.31806e-06 3.28215e-06 3.84767e-06 6.78209e-06 9.55348e-06 7.76424e-06 4.57611e-06 3.32036e-06 3.40193e-06 4.69867e-06 5.48751e-06 3.69654e-06 1.2805e-06 2.89866e-07 7.83975e-08 2.6148e-07 1.06334e-06 1.74289e-06 1.52401e-06 9.07056e-07 5.1625e-07 8.31187e-07 2.47749e-06 4.2339e-06 3.97655e-06 2.17198e-06 7.20291e-07 1.50117e-07 8.41709e-07 3.65886e-06 6.7976e-06 7.03373e-06 4.57005e-06 1.9335e-06 1.12986e-06 3.40076e-06 7.19508e-06 7.86113e-06 4.68721e-06 2.46511e-06 2.39414e-06 1.93741e-06 1.27594e-06 1.48226e-06 2.30749e-06 2.97352e-06 2.52344e-06 2.31968e-06 4.53879e-06 6.29353e-06 4.15418e-06 1.99749e-06 4.0946e-06 6.78898e-06 5.42395e-06 2.19728e-06 1.49087e-06 3.60187e-06 5.48598e-06 5.55927e-06 4.70616e-06 3.05027e-06 1.49419e-06 1.77041e-06 3.28006e-06 4.91242e-06 5.31697e-06 3.27109e-06 8.17772e-07 2.0556e-09 8.22241e-09 2.73776e-08 6.83982e-08 1.19281e-07 1.68023e-07 1.78207e-07 1.13419e-07 3.08581e-07 1.09862e-06 2.20692e-06 3.35688e-06 4.99332e-06 7.74224e-06 9.23651e-06 6.38429e-06 2.64563e-06 4.40649e-06 1.09547e-05 1.3498e-05 9.01164e-06 5.95876e-06 6.76799e-06 6.08158e-06 5.24991e-06 6.45314e-06 5.96304e-06 2.93128e-06 6.59683e-07 7.47147e-08 1.99209e-08 9.9379e-10 4.56574e-07 1.8253e-06 2.73935e-06 1.83091e-06 8.73364e-07 1.64011e-06 2.45315e-06 3.43558e-06 7.7112e-06 1.19341e-05 1.2711e-05 1.45177e-05 1.4914e-05 8.6575e-06 1.98422e-06 8.47947e-08 3.3357e-07 1.23407e-06 3.26845e-06 4.48571e-06 2.93488e-06 7.3372e-07 8.48451e-20 8.96793e-07 3.59294e-06 5.40385e-06 3.63152e-06 9.58739e-07 6.40541e-08 3.88541e-08 4.80455e-08 3.30967e-07 9.40549e-07 1.21916e-06 7.48889e-07 1.77639e-07 8.48451e-20 8.48451e-20 3.74019e-10 1.24594e-07 4.9984e-07 1.65769e-06 4.85254e-06 8.49019e-06 8.04065e-06 3.86231e-06 7.51093e-07 3.88541e-08 1.42289e-07 3.74887e-07 5.13763e-07 5.22964e-07 1.3609e-06 3.23852e-06 3.92375e-06 2.4373e-06 1.49085e-06 2.52107e-06 3.62893e-06 3.89446e-06 3.4838e-06 2.38137e-06 2.43245e-06 4.29959e-06 5.14334e-06 4.42458e-06 5.07748e-06 7.05396e-06 6.70794e-06 3.56321e-06 1.09354e-06 5.94004e-07 2.23031e-06 6.82104e-06 9.6855e-06 6.31699e-06 1.55824e-06 2.43299e-08 9.73194e-08 1.45979e-07 9.73194e-08 2.43299e-08 5.65959e-07 2.86045e-06 5.78219e-06 5.87574e-06 3.0814e-06 7.90119e-07 4.3638e-07 1.26769e-06 1.86803e-06 3.32101e-06 8.55452e-06 1.2341e-05 8.22336e-06 2.0626e-06 2.28594e-07 8.46747e-07 1.23631e-06 8.12933e-07 2.01542e-07 8.48451e-20 6.62153e-07 2.64861e-06 3.97306e-06 2.64918e-06 6.63001e-07 5.65634e-10 1.41408e-10 5.08647e-07 2.69674e-06 5.74233e-06 6.20182e-06 3.51613e-06 9.91274e-07 1.49684e-07 2.94087e-08 9.78813e-09 1.46822e-08 2.48321e-08 1.24873e-07 4.67214e-07 9.51419e-07 1.05552e-06 6.09723e-07 1.51734e-07 8.0021e-09 8.22241e-09 7.6778e-07 3.48633e-06 6.56158e-06 6.56591e-06 3.83529e-06 1.87558e-06 2.86313e-06 5.46522e-06 6.77583e-06 6.76114e-06 5.96453e-06 3.46521e-06 8.60546e-07 8.57557e-07 3.41456e-06 5.12027e-06 3.97947e-06 3.37465e-06 5.5051e-06 8.12692e-06 8.17751e-06 4.99229e-06 1.70417e-06 4.16364e-07 1.04091e-07 8.48451e-20 8.48451e-20 1.03855e-06 4.17877e-06 7.31893e-06 8.25894e-06 7.07274e-06 3.98182e-06 1.10885e-06 4.78174e-07 7.17261e-07 4.78174e-07 1.06162e-06 3.76832e-06 5.65248e-06 3.76832e-06 1.00433e-06 9.46158e-07 3.69878e-06 6.57856e-06 6.0715e-06 2.84656e-06 5.40835e-07 6.62769e-07 2.64063e-06 3.95989e-06 2.63993e-06 6.65929e-07 2.3786e-08 3.5679e-08 2.3786e-08 5.9465e-09 8.48451e-20 8.48451e-20 1.05325e-06 4.213e-06 6.31951e-06 4.213e-06 1.74237e-06 2.75646e-06 4.14557e-06 2.79999e-06 7.54417e-07 4.35348e-08 1.08837e-08 1.62467e-06 6.4987e-06 9.74804e-06 6.4987e-06 1.62467e-06 2.42376e-07 9.69503e-07 1.45515e-06 9.73101e-07 2.47772e-07 3.59728e-09 2.08228e-06 8.32552e-06 1.25152e-05 8.43337e-06 2.53305e-06 1.26743e-06 1.76634e-06 1.16823e-06 9.73446e-07 2.64779e-06 3.92848e-06 2.60459e-06 6.81238e-07 1.34953e-07 2.17296e-07 1.64686e-07 5.60377e-08 2.95843e-07 1.15959e-06 1.82339e-06 2.39241e-06 4.38112e-06 6.7061e-06 7.6585e-06 6.95299e-06 4.13776e-06 1.10966e-06 5.44951e-07 2.05945e-06 3.08987e-06 2.06224e-06 5.19564e-07 4.87571e-09 1.20166e-07 4.67429e-07 7.15222e-07 5.67288e-07 3.57226e-07 7.34211e-07 1.98274e-06 2.77314e-06 1.8253e-06 5.34391e-07 3.12261e-07 4.68391e-07 3.12261e-07 7.80652e-08 4.91325e-08 1.9653e-07 2.94795e-07 1.96778e-07 5.01263e-08 1.49069e-09 9.9379e-10 2.48448e-10 8.48451e-20 8.48451e-20 1.28319e-06 5.13871e-06 7.72294e-06 5.16845e-06 1.30698e-06 5.9465e-09 6.45033e-08 4.1415e-07 1.01157e-06 1.21721e-06 7.78569e-07 2.90415e-07 8.9519e-08 1.62661e-06 7.55928e-06 1.41948e-05 1.33201e-05 6.37014e-06 1.43714e-06 1.9653e-07 4.91325e-08 8.48451e-20 1.40225e-09 3.01961e-08 1.06762e-07 1.53132e-07 1.48883e-07 2.21117e-07 2.94795e-07 1.9653e-07 1.52023e-07 1.4224e-06 4.66068e-06 6.47657e-06 4.14623e-06 1.2079e-06 7.88265e-07 1.1824e-06 7.88265e-07 1.97066e-07 1.13356e-09 4.53426e-09 7.40038e-08 8.39303e-07 2.66819e-06 3.66457e-06 2.33104e-06 5.65959e-07 8.48451e-20 5.75979e-08 2.30392e-07 3.45587e-07 2.32447e-07 6.58203e-08 1.23336e-08 1.27549e-08 2.01854e-08 2.71947e-08 1.81298e-08 4.53244e-09 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 1.56137e-07 6.82145e-07 1.16721e-06 9.70134e-07 3.86528e-07 5.75979e-08 9.89308e-07 3.95723e-06 5.95252e-06 4.56652e-06 3.25974e-06 3.32229e-06 2.6434e-06 2.3679e-06 2.73795e-06 1.8253e-06 4.56325e-07 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 4.52923e-08 1.81169e-07 2.71754e-07 1.81169e-07 4.52923e-08 8.48451e-20 2.42376e-07 9.69503e-07 1.45426e-06 9.69503e-07 2.42376e-07 8.48451e-20 1.27948e-07 5.11793e-07 7.72222e-07 5.29923e-07 3.56237e-07 8.22506e-07 1.2111e-06 8.04377e-07 2.01094e-07 1.19543e-07 4.85833e-07 7.47897e-07 5.59316e-07 2.9093e-07 2.18785e-07 1.4075e-07 3.51876e-08 8.48451e-20 1.7085e-09 6.83399e-09 1.0251e-08 4.48392e-07 1.76794e-06 2.64935e-06 1.76623e-06 4.41558e-07 2.28063e-07 9.20891e-07 1.40294e-06 9.70858e-07 3.1919e-07 1.67271e-07 2.04131e-07 9.36586e-07 3.27659e-06 4.87062e-06 3.25897e-06 8.59342e-07 7.1358e-08 4.7572e-08 1.1893e-08 8.48451e-20 1.19543e-07 4.78174e-07 7.17261e-07 4.78174e-07 1.19543e-07 8.48451e-20 8.48451e-20 8.48451e-20 3.652e-07 1.4608e-06 2.1912e-06 1.4608e-06 3.652e-07 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 2.88646e-09 1.31089e-07 4.95492e-07 7.28806e-07 4.8106e-07 1.19543e-07 8.48451e-20 2.11966e-06 8.47864e-06 1.2718e-05 8.49079e-06 2.16829e-06 3.62843e-07 1.88217e-06 4.44733e-06 5.20328e-06 2.98569e-06 6.76004e-07 8.22241e-09 1.23336e-08 8.22241e-09 4.1112e-09 8.22241e-09 1.23336e-08 8.22241e-09 2.0556e-09 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 8.48451e-20 5.08647e-07 2.89843e-06 6.66338e-06 7.84217e-06 4.90082e-06 2.61356e-05 9.87451e-05 0.000147884 + diff -r 000000000000 -r 3bad335ccea9 test-data/samblaster.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samblaster.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,15 @@ +samblaster: Version 0.1.22 +samblaster: Inputting from stdin +samblaster: Outputting to stdout +samblaster: Opening /vagrant/test-out6/virtual-normal-samblaster-markdups.txt for write. +[bam_header_read] EOF marker is absent. The input is probably truncated. +[M::mem_pestat] skip orientation FF as there are not enough pairs +[M::mem_pestat] skip orientation FR as there are not enough pairs +[M::mem_pestat] skip orientation RF as there are not enough pairs +[M::mem_pestat] skip orientation RR as there are not enough pairs +samblaster: Loaded 86 header sequence entries. +samblaster: Removed 1 of 78 (1.28%) read ids as duplicates using 1724k memory in 0.000S CPU seconds and 31S wall time. +[main] Version: 0.7.7-r441 +[main] CMD:[samopen] SAM header is present: 86 sequences. + bwa mem -M -v 1 -R @RG\tID:virtual-normal\tSM:virtual-normal\tLB:virtual-normal\tPL:ILLUMINA -t 2 /proj/b2010040/private/nobackup/autoseq-genome/bwa/human_g1k_v37_decoy.fasta /vagrant/test-out6/skewer/virtual-normal_1.fastq.gz /vagrant/test-out6/skewer/virtual-normal_2.fastq.gz +[main] Real time: 30.780 sec; CPU: 13.292 sec diff -r 000000000000 -r 3bad335ccea9 test-data/samblaster_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samblaster_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample n_dups pct_dups n_tot n_nondups +virtual-normal 1 1.28 78 77 diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_flagstat.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_flagstat.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,13 @@ +21040602 + 0 in total (QC-passed reads + QC-failed reads) +0 + 0 secondary +0 + 0 supplementary +5448463 + 0 duplicates +20689039 + 0 mapped (98.33%:-nan%) +0 + 0 paired in sequencing +0 + 0 read1 +0 + 0 read2 +0 + 0 properly paired (-nan%:-nan%) +0 + 0 with itself and mate mapped +0 + 0 singletons (-nan%:-nan%) +0 + 0 with mate mapped to a different chr +0 + 0 with mate mapped to a different chr (mapQ>=5) diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_flagstat_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_flagstat_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample mapped_passed duplicates_failed secondary_passed paired in sequencing_failed duplicates_passed read2_passed read1_failed read1_passed with mate mapped to a different chr_passed total_failed properly paired_passed_pct singletons_passed supplementary_passed singletons_passed_pct mapped_failed_pct mapped_passed_pct supplementary_failed with itself and mate mapped_failed mapped_failed total_passed properly paired_failed flagstat_total with mate mapped to a different chr (mapQ >= 5)_passed properly paired_failed_pct with mate mapped to a different chr (mapQ >= 5)_failed with itself and mate mapped_passed read2_failed with mate mapped to a different chr_failed properly paired_passed paired in sequencing_passed singletons_failed secondary_failed singletons_failed_pct +samtools_flagstat 20689039 0 0 0 5448463 0 0 0 0 0 nan 0 0 nan nan 98.33 0 0 0 21040602 0 21040602 0 nan 0 0 0 0 0 0 0 0 nan diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_idxstats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_idxstats.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,67 @@ +1 195471971 977171 0 +10 130694993 637405 0 +11 122082543 557954 0 +12 120129022 822778 0 +13 120421639 595176 0 +14 124902244 1179793 0 +15 104043685 474303 0 +16 98207768 450478 0 +17 94987271 442543 0 +18 90702639 423431 0 +19 61431566 269193 0 +2 182113224 2369317 0 +3 160039680 802543 0 +4 156508116 738160 0 +5 151834684 703632 0 +6 149736546 768256 0 +7 145441459 685296 0 +8 129401213 895718 0 +9 124595110 1144967 0 +MT 16299 141 0 +X 171031299 506800 0 +Y 91744698 132190 0 +JH584299.1 953012 2185 0 +GL456233.1 336933 1053 0 +JH584301.1 259875 303 0 +GL456211.1 241735 2348 0 +GL456350.1 227966 283 0 +JH584293.1 207968 236 0 +GL456221.1 206961 2196 0 +JH584297.1 205776 366 0 +JH584296.1 199368 368 0 +GL456354.1 195993 591 0 +JH584294.1 191905 313 0 +JH584298.1 184189 277 0 +JH584300.1 182347 230 0 +GL456219.1 175968 622 0 +GL456210.1 169725 1661 0 +JH584303.1 158099 214 0 +JH584302.1 155838 185 0 +GL456212.1 153618 1979 0 +JH584304.1 114452 278844 0 +GL456379.1 72385 210 0 +GL456216.1 66673 341 0 +GL456393.1 55711 629 0 +GL456366.1 47073 244 0 +GL456367.1 42057 245 0 +GL456239.1 40056 214 0 +GL456213.1 39340 99 0 +GL456383.1 38659 848 0 +GL456385.1 35240 155 0 +GL456360.1 31704 165 0 +GL456378.1 31602 444 0 +GL456389.1 28772 6166 0 +GL456372.1 28664 211 0 +GL456370.1 26764 502 0 +GL456381.1 25871 55 0 +GL456387.1 24685 156 0 +GL456390.1 24668 780 0 +GL456394.1 24323 114 0 +GL456392.1 23629 21116 0 +GL456382.1 23158 57 0 +GL456359.1 22974 85 0 +GL456396.1 21240 20375 0 +GL456368.1 20208 319 0 +JH584292.1 14945 85 0 +JH584295.1 1976 4 0 +* 0 0 274008 diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,9736 @@ +# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats +# The command line was: stats --coverage 1,1000,1 --GC-depth 20000.0 --insert-size 8000 --most-inserts 0.99 --trim-quality 0 --ref-seq /omaha-beach/cloud_26/files/000/dataset_20.dat /omaha-beach/cloud_26/files/000/dataset_114.dat +# CHK, Checksum [2]Read Names [3]Sequences [4]Qualities +# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) +CHK 7742088d 2cf80e59 99341a6a +# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. +SN raw total sequences: 641821 +SN filtered sequences: 0 +SN sequences: 641821 +SN is sorted: 1 +SN 1st fragments: 320981 +SN last fragments: 320840 +SN reads mapped: 641821 +SN reads mapped and paired: 638746 # paired-end technology bit set + both mates mapped +SN reads unmapped: 0 +SN reads properly paired: 635626 # proper-pair bit set +SN reads paired: 641821 # paired-end technology bit set +SN reads duplicated: 0 # PCR or optical duplicate bit set +SN reads MQ0: 70 # mapped and MQ=0 +SN reads QC failed: 0 +SN non-primary alignments: 12111 +SN total length: 64823921 # ignores clipping +SN bases mapped: 64823921 # ignores clipping +SN bases mapped (cigar): 64823921 # more accurate +SN bases trimmed: 0 +SN bases duplicated: 0 +SN mismatches: 275405 # from NM fields +SN error rate: 4.248509e-03 # mismatches / bases mapped (cigar) +SN average length: 101 +SN maximum length: 101 +SN average quality: 26.0 +SN insert size average: 719.7 +SN insert size standard deviation: 1223.0 +SN inward oriented pairs: 317512 +SN outward oriented pairs: 1294 +SN pairs with other orientation: 30 +SN pairs on different chromosomes: 0 +# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +FFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 113 0 0 0 0 320725 143 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 4 320810 71 91 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 3 320877 25 75 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 5 320905 26 44 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 8 320816 67 86 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 8 320839 42 84 5 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 0 0 0 0 6 320867 57 47 1 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 8 320845 59 64 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 2 320851 46 78 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 4 320836 57 77 3 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 7 320849 46 67 5 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 8 320812 80 78 2 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 9 320826 56 82 4 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 0 0 0 10 320774 77 107 7 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 7 320808 60 95 3 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 1 0 0 0 12 320786 68 101 6 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 0 0 0 8 320758 89 116 6 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 9 320768 86 106 6 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 12 320795 77 91 4 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 20 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 11 320739 99 110 14 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 21 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 16 320681 115 143 21 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 22 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 11 320699 111 144 11 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 23 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 0 0 0 14 320659 111 171 15 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 24 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 11 1 0 0 0 18 320626 139 165 20 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 1 0 0 0 13 320630 125 180 23 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 26 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 1 0 0 1 32 320502 176 228 32 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 27 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 0 0 0 25 320413 219 270 43 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 40 320323 222 317 74 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 29 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 14 0 0 0 0 33 320324 240 300 68 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 30 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 0 0 0 32 320438 208 249 47 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 31 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 2 0 0 0 30 320518 136 220 63 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 32 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 7 2 0 0 0 22 320539 158 199 52 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 33 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 10 3 0 0 0 31 320501 143 234 58 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 34 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 14 5 0 0 0 28 320475 168 216 73 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 14 2 0 0 2 14 320498 164 217 65 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 6 7 0 0 0 25 320419 210 229 82 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 37 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 10 2 0 0 0 27 320497 146 216 79 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 38 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 15 2 0 0 0 35 320379 186 277 85 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 39 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 11 4 0 0 2 36 320412 186 271 58 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 40 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 8 4 0 0 0 31 320420 187 261 67 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 4 6 0 0 0 19 320375 205 268 92 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 9 2 0 0 0 34 320376 202 287 65 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 2 8 0 0 0 33 320367 206 289 68 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 4 13 0 0 2 41 320230 279 330 78 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 15 8 0 0 0 58 320276 209 341 68 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 13 8 0 0 0 53 320197 275 342 87 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 14 6 0 0 1 55 320225 219 388 67 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 11 9 0 0 0 53 320120 302 394 80 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 10 18 0 0 2 84 320118 260 419 63 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 10 12 0 0 0 60 319973 337 492 84 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 10 15 0 0 0 52 319932 333 537 90 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 5 18 0 0 0 61 319903 320 573 94 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 8 22 0 0 0 62 319897 359 544 78 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 14 25 0 0 0 89 319808 371 575 91 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 7 24 0 0 3 121 319810 320 633 57 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 4 42 0 0 0 66 319481 518 657 199 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 5 36 0 0 0 80 319309 575 777 183 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 7 40 0 0 0 79 319345 609 700 191 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 19 35 0 0 0 112 319419 487 785 110 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 9 54 0 0 0 88 319097 574 901 246 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 10 55 0 0 10 169 319174 475 997 74 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 7 75 0 0 0 111 318749 787 986 248 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 0 22 56 0 0 10 188 318870 589 1150 76 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 19 76 0 0 11 189 318737 648 1195 91 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 21 79 0 0 0 197 318550 705 1284 121 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 25 79 0 0 0 195 318333 783 1439 107 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 26 18 85 0 0 0 208 318101 829 1584 130 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 19 96 0 0 0 231 317865 961 1679 116 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 36 133 0 0 0 238 317621 994 1809 132 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 29 123 0 0 0 258 317369 1087 1947 143 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 32 0 123 0 0 109 316709 1180 1344 1464 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 35 0 133 0 0 125 316372 1317 1408 1576 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 0 34 138 0 0 7 406 316605 1310 2392 65 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 27 31 181 0 0 0 342 316340 1442 2510 108 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 24 36 187 0 0 8 395 316006 1568 2662 95 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 22 54 179 0 0 0 386 315780 1618 2865 77 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 77 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 46 206 0 0 11 436 315719 1579 2889 72 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 23 38 0 236 0 11 125 314395 1803 1935 2415 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 33 249 0 0 0 490 315017 1824 3294 60 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 19 42 285 0 0 8 548 314760 1875 3393 51 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 47 289 0 0 9 585 314291 2036 3653 55 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 82 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 2 46 359 0 0 14 604 313542 2274 4102 24 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 17 42 363 0 0 28 773 312837 2442 4461 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 61 357 0 0 22 706 312428 2610 4730 50 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 16 45 386 0 0 21 839 311516 2872 5269 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 27 57 431 0 0 31 937 310762 3053 5665 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 19 50 507 0 0 16 1056 309721 3328 6266 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 26 56 554 0 0 12 1030 309021 3568 6694 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 18 35 604 0 0 36 1137 308241 3708 7186 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 12 41 672 0 0 10 1127 307003 4124 7976 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 20 56 744 0 0 15 1358 305669 4425 8679 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 16 71 854 0 0 10 1290 304360 4896 9472 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 52 22 943 0 0 13 1582 302737 5311 10315 1 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 38 13 1011 0 0 13 1659 301116 5731 11394 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 95 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 48 1119 0 0 2 1835 299128 6219 12604 20 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 21 1338 0 0 0 1858 6469 296623 13924 730 12 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 8 1383 0 0 0 1987 6972 294224 15758 636 11 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 3 0 1574 0 0 6 2448 8066 291197 17253 422 6 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1610 2 0 0 2835 8983 8498 298741 142 169 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1699 0 0 0 3197 10141 285195 20749 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1758 0 0 0 3382 281089 11576 23176 0 0 0 0 0 0 0 0 0 0 0 0 0 +FFQ 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# Last Fragment Qualitites. Use `grep ^LFQ | cut -f 2-` to extract this part. +# Columns correspond to qualities and rows to cycles. First column is the cycle number. +LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 45 0 0 0 0 0 319823 972 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 34 15 0 0 0 5 320305 160 321 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 20 320305 132 370 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 0 6 0 0 17 320360 134 308 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 17 0 0 0 0 22 320335 165 301 0 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 20 320442 112 243 18 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 30 320503 109 179 9 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 0 0 0 7 320490 131 197 9 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 0 0 0 12 320539 123 159 2 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 0 11 320465 112 240 4 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 11 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 20 1 0 0 0 27 320344 160 278 10 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 0 0 0 0 25 320389 169 236 10 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 13 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 14 320331 166 308 8 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 14 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 3 0 0 0 24 320389 142 250 22 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 1 0 0 0 23 320394 156 236 15 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 30 320296 190 295 16 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 16 1 0 0 0 36 320300 198 269 19 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 0 0 0 0 32 320348 176 253 21 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 19 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 0 0 0 0 25 320363 163 250 26 0 0 0 0 0 0 0 0 0 0 0 0 +LFQ 20 0 0 0 0 0 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Use `grep ^MPC | cut -f 2-` to extract this part. +# Columns correspond to qualities, rows to cycles. 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0 0 0 0 0 0 0 0 0 0 0 1 0 7 4 0 0 1 20 84791 88 168 42 0 0 0 0 0 0 0 0 0 0 0 +MPC 41 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 2 0 0 0 14 84150 74 124 45 0 0 0 0 0 0 0 0 0 0 0 +MPC 42 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 3 2 0 0 0 13 83774 98 123 28 0 0 0 0 0 0 0 0 0 0 0 +MPC 43 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 2 4 2 0 0 2 28 83771 94 159 32 0 0 0 0 0 0 0 0 0 0 0 +MPC 44 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 6 5 0 0 1 23 83722 104 175 39 0 0 0 0 0 0 0 0 0 0 0 +MPC 45 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 10 6 0 0 1 41 84261 93 160 25 0 0 0 0 0 0 0 0 0 0 0 +MPC 46 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 7 1 0 0 0 39 84627 104 160 42 0 0 0 0 0 0 0 0 0 0 0 +MPC 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 0 7 3 0 0 0 34 84297 101 169 36 0 0 0 0 0 0 0 0 0 0 0 +MPC 48 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3 5 0 0 0 15 84963 121 171 48 0 0 0 0 0 0 0 0 0 0 0 +MPC 49 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 6 3 0 0 1 39 83942 137 169 32 0 0 0 0 0 0 0 0 0 0 0 +MPC 50 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 9 0 0 0 28 84075 143 194 66 0 0 0 0 0 0 0 0 0 0 0 +MPC 51 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 4 0 2 0 1 34 83331 123 177 64 0 0 0 0 0 0 0 0 0 0 0 +MPC 52 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 5 8 0 0 0 33 84009 111 218 49 0 0 0 0 0 0 0 0 0 0 0 +MPC 53 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 5 6 7 0 0 1 43 84258 125 209 35 0 0 0 0 0 0 0 0 0 0 0 +MPC 54 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 6 9 0 0 0 25 84920 133 194 29 0 0 0 0 0 0 0 0 0 0 0 +MPC 55 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 0 4 7 0 0 7 62 84793 109 211 26 0 0 0 0 0 0 0 0 0 0 0 +MPC 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 1 12 0 0 0 25 84246 173 244 47 0 0 0 0 0 0 0 0 0 0 0 +MPC 57 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 0 6 0 0 0 44 84546 193 256 53 0 0 0 0 0 0 0 0 0 0 0 +MPC 58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 1 16 0 0 0 23 84043 200 294 57 0 0 0 0 0 0 0 0 0 0 0 +MPC 59 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 10 7 0 0 0 46 85272 172 310 30 0 0 0 0 0 0 0 0 0 0 0 +MPC 60 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 2 12 0 0 0 45 84534 200 308 64 0 0 0 0 0 0 0 0 0 0 0 +MPC 61 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 0 7 6 0 0 5 90 84509 185 343 32 0 0 0 0 0 0 0 0 0 0 0 +MPC 62 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 4 15 0 0 0 37 84802 260 354 65 0 0 0 0 0 0 0 0 0 0 0 +MPC 63 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 1 5 11 0 0 3 86 84937 241 420 51 0 0 0 0 0 0 0 0 0 0 0 +MPC 64 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 9 9 0 0 7 84 84776 280 455 38 0 0 0 0 0 0 0 0 0 0 0 +MPC 65 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 6 14 0 0 0 65 83919 322 428 61 0 0 0 0 0 0 0 0 0 0 0 +MPC 66 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 12 19 0 0 0 58 84493 325 511 47 0 0 0 0 0 0 0 0 0 0 0 +MPC 67 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 7 23 0 0 0 58 84399 362 558 45 0 0 0 0 0 0 0 0 0 0 0 +MPC 68 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 10 16 0 0 0 68 83573 371 585 57 0 0 0 0 0 0 0 0 0 0 0 +MPC 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 7 43 0 0 0 85 84135 412 599 101 0 0 0 0 0 0 0 0 0 0 0 +MPC 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 11 6 36 0 0 0 89 84584 409 665 43 0 0 0 0 0 0 0 0 0 0 0 +MPC 71 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 15 15 15 10 0 0 60 84237 450 528 301 0 0 0 0 0 0 0 0 0 0 0 +MPC 72 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 8 17 16 0 0 75 82936 493 605 299 0 0 0 0 0 0 0 0 0 0 0 +MPC 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 4 17 44 0 0 2 157 84054 528 844 22 0 0 0 0 0 0 0 0 0 0 0 +MPC 74 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 12 54 0 0 0 96 83448 556 848 43 0 0 0 0 0 0 0 0 0 0 0 +MPC 75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 8 31 33 0 1 97 83325 652 739 350 0 0 0 0 0 0 0 0 0 0 0 +MPC 76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 19 34 0 0 0 130 82830 678 946 40 0 0 0 0 0 0 0 0 0 0 0 +MPC 77 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 13 41 0 0 0 143 82891 633 981 19 0 0 0 0 0 0 0 0 0 0 0 +MPC 78 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 13 43 27 0 2 100 82562 693 858 401 0 0 0 0 0 0 0 0 0 0 0 +MPC 79 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 14 16 82 0 0 3 163 82688 729 1061 25 0 0 0 0 0 0 0 0 0 0 0 +MPC 80 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 13 16 71 0 0 2 175 82962 828 1165 25 0 0 0 0 0 0 0 0 0 0 0 +MPC 81 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 3 17 74 0 0 8 231 82689 870 1289 15 0 0 0 0 0 0 0 0 0 0 0 +MPC 82 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 17 111 0 0 13 216 82308 966 1392 13 0 0 0 0 0 0 0 0 0 0 0 +MPC 83 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 4 25 99 0 0 9 267 81839 1044 1442 5 0 0 0 0 0 0 0 0 0 0 0 +MPC 84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 20 85 0 0 1 232 81465 1231 1663 7 0 0 0 0 0 0 0 0 0 0 0 +MPC 85 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 4 17 99 0 0 10 268 81759 1291 1819 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 86 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 6 19 117 0 0 10 316 81327 1341 1988 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 87 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 3 19 117 0 0 4 349 81046 1483 2232 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 5 2 25 159 0 0 7 363 80978 1554 2285 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 89 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 4 25 182 0 0 9 338 80443 1644 2682 2 0 0 0 0 0 0 0 0 0 0 0 +MPC 90 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 7 2 17 214 0 0 4 430 79591 1772 2930 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 91 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 7 17 208 0 0 11 441 80129 1730 3233 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 92 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 10 5 17 211 0 0 3 446 78437 2002 3480 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 4 14 8 254 0 0 7 572 78615 1997 3749 3 0 0 0 0 0 0 0 0 0 0 0 +MPC 94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6 5 8 251 0 0 1 462 77866 2241 4048 6 0 0 0 0 0 0 0 0 0 0 0 +MPC 95 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 9 314 0 0 6 655 76430 2514 4695 7 0 0 0 0 0 0 0 0 0 0 0 +MPC 96 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 12 391 0 0 0 566 2098 76969 5222 211 4 0 0 0 0 0 0 0 0 0 0 0 +MPC 97 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 9 401 0 0 0 614 2396 75564 5776 229 6 0 0 0 0 0 0 0 0 0 0 0 +MPC 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 3 271 219 0 0 406 1727 2800 77304 3035 141 1 0 0 0 0 0 0 0 0 0 0 0 +MPC 99 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 504 0 0 0 928 2885 3413 78669 64 44 1 0 0 0 0 0 0 0 0 0 0 0 +MPC 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 536 0 0 0 979 3339 73408 7776 0 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 101 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 728 0 0 0 1072 73777 4856 10378 0 0 0 0 0 0 0 0 0 0 0 0 +MPC 102 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +# GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. +GCF 7.29 0 +GCF 15.08 2 +GCF 16.08 3 +GCF 17.09 7 +GCF 18.59 17 +GCF 20.10 33 +GCF 21.11 42 +GCF 22.11 52 +GCF 23.12 114 +GCF 24.12 164 +GCF 25.13 326 +GCF 26.13 507 +GCF 27.14 691 +GCF 28.14 899 +GCF 29.15 1591 +GCF 30.15 1949 +GCF 31.16 2308 +GCF 32.16 2736 +GCF 32.91 3088 +GCF 33.67 3685 +GCF 34.67 4605 +GCF 35.68 5091 +GCF 36.68 6131 +GCF 37.69 6883 +GCF 38.69 7964 +GCF 39.70 8636 +GCF 40.70 10761 +GCF 41.71 12194 +GCF 42.71 12911 +GCF 43.72 13386 +GCF 44.72 13260 +GCF 45.73 13698 +GCF 46.73 13439 +GCF 47.74 15308 +GCF 48.74 14928 +GCF 49.75 14412 +GCF 50.75 13332 +GCF 51.76 12903 +GCF 52.76 11945 +GCF 53.77 12084 +GCF 54.77 11708 +GCF 55.78 9649 +GCF 56.78 9361 +GCF 57.79 8367 +GCF 58.79 6859 +GCF 59.80 5753 +GCF 60.80 4662 +GCF 61.81 4213 +GCF 62.81 3894 +GCF 63.82 3063 +GCF 64.82 2456 +GCF 65.83 1920 +GCF 66.58 1398 +GCF 67.34 1419 +GCF 68.34 1253 +GCF 69.35 963 +GCF 70.35 713 +GCF 71.36 414 +GCF 72.36 265 +GCF 73.37 187 +GCF 74.37 115 +GCF 75.38 74 +GCF 76.38 50 +GCF 77.39 32 +GCF 78.39 23 +GCF 79.90 14 +GCF 81.41 19 +GCF 82.41 13 +GCF 83.42 5 +GCF 84.42 2 +GCF 85.43 1 +# GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. +GCL 6.78 0 +GCL 14.57 1 +GCL 16.08 3 +GCL 17.09 4 +GCL 18.09 7 +GCL 19.10 14 +GCL 20.10 31 +GCL 21.11 43 +GCL 22.11 65 +GCL 23.12 110 +GCL 24.12 186 +GCL 25.13 318 +GCL 26.13 565 +GCL 27.14 698 +GCL 28.14 919 +GCL 29.15 1512 +GCL 30.15 1962 +GCL 31.16 2348 +GCL 32.16 2693 +GCL 32.91 3148 +GCL 33.67 3657 +GCL 34.67 4472 +GCL 35.68 5072 +GCL 36.68 5943 +GCL 37.69 6932 +GCL 38.69 7875 +GCL 39.70 8778 +GCL 40.70 10644 +GCL 41.71 11773 +GCL 42.71 12979 +GCL 43.72 13566 +GCL 44.72 13217 +GCL 45.73 13362 +GCL 46.73 13338 +GCL 47.74 15116 +GCL 48.74 14791 +GCL 49.75 14361 +GCL 50.75 13389 +GCL 51.76 12939 +GCL 52.76 12428 +GCL 53.77 12023 +GCL 54.77 11736 +GCL 55.78 9713 +GCL 56.78 9335 +GCL 57.79 8514 +GCL 58.79 6846 +GCL 59.80 5874 +GCL 60.80 4865 +GCL 61.81 4274 +GCL 62.81 3973 +GCL 63.82 3008 +GCL 64.82 2400 +GCL 65.83 1929 +GCL 66.58 1438 +GCL 67.34 1428 +GCL 68.34 1299 +GCL 69.35 988 +GCL 70.35 739 +GCL 71.36 392 +GCL 72.36 258 +GCL 73.37 156 +GCL 74.37 118 +GCL 75.38 81 +GCL 76.38 51 +GCL 77.39 28 +GCL 78.39 32 +GCL 79.40 25 +GCL 80.40 21 +GCL 81.41 12 +GCL 82.41 14 +GCL 83.92 4 +GCL 85.43 2 +# ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle, and A,C,G,T counts [%] +GCC 1 12.32 37.19 37.45 13.05 +GCC 2 30.22 19.07 19.01 31.70 +GCC 3 23.59 25.79 25.71 24.90 +GCC 4 24.89 24.36 24.80 25.95 +GCC 5 26.37 23.14 23.40 27.09 +GCC 6 27.80 21.60 21.70 28.90 +GCC 7 27.71 21.52 21.77 29.00 +GCC 8 25.01 24.21 24.68 26.10 +GCC 9 25.54 23.74 23.93 26.79 +GCC 10 27.83 21.53 21.61 29.03 +GCC 11 22.59 26.73 26.96 23.72 +GCC 12 24.80 24.68 24.80 25.72 +GCC 13 26.25 23.19 22.90 27.66 +GCC 14 25.68 23.77 23.72 26.83 +GCC 15 25.57 23.95 23.87 26.61 +GCC 16 25.07 24.41 24.49 26.03 +GCC 17 25.26 24.27 24.24 26.23 +GCC 18 25.39 24.07 23.99 26.55 +GCC 19 25.14 24.57 24.36 25.93 +GCC 20 25.54 23.86 23.89 26.71 +GCC 21 25.45 23.91 24.04 26.60 +GCC 22 25.38 23.88 24.40 26.34 +GCC 23 25.68 23.61 24.05 26.65 +GCC 24 25.78 23.77 23.42 27.03 +GCC 25 25.33 24.02 24.16 26.49 +GCC 26 25.76 23.85 23.76 26.63 +GCC 27 25.79 23.86 23.85 26.50 +GCC 28 25.39 24.28 24.11 26.23 +GCC 29 25.76 24.03 23.60 26.62 +GCC 30 25.85 23.95 23.84 26.35 +GCC 31 25.55 24.04 24.10 26.31 +GCC 32 25.91 23.72 23.70 26.66 +GCC 33 25.71 23.88 23.80 26.62 +GCC 34 25.47 24.24 24.41 25.87 +GCC 35 25.73 23.66 23.83 26.78 +GCC 36 25.56 23.78 23.97 26.69 +GCC 37 25.71 24.17 23.94 26.18 +GCC 38 25.76 23.66 23.92 26.66 +GCC 39 25.66 23.95 23.94 26.45 +GCC 40 25.54 24.12 24.01 26.33 +GCC 41 25.47 23.92 23.71 26.90 +GCC 42 25.78 23.69 23.74 26.79 +GCC 43 25.41 24.09 24.14 26.36 +GCC 44 25.94 23.70 23.59 26.77 +GCC 45 25.84 23.84 23.78 26.54 +GCC 46 25.47 24.14 24.07 26.32 +GCC 47 25.69 23.93 23.94 26.44 +GCC 48 25.71 24.00 23.78 26.51 +GCC 49 25.25 23.94 24.25 26.57 +GCC 50 25.78 23.80 23.68 26.74 +GCC 51 25.46 23.99 23.90 26.66 +GCC 52 25.32 23.97 24.09 26.62 +GCC 53 25.76 23.74 23.72 26.79 +GCC 54 25.69 23.87 23.88 26.55 +GCC 55 25.34 24.00 24.22 26.44 +GCC 56 25.68 23.94 23.77 26.61 +GCC 57 25.68 23.82 23.92 26.57 +GCC 58 25.74 23.69 24.16 26.41 +GCC 59 25.69 23.87 23.83 26.61 +GCC 60 25.83 23.70 23.85 26.63 +GCC 61 25.57 23.87 24.19 26.37 +GCC 62 25.87 23.75 23.88 26.51 +GCC 63 26.09 23.89 23.56 26.46 +GCC 64 25.68 24.31 23.96 26.06 +GCC 65 25.74 24.02 23.86 26.38 +GCC 66 25.73 23.92 23.70 26.65 +GCC 67 25.44 24.05 24.26 26.26 +GCC 68 25.76 23.92 23.83 26.49 +GCC 69 25.58 23.96 23.74 26.72 +GCC 70 25.91 23.86 24.02 26.21 +GCC 71 25.93 23.70 23.76 26.61 +GCC 72 25.95 23.42 23.76 26.87 +GCC 73 25.36 24.10 24.11 26.42 +GCC 74 25.91 23.79 23.67 26.64 +GCC 75 25.67 23.81 23.92 26.59 +GCC 76 25.79 23.88 24.29 26.05 +GCC 77 25.80 23.81 23.66 26.74 +GCC 78 26.11 23.71 23.57 26.61 +GCC 79 25.69 24.25 23.89 26.17 +GCC 80 25.79 23.81 23.80 26.60 +GCC 81 25.91 23.89 23.56 26.64 +GCC 82 25.47 23.98 23.96 26.59 +GCC 83 25.76 23.85 23.90 26.49 +GCC 84 26.10 23.65 23.62 26.63 +GCC 85 25.35 24.06 24.19 26.39 +GCC 86 26.07 23.85 23.69 26.39 +GCC 87 26.02 23.96 23.45 26.57 +GCC 88 25.63 24.31 23.85 26.20 +GCC 89 25.89 23.88 23.55 26.69 +GCC 90 25.81 24.05 23.77 26.37 +GCC 91 25.36 24.23 24.29 26.12 +GCC 92 25.90 23.55 23.90 26.65 +GCC 93 25.85 23.76 23.75 26.65 +GCC 94 25.50 24.35 24.15 26.00 +GCC 95 25.77 23.83 23.88 26.52 +GCC 96 25.71 23.78 23.88 26.62 +GCC 97 25.67 24.09 24.05 26.19 +GCC 98 25.81 23.71 23.97 26.51 +GCC 99 25.43 23.88 24.11 26.58 +GCC 100 25.46 23.99 24.27 26.28 +GCC 101 25.52 24.12 24.24 26.11 +# Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs +IS 0 0 0 0 0 +IS 1 0 0 0 0 +IS 2 0 0 0 0 +IS 3 0 0 0 0 +IS 4 0 0 0 0 +IS 5 0 0 0 0 +IS 6 0 0 0 0 +IS 7 0 0 0 0 +IS 8 0 0 0 0 +IS 9 0 0 0 0 +IS 10 0 0 0 0 +IS 11 0 0 0 0 +IS 12 0 0 0 0 +IS 13 0 0 0 0 +IS 14 0 0 0 0 +IS 15 0 0 0 0 +IS 16 0 0 0 0 +IS 17 0 0 0 0 +IS 18 0 0 0 0 +IS 19 0 0 0 0 +IS 20 0 0 0 0 +IS 21 0 0 0 0 +IS 22 0 0 0 0 +IS 23 0 0 0 0 +IS 24 0 0 0 0 +IS 25 0 0 0 0 +IS 26 0 0 0 0 +IS 27 0 0 0 0 +IS 28 0 0 0 0 +IS 29 0 0 0 0 +IS 30 0 0 0 0 +IS 31 0 0 0 0 +IS 32 0 0 0 0 +IS 33 0 0 0 0 +IS 34 0 0 0 0 +IS 35 0 0 0 0 +IS 36 0 0 0 0 +IS 37 0 0 0 0 +IS 38 0 0 0 0 +IS 39 0 0 0 0 +IS 40 0 0 0 0 +IS 41 0 0 0 0 +IS 42 0 0 0 0 +IS 43 0 0 0 0 +IS 44 0 0 0 0 +IS 45 0 0 0 0 +IS 46 0 0 0 0 +IS 47 0 0 0 0 +IS 48 0 0 0 0 +IS 49 0 0 0 0 +IS 50 0 0 0 0 +IS 51 0 0 0 0 +IS 52 0 0 0 0 +IS 53 0 0 0 0 +IS 54 0 0 0 0 +IS 55 0 0 0 0 +IS 56 0 0 0 0 +IS 57 0 0 0 0 +IS 58 0 0 0 0 +IS 59 0 0 0 0 +IS 60 0 0 0 0 +IS 61 0 0 0 0 +IS 62 0 0 0 0 +IS 63 0 0 0 0 +IS 64 0 0 0 0 +IS 65 0 0 0 0 +IS 66 0 0 0 0 +IS 67 0 0 0 0 +IS 68 0 0 0 0 +IS 69 0 0 0 0 +IS 70 0 0 0 0 +IS 71 0 0 0 0 +IS 72 0 0 0 0 +IS 73 0 0 0 0 +IS 74 0 0 0 0 +IS 75 0 0 0 0 +IS 76 0 0 0 0 +IS 77 0 0 0 0 +IS 78 0 0 0 0 +IS 79 0 0 0 0 +IS 80 0 0 0 0 +IS 81 0 0 0 0 +IS 82 0 0 0 0 +IS 83 0 0 0 0 +IS 84 0 0 0 0 +IS 85 0 0 0 0 +IS 86 0 0 0 0 +IS 87 0 0 0 0 +IS 88 0 0 0 0 +IS 89 0 0 0 0 +IS 90 0 0 0 0 +IS 91 0 0 0 0 +IS 92 0 0 0 0 +IS 93 0 0 0 0 +IS 94 0 0 0 0 +IS 95 0 0 0 0 +IS 96 0 0 0 0 +IS 97 0 0 0 0 +IS 98 0 0 0 0 +IS 99 0 0 0 0 +IS 100 0 0 0 0 +IS 101 5 4 1 0 +IS 102 537 308 229 0 +IS 103 481 296 185 0 +IS 104 401 345 56 0 +IS 105 348 332 16 0 +IS 106 367 358 9 0 +IS 107 346 346 0 0 +IS 108 356 356 0 0 +IS 109 391 391 0 0 +IS 110 349 349 0 0 +IS 111 368 368 0 0 +IS 112 452 452 0 0 +IS 113 461 461 0 0 +IS 114 474 474 0 0 +IS 115 515 515 0 0 +IS 116 481 481 0 0 +IS 117 521 521 0 0 +IS 118 561 561 0 0 +IS 119 601 601 0 0 +IS 120 605 605 0 0 +IS 121 605 605 0 0 +IS 122 702 702 0 0 +IS 123 707 707 0 0 +IS 124 658 658 0 0 +IS 125 755 755 0 0 +IS 126 738 738 0 0 +IS 127 761 761 0 0 +IS 128 828 828 0 0 +IS 129 884 884 0 0 +IS 130 929 929 0 0 +IS 131 935 935 0 0 +IS 132 957 957 0 0 +IS 133 1008 1008 0 0 +IS 134 1091 1091 0 0 +IS 135 1138 1138 0 0 +IS 136 1183 1183 0 0 +IS 137 1285 1285 0 0 +IS 138 1387 1387 0 0 +IS 139 1430 1430 0 0 +IS 140 1500 1500 0 0 +IS 141 1630 1630 0 0 +IS 142 1701 1701 0 0 +IS 143 1848 1848 0 0 +IS 144 1908 1908 0 0 +IS 145 1969 1969 0 0 +IS 146 2217 2217 0 0 +IS 147 2223 2223 0 0 +IS 148 2284 2284 0 0 +IS 149 2464 2464 0 0 +IS 150 2580 2580 0 0 +IS 151 2545 2545 0 0 +IS 152 2644 2644 0 0 +IS 153 2605 2605 0 0 +IS 154 2592 2592 0 0 +IS 155 2759 2759 0 0 +IS 156 2770 2770 0 0 +IS 157 2732 2732 0 0 +IS 158 2781 2781 0 0 +IS 159 2796 2796 0 0 +IS 160 2897 2897 0 0 +IS 161 2839 2839 0 0 +IS 162 2795 2795 0 0 +IS 163 2726 2726 0 0 +IS 164 2790 2790 0 0 +IS 165 2868 2868 0 0 +IS 166 2815 2815 0 0 +IS 167 2874 2874 0 0 +IS 168 2908 2908 0 0 +IS 169 2826 2826 0 0 +IS 170 2856 2856 0 0 +IS 171 2827 2827 0 0 +IS 172 2857 2857 0 0 +IS 173 2864 2863 0 1 +IS 174 2785 2785 0 0 +IS 175 2695 2695 0 0 +IS 176 2713 2713 0 0 +IS 177 2594 2594 0 0 +IS 178 2525 2525 0 0 +IS 179 2584 2584 0 0 +IS 180 2505 2505 0 0 +IS 181 2379 2378 1 0 +IS 182 2330 2330 0 0 +IS 183 2195 2195 0 0 +IS 184 2121 2121 0 0 +IS 185 2002 2001 0 1 +IS 186 1921 1921 0 0 +IS 187 1839 1839 0 0 +IS 188 1891 1891 0 0 +IS 189 1711 1711 0 0 +IS 190 1618 1618 0 0 +IS 191 1489 1489 0 0 +IS 192 1489 1489 0 0 +IS 193 1363 1363 0 0 +IS 194 1295 1295 0 0 +IS 195 1181 1181 0 0 +IS 196 1156 1154 2 0 +IS 197 1020 1018 2 0 +IS 198 982 981 1 0 +IS 199 901 893 8 0 +IS 200 817 816 1 0 +IS 201 720 717 3 0 +IS 202 703 703 0 0 +IS 203 617 617 0 0 +IS 204 508 508 0 0 +IS 205 503 503 0 0 +IS 206 429 429 0 0 +IS 207 379 379 0 0 +IS 208 352 349 3 0 +IS 209 304 304 0 0 +IS 210 288 288 0 0 +IS 211 182 182 0 0 +IS 212 205 204 1 0 +IS 213 178 178 0 0 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0 0 +IS 7412 0 0 0 0 +IS 7413 0 0 0 0 +IS 7414 2 2 0 0 +IS 7415 0 0 0 0 +IS 7416 1 1 0 0 +IS 7417 0 0 0 0 +IS 7418 0 0 0 0 +IS 7419 1 1 0 0 +IS 7420 0 0 0 0 +IS 7421 0 0 0 0 +IS 7422 0 0 0 0 +IS 7423 0 0 0 0 +IS 7424 1 1 0 0 +IS 7425 0 0 0 0 +IS 7426 1 1 0 0 +IS 7427 2 2 0 0 +IS 7428 0 0 0 0 +IS 7429 2 2 0 0 +IS 7430 1 1 0 0 +IS 7431 0 0 0 0 +IS 7432 0 0 0 0 +IS 7433 1 1 0 0 +IS 7434 0 0 0 0 +IS 7435 0 0 0 0 +IS 7436 0 0 0 0 +IS 7437 0 0 0 0 +IS 7438 0 0 0 0 +IS 7439 0 0 0 0 +IS 7440 0 0 0 0 +IS 7441 0 0 0 0 +IS 7442 0 0 0 0 +IS 7443 1 1 0 0 +IS 7444 0 0 0 0 +IS 7445 0 0 0 0 +IS 7446 0 0 0 0 +IS 7447 1 1 0 0 +IS 7448 0 0 0 0 +IS 7449 0 0 0 0 +IS 7450 0 0 0 0 +IS 7451 1 1 0 0 +IS 7452 1 1 0 0 +IS 7453 0 0 0 0 +IS 7454 1 1 0 0 +IS 7455 0 0 0 0 +IS 7456 0 0 0 0 +IS 7457 1 1 0 0 +IS 7458 1 1 0 0 +IS 7459 0 0 0 0 +IS 7460 0 0 0 0 +IS 7461 0 0 0 0 +IS 7462 0 0 0 0 +IS 7463 0 0 0 0 +IS 7464 0 0 0 0 +IS 7465 0 0 0 0 +IS 7466 1 1 0 0 +IS 7467 1 1 0 0 +IS 7468 0 0 0 0 +IS 7469 0 0 0 0 +IS 7470 2 2 0 0 +IS 7471 0 0 0 0 +IS 7472 1 1 0 0 +IS 7473 1 1 0 0 +IS 7474 1 1 0 0 +IS 7475 1 1 0 0 +IS 7476 2 2 0 0 +IS 7477 0 0 0 0 +IS 7478 2 2 0 0 +IS 7479 0 0 0 0 +IS 7480 1 1 0 0 +IS 7481 1 1 0 0 +IS 7482 1 1 0 0 +IS 7483 1 1 0 0 +IS 7484 0 0 0 0 +IS 7485 2 2 0 0 +IS 7486 0 0 0 0 +IS 7487 2 2 0 0 +IS 7488 3 3 0 0 +IS 7489 0 0 0 0 +IS 7490 1 1 0 0 +IS 7491 2 2 0 0 +IS 7492 2 2 0 0 +IS 7493 0 0 0 0 +IS 7494 2 2 0 0 +IS 7495 4 4 0 0 +IS 7496 3 3 0 0 +IS 7497 0 0 0 0 +IS 7498 0 0 0 0 +IS 7499 1 1 0 0 +IS 7500 2 2 0 0 +IS 7501 1 1 0 0 +IS 7502 4 4 0 0 +IS 7503 1 1 0 0 +IS 7504 3 3 0 0 +IS 7505 1 1 0 0 +IS 7506 6 6 0 0 +IS 7507 1 1 0 0 +IS 7508 9 9 0 0 +IS 7509 1 1 0 0 +IS 7510 4 4 0 0 +IS 7511 6 6 0 0 +IS 7512 6 6 0 0 +IS 7513 3 3 0 0 +IS 7514 3 3 0 0 +IS 7515 6 6 0 0 +IS 7516 7 7 0 0 +IS 7517 7 7 0 0 +IS 7518 3 3 0 0 +IS 7519 7 7 0 0 +IS 7520 12 12 0 0 +IS 7521 5 5 0 0 +IS 7522 10 10 0 0 +IS 7523 7 7 0 0 +IS 7524 8 8 0 0 +IS 7525 6 6 0 0 +IS 7526 6 6 0 0 +IS 7527 6 6 0 0 +IS 7528 5 5 0 0 +IS 7529 8 8 0 0 +IS 7530 5 5 0 0 +IS 7531 9 9 0 0 +IS 7532 10 10 0 0 +IS 7533 9 9 0 0 +IS 7534 4 4 0 0 +IS 7535 3 3 0 0 +IS 7536 8 8 0 0 +IS 7537 9 9 0 0 +IS 7538 10 10 0 0 +IS 7539 12 12 0 0 +IS 7540 10 10 0 0 +IS 7541 8 8 0 0 +IS 7542 7 7 0 0 +IS 7543 14 14 0 0 +IS 7544 6 6 0 0 +IS 7545 7 7 0 0 +IS 7546 9 9 0 0 +IS 7547 9 9 0 0 +IS 7548 10 10 0 0 +IS 7549 13 13 0 0 +IS 7550 7 7 0 0 +IS 7551 9 9 0 0 +IS 7552 6 6 0 0 +IS 7553 4 4 0 0 +IS 7554 3 3 0 0 +IS 7555 4 4 0 0 +IS 7556 7 7 0 0 +IS 7557 4 4 0 0 +IS 7558 8 8 0 0 +IS 7559 4 4 0 0 +IS 7560 9 9 0 0 +IS 7561 6 6 0 0 +IS 7562 2 2 0 0 +IS 7563 3 3 0 0 +IS 7564 2 2 0 0 +IS 7565 3 3 0 0 +IS 7566 3 3 0 0 +IS 7567 4 4 0 0 +IS 7568 4 4 0 0 +IS 7569 2 2 0 0 +IS 7570 0 0 0 0 +IS 7571 2 2 0 0 +IS 7572 1 1 0 0 +IS 7573 4 4 0 0 +IS 7574 2 2 0 0 +IS 7575 1 1 0 0 +IS 7576 2 2 0 0 +IS 7577 1 1 0 0 +IS 7578 0 0 0 0 +IS 7579 0 0 0 0 +IS 7580 0 0 0 0 +IS 7581 2 2 0 0 +IS 7582 0 0 0 0 +IS 7583 1 1 0 0 +IS 7584 0 0 0 0 +IS 7585 0 0 0 0 +IS 7586 2 2 0 0 +IS 7587 0 0 0 0 +IS 7588 0 0 0 0 +IS 7589 2 2 0 0 +IS 7590 0 0 0 0 +IS 7591 0 0 0 0 +IS 7592 0 0 0 0 +IS 7593 2 2 0 0 +IS 7594 0 0 0 0 +IS 7595 1 1 0 0 +IS 7596 0 0 0 0 +IS 7597 0 0 0 0 +IS 7598 2 2 0 0 +IS 7599 0 0 0 0 +IS 7600 0 0 0 0 +IS 7601 2 2 0 0 +IS 7602 0 0 0 0 +IS 7603 0 0 0 0 +IS 7604 0 0 0 0 +IS 7605 0 0 0 0 +IS 7606 2 2 0 0 +IS 7607 0 0 0 0 +IS 7608 0 0 0 0 +IS 7609 1 1 0 0 +IS 7610 0 0 0 0 +IS 7611 2 2 0 0 +IS 7612 0 0 0 0 +IS 7613 0 0 0 0 +IS 7614 0 0 0 0 +IS 7615 1 1 0 0 +IS 7616 0 0 0 0 +IS 7617 0 0 0 0 +IS 7618 0 0 0 0 +IS 7619 1 1 0 0 +IS 7620 0 0 0 0 +IS 7621 1 1 0 0 +IS 7622 1 1 0 0 +IS 7623 0 0 0 0 +IS 7624 2 2 0 0 +IS 7625 0 0 0 0 +IS 7626 0 0 0 0 +IS 7627 1 1 0 0 +IS 7628 1 1 0 0 +IS 7629 0 0 0 0 +IS 7630 1 1 0 0 +IS 7631 0 0 0 0 +IS 7632 0 0 0 0 +IS 7633 0 0 0 0 +IS 7634 0 0 0 0 +IS 7635 0 0 0 0 +IS 7636 0 0 0 0 +IS 7637 0 0 0 0 +IS 7638 0 0 0 0 +IS 7639 0 0 0 0 +IS 7640 0 0 0 0 +IS 7641 0 0 0 0 +IS 7642 0 0 0 0 +IS 7643 0 0 0 0 +IS 7644 0 0 0 0 +IS 7645 0 0 0 0 +IS 7646 0 0 0 0 +IS 7647 0 0 0 0 +IS 7648 0 0 0 0 +IS 7649 0 0 0 0 +IS 7650 0 0 0 0 +IS 7651 0 0 0 0 +IS 7652 0 0 0 0 +IS 7653 0 0 0 0 +IS 7654 0 0 0 0 +IS 7655 0 0 0 0 +IS 7656 0 0 0 0 +IS 7657 1 1 0 0 +IS 7658 1 1 0 0 +IS 7659 0 0 0 0 +IS 7660 0 0 0 0 +IS 7661 2 2 0 0 +IS 7662 0 0 0 0 +IS 7663 0 0 0 0 +IS 7664 0 0 0 0 +IS 7665 0 0 0 0 +IS 7666 0 0 0 0 +IS 7667 0 0 0 0 +IS 7668 0 0 0 0 +IS 7669 0 0 0 0 +IS 7670 0 0 0 0 +IS 7671 0 0 0 0 +IS 7672 0 0 0 0 +IS 7673 0 0 0 0 +IS 7674 0 0 0 0 +IS 7675 0 0 0 0 +IS 7676 1 1 0 0 +IS 7677 0 0 0 0 +IS 7678 0 0 0 0 +IS 7679 0 0 0 0 +IS 7680 0 0 0 0 +IS 7681 0 0 0 0 +IS 7682 0 0 0 0 +IS 7683 0 0 0 0 +IS 7684 0 0 0 0 +IS 7685 0 0 0 0 +IS 7686 0 0 0 0 +IS 7687 0 0 0 0 +IS 7688 1 1 0 0 +IS 7689 0 0 0 0 +IS 7690 0 0 0 0 +IS 7691 0 0 0 0 +IS 7692 0 0 0 0 +IS 7693 0 0 0 0 +IS 7694 0 0 0 0 +IS 7695 0 0 0 0 +IS 7696 1 1 0 0 +IS 7697 1 1 0 0 +IS 7698 0 0 0 0 +IS 7699 0 0 0 0 +IS 7700 1 1 0 0 +IS 7701 1 1 0 0 +IS 7702 1 1 0 0 +IS 7703 0 0 0 0 +IS 7704 0 0 0 0 +IS 7705 0 0 0 0 +IS 7706 0 0 0 0 +IS 7707 0 0 0 0 +IS 7708 0 0 0 0 +IS 7709 0 0 0 0 +IS 7710 0 0 0 0 +IS 7711 0 0 0 0 +IS 7712 0 0 0 0 +IS 7713 0 0 0 0 +IS 7714 0 0 0 0 +IS 7715 0 0 0 0 +IS 7716 0 0 0 0 +IS 7717 0 0 0 0 +IS 7718 0 0 0 0 +IS 7719 0 0 0 0 +IS 7720 0 0 0 0 +IS 7721 0 0 0 0 +IS 7722 0 0 0 0 +IS 7723 0 0 0 0 +IS 7724 0 0 0 0 +IS 7725 0 0 0 0 +IS 7726 0 0 0 0 +IS 7727 0 0 0 0 +IS 7728 0 0 0 0 +IS 7729 0 0 0 0 +IS 7730 0 0 0 0 +IS 7731 0 0 0 0 +IS 7732 0 0 0 0 +IS 7733 0 0 0 0 +IS 7734 0 0 0 0 +IS 7735 0 0 0 0 +IS 7736 0 0 0 0 +IS 7737 0 0 0 0 +IS 7738 0 0 0 0 +IS 7739 0 0 0 0 +IS 7740 2 1 1 0 +IS 7741 1 0 1 0 +IS 7742 4 4 0 0 +IS 7743 0 0 0 0 +IS 7744 2 2 0 0 +IS 7745 1 1 0 0 +IS 7746 0 0 0 0 +IS 7747 1 1 0 0 +IS 7748 2 2 0 0 +IS 7749 0 0 0 0 +IS 7750 1 1 0 0 +IS 7751 0 0 0 0 +IS 7752 1 1 0 0 +IS 7753 1 1 0 0 +IS 7754 0 0 0 0 +IS 7755 1 1 0 0 +IS 7756 1 1 0 0 +IS 7757 3 3 0 0 +IS 7758 1 1 0 0 +IS 7759 1 1 0 0 +IS 7760 2 2 0 0 +IS 7761 0 0 0 0 +IS 7762 3 3 0 0 +IS 7763 1 1 0 0 +IS 7764 3 3 0 0 +IS 7765 3 3 0 0 +IS 7766 2 2 0 0 +IS 7767 3 3 0 0 +IS 7768 1 1 0 0 +IS 7769 4 4 0 0 +IS 7770 2 2 0 0 +IS 7771 2 2 0 0 +IS 7772 3 3 0 0 +IS 7773 4 4 0 0 +IS 7774 4 4 0 0 +IS 7775 1 1 0 0 +IS 7776 3 3 0 0 +IS 7777 4 4 0 0 +IS 7778 3 3 0 0 +IS 7779 4 4 0 0 +IS 7780 9 9 0 0 +IS 7781 8 8 0 0 +IS 7782 8 8 0 0 +IS 7783 7 7 0 0 +IS 7784 6 6 0 0 +IS 7785 11 11 0 0 +IS 7786 8 8 0 0 +IS 7787 7 7 0 0 +IS 7788 10 10 0 0 +IS 7789 9 9 0 0 +IS 7790 8 8 0 0 +IS 7791 10 10 0 0 +IS 7792 7 7 0 0 +IS 7793 11 11 0 0 +IS 7794 11 11 0 0 +IS 7795 11 11 0 0 +IS 7796 14 14 0 0 +IS 7797 11 11 0 0 +IS 7798 9 9 0 0 +IS 7799 12 12 0 0 +IS 7800 14 14 0 0 +IS 7801 13 13 0 0 +IS 7802 14 14 0 0 +IS 7803 13 13 0 0 +IS 7804 13 13 0 0 +IS 7805 12 12 0 0 +IS 7806 12 12 0 0 +IS 7807 9 9 0 0 +IS 7808 13 13 0 0 +IS 7809 12 12 0 0 +IS 7810 10 10 0 0 +IS 7811 14 14 0 0 +IS 7812 15 15 0 0 +IS 7813 13 13 0 0 +IS 7814 10 10 0 0 +IS 7815 12 12 0 0 +IS 7816 8 8 0 0 +IS 7817 6 6 0 0 +IS 7818 11 11 0 0 +IS 7819 8 8 0 0 +IS 7820 10 10 0 0 +IS 7821 8 8 0 0 +IS 7822 12 12 0 0 +IS 7823 9 9 0 0 +IS 7824 8 8 0 0 +IS 7825 8 8 0 0 +IS 7826 5 5 0 0 +IS 7827 10 10 0 0 +IS 7828 7 7 0 0 +IS 7829 7 7 0 0 +IS 7830 9 9 0 0 +IS 7831 4 4 0 0 +IS 7832 5 5 0 0 +IS 7833 4 4 0 0 +IS 7834 6 6 0 0 +IS 7835 4 4 0 0 +IS 7836 3 3 0 0 +IS 7837 5 5 0 0 +IS 7838 6 6 0 0 +IS 7839 6 6 0 0 +IS 7840 4 4 0 0 +IS 7841 1 1 0 0 +IS 7842 0 0 0 0 +IS 7843 0 0 0 0 +IS 7844 1 1 0 0 +IS 7845 2 2 0 0 +IS 7846 1 1 0 0 +IS 7847 2 2 0 0 +IS 7848 0 0 0 0 +IS 7849 1 1 0 0 +IS 7850 0 0 0 0 +IS 7851 0 0 0 0 +IS 7852 0 0 0 0 +IS 7853 0 0 0 0 +IS 7854 0 0 0 0 +IS 7855 0 0 0 0 +IS 7856 0 0 0 0 +IS 7857 0 0 0 0 +IS 7858 0 0 0 0 +IS 7859 0 0 0 0 +IS 7860 1 1 0 0 +IS 7861 1 1 0 0 +IS 7862 1 1 0 0 +IS 7863 0 0 0 0 +IS 7864 0 0 0 0 +IS 7865 0 0 0 0 +IS 7866 0 0 0 0 +IS 7867 1 1 0 0 +IS 7868 0 0 0 0 +IS 7869 0 0 0 0 +IS 7870 1 1 0 0 +IS 7871 0 0 0 0 +IS 7872 0 0 0 0 +IS 7873 1 1 0 0 +IS 7874 0 0 0 0 +IS 7875 0 0 0 0 +IS 7876 0 0 0 0 +IS 7877 0 0 0 0 +IS 7878 1 1 0 0 +IS 7879 0 0 0 0 +IS 7880 0 0 0 0 +IS 7881 0 0 0 0 +IS 7882 0 0 0 0 +IS 7883 0 0 0 0 +IS 7884 0 0 0 0 +IS 7885 0 0 0 0 +IS 7886 0 0 0 0 +IS 7887 0 0 0 0 +IS 7888 0 0 0 0 +IS 7889 1 1 0 0 +IS 7890 0 0 0 0 +IS 7891 0 0 0 0 +IS 7892 1 1 0 0 +IS 7893 0 0 0 0 +IS 7894 1 1 0 0 +IS 7895 0 0 0 0 +IS 7896 1 1 0 0 +IS 7897 0 0 0 0 +IS 7898 1 1 0 0 +IS 7899 0 0 0 0 +IS 7900 0 0 0 0 +IS 7901 0 0 0 0 +IS 7902 0 0 0 0 +IS 7903 0 0 0 0 +IS 7904 1 1 0 0 +IS 7905 0 0 0 0 +IS 7906 0 0 0 0 +IS 7907 0 0 0 0 +IS 7908 0 0 0 0 +IS 7909 0 0 0 0 +IS 7910 0 0 0 0 +IS 7911 0 0 0 0 +IS 7912 0 0 0 0 +IS 7913 0 0 0 0 +IS 7914 0 0 0 0 +IS 7915 0 0 0 0 +IS 7916 0 0 0 0 +IS 7917 0 0 0 0 +IS 7918 0 0 0 0 +IS 7919 0 0 0 0 +IS 7920 0 0 0 0 +IS 7921 0 0 0 0 +IS 7922 0 0 0 0 +IS 7923 0 0 0 0 +IS 7924 0 0 0 0 +IS 7925 0 0 0 0 +IS 7926 0 0 0 0 +IS 7927 0 0 0 0 +IS 7928 0 0 0 0 +IS 7929 0 0 0 0 +IS 7930 0 0 0 0 +IS 7931 0 0 0 0 +IS 7932 0 0 0 0 +IS 7933 0 0 0 0 +IS 7934 0 0 0 0 +IS 7935 0 0 0 0 +IS 7936 0 0 0 0 +IS 7937 0 0 0 0 +IS 7938 0 0 0 0 +IS 7939 0 0 0 0 +IS 7940 0 0 0 0 +IS 7941 0 0 0 0 +IS 7942 0 0 0 0 +IS 7943 0 0 0 0 +IS 7944 1 1 0 0 +IS 7945 0 0 0 0 +IS 7946 0 0 0 0 +IS 7947 0 0 0 0 +IS 7948 0 0 0 0 +IS 7949 0 0 0 0 +IS 7950 0 0 0 0 +IS 7951 0 0 0 0 +IS 7952 0 0 0 0 +IS 7953 0 0 0 0 +IS 7954 0 0 0 0 +IS 7955 0 0 0 0 +IS 7956 0 0 0 0 +IS 7957 0 0 0 0 +IS 7958 0 0 0 0 +IS 7959 1 1 0 0 +IS 7960 1 1 0 0 +IS 7961 0 0 0 0 +IS 7962 0 0 0 0 +IS 7963 0 0 0 0 +IS 7964 0 0 0 0 +IS 7965 0 0 0 0 +IS 7966 0 0 0 0 +IS 7967 0 0 0 0 +IS 7968 0 0 0 0 +IS 7969 1 1 0 0 +IS 7970 0 0 0 0 +IS 7971 0 0 0 0 +IS 7972 0 0 0 0 +IS 7973 0 0 0 0 +IS 7974 0 0 0 0 +IS 7975 0 0 0 0 +IS 7976 0 0 0 0 +IS 7977 1 1 0 0 +IS 7978 0 0 0 0 +IS 7979 0 0 0 0 +IS 7980 0 0 0 0 +IS 7981 0 0 0 0 +IS 7982 0 0 0 0 +IS 7983 0 0 0 0 +IS 7984 0 0 0 0 +IS 7985 1 1 0 0 +IS 7986 0 0 0 0 +IS 7987 0 0 0 0 +IS 7988 1 1 0 0 +IS 7989 0 0 0 0 +IS 7990 0 0 0 0 +IS 7991 1 1 0 0 +IS 7992 0 0 0 0 +IS 7993 1 1 0 0 +IS 7994 1 1 0 0 +IS 7995 0 0 0 0 +IS 7996 0 0 0 0 +IS 7997 0 0 0 0 +IS 7998 2 2 0 0 +IS 7999 3573 3553 11 9 +# Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count +RL 101 641821 +# Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions +ID 1 4895 3362 +ID 2 826 512 +# Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) +IC 2 0 3 0 0 +IC 3 8 9 2 2 +IC 4 14 13 33 36 +IC 5 58 65 31 35 +IC 6 58 67 19 20 +IC 7 31 30 14 13 +IC 8 32 32 12 13 +IC 9 27 41 15 13 +IC 10 15 21 25 17 +IC 11 29 24 27 22 +IC 12 20 18 19 18 +IC 13 31 23 29 21 +IC 14 25 32 15 16 +IC 15 33 29 22 20 +IC 16 24 15 23 23 +IC 17 24 20 25 22 +IC 18 27 30 20 35 +IC 19 30 39 35 47 +IC 20 30 25 38 22 +IC 21 36 29 30 25 +IC 22 31 23 26 24 +IC 23 25 43 32 29 +IC 24 31 35 20 19 +IC 25 30 33 17 13 +IC 26 39 28 16 15 +IC 27 50 56 24 18 +IC 28 31 26 10 17 +IC 29 34 31 21 20 +IC 30 26 28 25 19 +IC 31 27 27 22 20 +IC 32 28 37 20 22 +IC 33 24 24 25 10 +IC 34 22 32 24 23 +IC 35 36 25 19 15 +IC 36 26 23 15 29 +IC 37 15 20 30 29 +IC 38 25 32 18 21 +IC 39 20 23 25 24 +IC 40 31 47 26 21 +IC 41 23 29 29 29 +IC 42 27 24 16 17 +IC 43 25 29 21 29 +IC 44 27 32 19 13 +IC 45 36 40 19 26 +IC 46 24 29 21 24 +IC 47 33 28 16 14 +IC 48 41 38 10 16 +IC 49 32 39 22 24 +IC 50 34 29 18 15 +IC 51 15 21 31 28 +IC 52 40 37 28 13 +IC 53 26 21 24 19 +IC 54 20 21 12 22 +IC 55 29 28 17 21 +IC 56 22 20 13 15 +IC 57 23 15 33 30 +IC 58 28 23 19 19 +IC 59 43 39 21 20 +IC 60 38 39 20 21 +IC 61 25 23 21 24 +IC 62 29 21 15 18 +IC 63 39 25 17 14 +IC 64 27 23 11 17 +IC 65 20 35 26 31 +IC 66 23 30 24 13 +IC 67 35 29 22 29 +IC 68 20 24 21 27 +IC 69 28 27 21 14 +IC 70 41 28 21 13 +IC 71 36 35 15 22 +IC 72 25 24 15 18 +IC 73 15 27 18 15 +IC 74 24 27 22 19 +IC 75 28 38 18 22 +IC 76 29 46 24 16 +IC 77 28 48 22 14 +IC 78 23 21 15 28 +IC 79 30 34 26 23 +IC 80 34 30 29 19 +IC 81 31 32 14 17 +IC 82 33 28 20 15 +IC 83 37 20 28 9 +IC 84 27 26 19 12 +IC 85 31 25 16 14 +IC 86 22 26 14 13 +IC 87 30 23 20 23 +IC 88 33 24 8 13 +IC 89 31 26 17 24 +IC 90 34 30 11 19 +IC 91 34 17 16 17 +IC 92 29 29 14 16 +IC 93 23 29 9 9 +IC 94 18 40 13 18 +IC 95 28 48 18 12 +IC 96 42 49 26 27 +IC 97 48 64 36 35 +IC 98 25 28 1 1 +IC 99 10 9 0 0 +# Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. +COV [1-1] 1 639227 +COV [2-2] 2 385861 +COV [3-3] 3 200311 +COV [4-4] 4 140538 +COV [5-5] 5 100920 +COV [6-6] 6 78198 +COV [7-7] 7 63261 +COV [8-8] 8 53571 +COV [9-9] 9 45160 +COV [10-10] 10 40242 +COV [11-11] 11 35638 +COV [12-12] 12 32108 +COV [13-13] 13 28874 +COV [14-14] 14 26269 +COV [15-15] 15 24346 +COV [16-16] 16 22055 +COV [17-17] 17 19763 +COV [18-18] 18 18165 +COV [19-19] 19 17543 +COV [20-20] 20 16315 +COV [21-21] 21 16254 +COV [22-22] 22 14587 +COV [23-23] 23 13217 +COV [24-24] 24 12790 +COV [25-25] 25 12207 +COV [26-26] 26 11415 +COV [27-27] 27 10704 +COV [28-28] 28 9967 +COV [29-29] 29 9972 +COV [30-30] 30 9503 +COV [31-31] 31 9486 +COV [32-32] 32 8859 +COV [33-33] 33 8810 +COV [34-34] 34 8445 +COV [35-35] 35 7811 +COV [36-36] 36 7790 +COV [37-37] 37 7349 +COV [38-38] 38 7298 +COV [39-39] 39 6735 +COV [40-40] 40 6474 +COV [41-41] 41 6543 +COV [42-42] 42 6136 +COV [43-43] 43 6119 +COV [44-44] 44 5783 +COV [45-45] 45 5411 +COV [46-46] 46 5548 +COV [47-47] 47 5121 +COV [48-48] 48 5074 +COV [49-49] 49 4915 +COV [50-50] 50 4760 +COV [51-51] 51 4813 +COV [52-52] 52 4591 +COV [53-53] 53 4309 +COV [54-54] 54 3935 +COV [55-55] 55 4026 +COV [56-56] 56 3923 +COV [57-57] 57 3709 +COV [58-58] 58 3561 +COV [59-59] 59 3609 +COV [60-60] 60 3413 +COV [61-61] 61 3414 +COV [62-62] 62 3233 +COV [63-63] 63 3285 +COV [64-64] 64 3172 +COV [65-65] 65 3188 +COV [66-66] 66 2992 +COV [67-67] 67 2840 +COV [68-68] 68 3046 +COV [69-69] 69 2891 +COV [70-70] 70 2646 +COV [71-71] 71 2584 +COV [72-72] 72 2724 +COV [73-73] 73 2563 +COV [74-74] 74 2439 +COV [75-75] 75 2286 +COV [76-76] 76 2219 +COV [77-77] 77 2212 +COV [78-78] 78 2172 +COV [79-79] 79 2027 +COV [80-80] 80 1978 +COV [81-81] 81 2120 +COV [82-82] 82 2141 +COV [83-83] 83 1983 +COV [84-84] 84 2075 +COV [85-85] 85 1855 +COV [86-86] 86 1761 +COV [87-87] 87 1824 +COV [88-88] 88 1805 +COV [89-89] 89 1663 +COV [90-90] 90 1661 +COV [91-91] 91 1671 +COV [92-92] 92 1618 +COV [93-93] 93 1675 +COV [94-94] 94 1480 +COV [95-95] 95 1460 +COV [96-96] 96 1400 +COV [97-97] 97 1447 +COV [98-98] 98 1402 +COV [99-99] 99 1484 +COV [100-100] 100 1364 +COV [101-101] 101 1364 +COV [102-102] 102 1435 +COV [103-103] 103 1373 +COV [104-104] 104 1299 +COV [105-105] 105 1267 +COV [106-106] 106 1208 +COV [107-107] 107 1157 +COV [108-108] 108 1171 +COV [109-109] 109 1115 +COV [110-110] 110 1089 +COV [111-111] 111 1109 +COV [112-112] 112 1057 +COV [113-113] 113 1018 +COV [114-114] 114 1011 +COV [115-115] 115 976 +COV [116-116] 116 970 +COV [117-117] 117 887 +COV [118-118] 118 889 +COV [119-119] 119 876 +COV [120-120] 120 914 +COV [121-121] 121 835 +COV [122-122] 122 819 +COV [123-123] 123 751 +COV [124-124] 124 753 +COV [125-125] 125 766 +COV [126-126] 126 733 +COV [127-127] 127 650 +COV [128-128] 128 737 +COV [129-129] 129 745 +COV [130-130] 130 636 +COV [131-131] 131 643 +COV [132-132] 132 612 +COV [133-133] 133 668 +COV [134-134] 134 668 +COV [135-135] 135 645 +COV [136-136] 136 570 +COV [137-137] 137 587 +COV [138-138] 138 571 +COV [139-139] 139 616 +COV [140-140] 140 618 +COV [141-141] 141 571 +COV [142-142] 142 582 +COV [143-143] 143 535 +COV [144-144] 144 547 +COV [145-145] 145 519 +COV [146-146] 146 500 +COV [147-147] 147 500 +COV [148-148] 148 483 +COV [149-149] 149 463 +COV [150-150] 150 494 +COV [151-151] 151 474 +COV [152-152] 152 445 +COV [153-153] 153 477 +COV [154-154] 154 457 +COV [155-155] 155 427 +COV [156-156] 156 444 +COV [157-157] 157 436 +COV [158-158] 158 393 +COV [159-159] 159 382 +COV [160-160] 160 400 +COV [161-161] 161 436 +COV [162-162] 162 395 +COV [163-163] 163 387 +COV [164-164] 164 397 +COV [165-165] 165 419 +COV [166-166] 166 404 +COV [167-167] 167 393 +COV [168-168] 168 413 +COV [169-169] 169 415 +COV [170-170] 170 358 +COV [171-171] 171 335 +COV [172-172] 172 328 +COV [173-173] 173 334 +COV [174-174] 174 286 +COV [175-175] 175 315 +COV [176-176] 176 290 +COV [177-177] 177 305 +COV [178-178] 178 290 +COV [179-179] 179 285 +COV [180-180] 180 303 +COV [181-181] 181 251 +COV [182-182] 182 261 +COV [183-183] 183 265 +COV [184-184] 184 269 +COV [185-185] 185 242 +COV [186-186] 186 301 +COV [187-187] 187 284 +COV [188-188] 188 291 +COV [189-189] 189 293 +COV [190-190] 190 225 +COV [191-191] 191 255 +COV [192-192] 192 242 +COV [193-193] 193 247 +COV [194-194] 194 245 +COV [195-195] 195 205 +COV [196-196] 196 235 +COV [197-197] 197 236 +COV [198-198] 198 213 +COV [199-199] 199 217 +COV [200-200] 200 215 +COV [201-201] 201 175 +COV [202-202] 202 182 +COV [203-203] 203 206 +COV [204-204] 204 181 +COV [205-205] 205 212 +COV [206-206] 206 210 +COV [207-207] 207 212 +COV [208-208] 208 163 +COV [209-209] 209 216 +COV [210-210] 210 174 +COV [211-211] 211 195 +COV [212-212] 212 161 +COV [213-213] 213 182 +COV [214-214] 214 174 +COV [215-215] 215 147 +COV [216-216] 216 176 +COV [217-217] 217 185 +COV [218-218] 218 143 +COV [219-219] 219 154 +COV [220-220] 220 137 +COV [221-221] 221 159 +COV [222-222] 222 209 +COV [223-223] 223 168 +COV [224-224] 224 152 +COV [225-225] 225 161 +COV [226-226] 226 162 +COV [227-227] 227 177 +COV [228-228] 228 136 +COV [229-229] 229 127 +COV [230-230] 230 149 +COV [231-231] 231 151 +COV [232-232] 232 108 +COV [233-233] 233 139 +COV [234-234] 234 150 +COV [235-235] 235 153 +COV [236-236] 236 120 +COV [237-237] 237 128 +COV [238-238] 238 142 +COV [239-239] 239 113 +COV [240-240] 240 130 +COV [241-241] 241 112 +COV [242-242] 242 134 +COV [243-243] 243 145 +COV [244-244] 244 111 +COV [245-245] 245 174 +COV [246-246] 246 166 +COV [247-247] 247 144 +COV [248-248] 248 186 +COV [249-249] 249 130 +COV [250-250] 250 107 +COV [251-251] 251 153 +COV [252-252] 252 134 +COV [253-253] 253 135 +COV [254-254] 254 131 +COV [255-255] 255 110 +COV [256-256] 256 117 +COV [257-257] 257 113 +COV [258-258] 258 131 +COV [259-259] 259 107 +COV [260-260] 260 104 +COV [261-261] 261 131 +COV [262-262] 262 112 +COV [263-263] 263 128 +COV [264-264] 264 97 +COV [265-265] 265 129 +COV [266-266] 266 132 +COV [267-267] 267 95 +COV [268-268] 268 98 +COV [269-269] 269 115 +COV [270-270] 270 105 +COV [271-271] 271 121 +COV [272-272] 272 109 +COV [273-273] 273 115 +COV [274-274] 274 101 +COV [275-275] 275 97 +COV [276-276] 276 134 +COV [277-277] 277 112 +COV [278-278] 278 134 +COV [279-279] 279 133 +COV [280-280] 280 113 +COV [281-281] 281 104 +COV [282-282] 282 127 +COV [283-283] 283 126 +COV [284-284] 284 115 +COV [285-285] 285 115 +COV [286-286] 286 116 +COV [287-287] 287 99 +COV [288-288] 288 109 +COV [289-289] 289 107 +COV [290-290] 290 106 +COV [291-291] 291 96 +COV [292-292] 292 92 +COV [293-293] 293 93 +COV [294-294] 294 98 +COV [295-295] 295 95 +COV [296-296] 296 98 +COV [297-297] 297 116 +COV [298-298] 298 104 +COV [299-299] 299 108 +COV [300-300] 300 107 +COV [301-301] 301 106 +COV [302-302] 302 105 +COV [303-303] 303 114 +COV [304-304] 304 116 +COV [305-305] 305 91 +COV [306-306] 306 107 +COV [307-307] 307 114 +COV [308-308] 308 109 +COV [309-309] 309 111 +COV [310-310] 310 101 +COV [311-311] 311 132 +COV [312-312] 312 115 +COV [313-313] 313 120 +COV [314-314] 314 86 +COV [315-315] 315 109 +COV [316-316] 316 125 +COV [317-317] 317 126 +COV [318-318] 318 111 +COV [319-319] 319 106 +COV [320-320] 320 110 +COV [321-321] 321 107 +COV [322-322] 322 91 +COV [323-323] 323 100 +COV [324-324] 324 99 +COV [325-325] 325 100 +COV [326-326] 326 97 +COV [327-327] 327 122 +COV [328-328] 328 97 +COV [329-329] 329 142 +COV [330-330] 330 109 +COV [331-331] 331 114 +COV [332-332] 332 105 +COV [333-333] 333 109 +COV [334-334] 334 107 +COV [335-335] 335 97 +COV [336-336] 336 108 +COV [337-337] 337 86 +COV [338-338] 338 101 +COV [339-339] 339 95 +COV [340-340] 340 90 +COV [341-341] 341 93 +COV [342-342] 342 84 +COV [343-343] 343 92 +COV [344-344] 344 96 +COV [345-345] 345 105 +COV [346-346] 346 88 +COV [347-347] 347 90 +COV [348-348] 348 84 +COV [349-349] 349 85 +COV [350-350] 350 73 +COV [351-351] 351 99 +COV [352-352] 352 104 +COV [353-353] 353 95 +COV [354-354] 354 95 +COV [355-355] 355 95 +COV [356-356] 356 98 +COV [357-357] 357 125 +COV [358-358] 358 72 +COV [359-359] 359 71 +COV [360-360] 360 84 +COV [361-361] 361 84 +COV [362-362] 362 75 +COV [363-363] 363 95 +COV [364-364] 364 74 +COV [365-365] 365 78 +COV [366-366] 366 82 +COV [367-367] 367 81 +COV [368-368] 368 67 +COV [369-369] 369 79 +COV [370-370] 370 81 +COV [371-371] 371 74 +COV [372-372] 372 85 +COV [373-373] 373 72 +COV [374-374] 374 76 +COV [375-375] 375 62 +COV [376-376] 376 81 +COV [377-377] 377 82 +COV [378-378] 378 74 +COV [379-379] 379 55 +COV [380-380] 380 71 +COV [381-381] 381 80 +COV [382-382] 382 74 +COV [383-383] 383 69 +COV [384-384] 384 65 +COV [385-385] 385 78 +COV [386-386] 386 80 +COV [387-387] 387 72 +COV [388-388] 388 67 +COV [389-389] 389 81 +COV [390-390] 390 71 +COV [391-391] 391 53 +COV [392-392] 392 67 +COV [393-393] 393 49 +COV [394-394] 394 78 +COV [395-395] 395 85 +COV [396-396] 396 65 +COV [397-397] 397 69 +COV [398-398] 398 62 +COV [399-399] 399 68 +COV [400-400] 400 68 +COV [401-401] 401 56 +COV [402-402] 402 64 +COV [403-403] 403 45 +COV [404-404] 404 64 +COV [405-405] 405 64 +COV [406-406] 406 76 +COV [407-407] 407 82 +COV [408-408] 408 76 +COV [409-409] 409 69 +COV [410-410] 410 63 +COV [411-411] 411 66 +COV [412-412] 412 79 +COV [413-413] 413 56 +COV [414-414] 414 62 +COV [415-415] 415 63 +COV [416-416] 416 75 +COV [417-417] 417 61 +COV [418-418] 418 53 +COV [419-419] 419 57 +COV [420-420] 420 59 +COV [421-421] 421 50 +COV [422-422] 422 63 +COV [423-423] 423 63 +COV [424-424] 424 41 +COV [425-425] 425 71 +COV [426-426] 426 70 +COV [427-427] 427 59 +COV [428-428] 428 54 +COV [429-429] 429 52 +COV [430-430] 430 54 +COV [431-431] 431 56 +COV [432-432] 432 58 +COV [433-433] 433 59 +COV [434-434] 434 55 +COV [435-435] 435 43 +COV [436-436] 436 52 +COV [437-437] 437 50 +COV [438-438] 438 57 +COV [439-439] 439 66 +COV [440-440] 440 70 +COV [441-441] 441 55 +COV [442-442] 442 68 +COV [443-443] 443 61 +COV [444-444] 444 63 +COV [445-445] 445 64 +COV [446-446] 446 73 +COV [447-447] 447 61 +COV [448-448] 448 54 +COV [449-449] 449 56 +COV [450-450] 450 46 +COV [451-451] 451 69 +COV [452-452] 452 64 +COV [453-453] 453 53 +COV [454-454] 454 68 +COV [455-455] 455 65 +COV [456-456] 456 52 +COV [457-457] 457 68 +COV [458-458] 458 70 +COV [459-459] 459 59 +COV [460-460] 460 52 +COV [461-461] 461 60 +COV [462-462] 462 37 +COV [463-463] 463 59 +COV [464-464] 464 42 +COV [465-465] 465 70 +COV [466-466] 466 59 +COV [467-467] 467 44 +COV [468-468] 468 42 +COV [469-469] 469 52 +COV [470-470] 470 57 +COV [471-471] 471 75 +COV [472-472] 472 58 +COV [473-473] 473 48 +COV [474-474] 474 65 +COV [475-475] 475 61 +COV [476-476] 476 47 +COV [477-477] 477 47 +COV [478-478] 478 52 +COV [479-479] 479 43 +COV [480-480] 480 57 +COV [481-481] 481 45 +COV [482-482] 482 58 +COV [483-483] 483 63 +COV [484-484] 484 62 +COV [485-485] 485 57 +COV [486-486] 486 67 +COV [487-487] 487 65 +COV [488-488] 488 63 +COV [489-489] 489 67 +COV [490-490] 490 63 +COV [491-491] 491 62 +COV [492-492] 492 72 +COV [493-493] 493 62 +COV [494-494] 494 60 +COV [495-495] 495 60 +COV [496-496] 496 61 +COV [497-497] 497 70 +COV [498-498] 498 57 +COV [499-499] 499 62 +COV [500-500] 500 59 +COV [501-501] 501 51 +COV [502-502] 502 55 +COV [503-503] 503 59 +COV [504-504] 504 61 +COV [505-505] 505 56 +COV [506-506] 506 57 +COV [507-507] 507 57 +COV [508-508] 508 45 +COV [509-509] 509 62 +COV [510-510] 510 65 +COV [511-511] 511 40 +COV [512-512] 512 69 +COV [513-513] 513 64 +COV [514-514] 514 37 +COV [515-515] 515 57 +COV [516-516] 516 47 +COV [517-517] 517 38 +COV [518-518] 518 69 +COV [519-519] 519 38 +COV [520-520] 520 58 +COV [521-521] 521 51 +COV [522-522] 522 40 +COV [523-523] 523 47 +COV [524-524] 524 40 +COV [525-525] 525 49 +COV [526-526] 526 47 +COV [527-527] 527 38 +COV [528-528] 528 44 +COV [529-529] 529 55 +COV [530-530] 530 44 +COV [531-531] 531 32 +COV [532-532] 532 43 +COV [533-533] 533 41 +COV [534-534] 534 36 +COV [535-535] 535 46 +COV [536-536] 536 41 +COV [537-537] 537 54 +COV [538-538] 538 39 +COV [539-539] 539 49 +COV [540-540] 540 36 +COV [541-541] 541 34 +COV [542-542] 542 39 +COV [543-543] 543 47 +COV [544-544] 544 33 +COV [545-545] 545 29 +COV [546-546] 546 34 +COV [547-547] 547 36 +COV [548-548] 548 29 +COV [549-549] 549 34 +COV [550-550] 550 33 +COV [551-551] 551 70 +COV [552-552] 552 32 +COV [553-553] 553 45 +COV [554-554] 554 38 +COV [555-555] 555 31 +COV [556-556] 556 43 +COV [557-557] 557 38 +COV [558-558] 558 42 +COV [559-559] 559 29 +COV [560-560] 560 26 +COV [561-561] 561 23 +COV [562-562] 562 35 +COV [563-563] 563 39 +COV [564-564] 564 28 +COV [565-565] 565 30 +COV [566-566] 566 29 +COV [567-567] 567 30 +COV [568-568] 568 42 +COV [569-569] 569 42 +COV [570-570] 570 30 +COV [571-571] 571 23 +COV [572-572] 572 26 +COV [573-573] 573 37 +COV [574-574] 574 34 +COV [575-575] 575 35 +COV [576-576] 576 39 +COV [577-577] 577 34 +COV [578-578] 578 32 +COV [579-579] 579 28 +COV [580-580] 580 29 +COV [581-581] 581 25 +COV [582-582] 582 29 +COV [583-583] 583 43 +COV [584-584] 584 30 +COV [585-585] 585 34 +COV [586-586] 586 29 +COV [587-587] 587 29 +COV [588-588] 588 35 +COV [589-589] 589 27 +COV [590-590] 590 26 +COV [591-591] 591 25 +COV [592-592] 592 34 +COV [593-593] 593 29 +COV [594-594] 594 21 +COV [595-595] 595 22 +COV [596-596] 596 28 +COV [597-597] 597 33 +COV [598-598] 598 40 +COV [599-599] 599 28 +COV [600-600] 600 29 +COV [601-601] 601 39 +COV [602-602] 602 36 +COV [603-603] 603 28 +COV [604-604] 604 27 +COV [605-605] 605 27 +COV [606-606] 606 32 +COV [607-607] 607 24 +COV [608-608] 608 40 +COV [609-609] 609 36 +COV [610-610] 610 37 +COV [611-611] 611 29 +COV [612-612] 612 35 +COV [613-613] 613 30 +COV [614-614] 614 41 +COV [615-615] 615 36 +COV [616-616] 616 42 +COV [617-617] 617 35 +COV [618-618] 618 27 +COV [619-619] 619 32 +COV [620-620] 620 33 +COV [621-621] 621 27 +COV [622-622] 622 43 +COV [623-623] 623 34 +COV [624-624] 624 39 +COV [625-625] 625 36 +COV [626-626] 626 31 +COV [627-627] 627 42 +COV [628-628] 628 29 +COV [629-629] 629 38 +COV [630-630] 630 32 +COV [631-631] 631 30 +COV [632-632] 632 38 +COV [633-633] 633 39 +COV [634-634] 634 26 +COV [635-635] 635 30 +COV [636-636] 636 23 +COV [637-637] 637 34 +COV [638-638] 638 23 +COV [639-639] 639 28 +COV [640-640] 640 36 +COV [641-641] 641 30 +COV [642-642] 642 43 +COV [643-643] 643 37 +COV [644-644] 644 36 +COV [645-645] 645 32 +COV [646-646] 646 39 +COV [647-647] 647 29 +COV [648-648] 648 37 +COV [649-649] 649 40 +COV [650-650] 650 31 +COV [651-651] 651 32 +COV [652-652] 652 24 +COV [653-653] 653 19 +COV [654-654] 654 28 +COV [655-655] 655 29 +COV [656-656] 656 27 +COV [657-657] 657 33 +COV [658-658] 658 28 +COV [659-659] 659 18 +COV [660-660] 660 25 +COV [661-661] 661 33 +COV [662-662] 662 29 +COV [663-663] 663 31 +COV [664-664] 664 26 +COV [665-665] 665 35 +COV [666-666] 666 21 +COV [667-667] 667 27 +COV [668-668] 668 26 +COV [669-669] 669 22 +COV [670-670] 670 30 +COV [671-671] 671 31 +COV [672-672] 672 21 +COV [673-673] 673 34 +COV [674-674] 674 40 +COV [675-675] 675 35 +COV [676-676] 676 36 +COV [677-677] 677 32 +COV [678-678] 678 40 +COV [679-679] 679 33 +COV [680-680] 680 32 +COV [681-681] 681 23 +COV [682-682] 682 32 +COV [683-683] 683 27 +COV [684-684] 684 32 +COV [685-685] 685 30 +COV [686-686] 686 31 +COV [687-687] 687 26 +COV [688-688] 688 28 +COV [689-689] 689 31 +COV [690-690] 690 22 +COV [691-691] 691 27 +COV [692-692] 692 22 +COV [693-693] 693 27 +COV [694-694] 694 27 +COV [695-695] 695 25 +COV [696-696] 696 25 +COV [697-697] 697 32 +COV [698-698] 698 25 +COV [699-699] 699 27 +COV [700-700] 700 27 +COV [701-701] 701 27 +COV [702-702] 702 24 +COV [703-703] 703 29 +COV [704-704] 704 22 +COV [705-705] 705 26 +COV [706-706] 706 16 +COV [707-707] 707 23 +COV [708-708] 708 23 +COV [709-709] 709 23 +COV [710-710] 710 28 +COV [711-711] 711 26 +COV [712-712] 712 28 +COV [713-713] 713 39 +COV [714-714] 714 22 +COV [715-715] 715 29 +COV [716-716] 716 16 +COV [717-717] 717 18 +COV [718-718] 718 26 +COV [719-719] 719 22 +COV [720-720] 720 21 +COV [721-721] 721 20 +COV [722-722] 722 30 +COV [723-723] 723 26 +COV [724-724] 724 25 +COV [725-725] 725 22 +COV [726-726] 726 24 +COV [727-727] 727 30 +COV [728-728] 728 21 +COV [729-729] 729 26 +COV [730-730] 730 20 +COV [731-731] 731 30 +COV [732-732] 732 27 +COV [733-733] 733 28 +COV [734-734] 734 25 +COV [735-735] 735 22 +COV [736-736] 736 32 +COV [737-737] 737 36 +COV [738-738] 738 32 +COV [739-739] 739 26 +COV [740-740] 740 22 +COV [741-741] 741 21 +COV [742-742] 742 18 +COV [743-743] 743 28 +COV [744-744] 744 28 +COV [745-745] 745 21 +COV [746-746] 746 16 +COV [747-747] 747 30 +COV [748-748] 748 28 +COV [749-749] 749 22 +COV [750-750] 750 21 +COV [751-751] 751 30 +COV [752-752] 752 12 +COV [753-753] 753 24 +COV [754-754] 754 28 +COV [755-755] 755 19 +COV [756-756] 756 36 +COV [757-757] 757 27 +COV [758-758] 758 26 +COV [759-759] 759 29 +COV [760-760] 760 26 +COV [761-761] 761 24 +COV [762-762] 762 21 +COV [763-763] 763 18 +COV [764-764] 764 19 +COV [765-765] 765 26 +COV [766-766] 766 21 +COV [767-767] 767 17 +COV [768-768] 768 26 +COV [769-769] 769 18 +COV [770-770] 770 14 +COV [771-771] 771 18 +COV [772-772] 772 20 +COV [773-773] 773 21 +COV [774-774] 774 20 +COV [775-775] 775 16 +COV [776-776] 776 17 +COV [777-777] 777 24 +COV [778-778] 778 12 +COV [779-779] 779 19 +COV [780-780] 780 14 +COV [781-781] 781 25 +COV [782-782] 782 21 +COV [783-783] 783 27 +COV [784-784] 784 21 +COV [785-785] 785 19 +COV [786-786] 786 23 +COV [787-787] 787 19 +COV [788-788] 788 24 +COV [789-789] 789 15 +COV [790-790] 790 17 +COV [791-791] 791 16 +COV [792-792] 792 23 +COV [793-793] 793 19 +COV [794-794] 794 17 +COV [795-795] 795 13 +COV [796-796] 796 18 +COV [797-797] 797 23 +COV [798-798] 798 22 +COV [799-799] 799 22 +COV [800-800] 800 13 +COV [801-801] 801 13 +COV [802-802] 802 13 +COV [803-803] 803 13 +COV [804-804] 804 23 +COV [805-805] 805 20 +COV [806-806] 806 17 +COV [807-807] 807 16 +COV [808-808] 808 11 +COV [809-809] 809 23 +COV [810-810] 810 17 +COV [811-811] 811 10 +COV [812-812] 812 17 +COV [813-813] 813 12 +COV [814-814] 814 14 +COV [815-815] 815 14 +COV [816-816] 816 14 +COV [817-817] 817 24 +COV [818-818] 818 17 +COV [819-819] 819 21 +COV [820-820] 820 21 +COV [821-821] 821 10 +COV [822-822] 822 20 +COV [823-823] 823 19 +COV [824-824] 824 17 +COV [825-825] 825 18 +COV [826-826] 826 21 +COV [827-827] 827 24 +COV [828-828] 828 14 +COV [829-829] 829 21 +COV [830-830] 830 25 +COV [831-831] 831 18 +COV [832-832] 832 23 +COV [833-833] 833 19 +COV [834-834] 834 17 +COV [835-835] 835 19 +COV [836-836] 836 19 +COV [837-837] 837 20 +COV [838-838] 838 24 +COV [839-839] 839 20 +COV [840-840] 840 16 +COV [841-841] 841 21 +COV [842-842] 842 20 +COV [843-843] 843 17 +COV [844-844] 844 18 +COV [845-845] 845 14 +COV [846-846] 846 16 +COV [847-847] 847 11 +COV [848-848] 848 17 +COV [849-849] 849 12 +COV [850-850] 850 18 +COV [851-851] 851 22 +COV [852-852] 852 15 +COV [853-853] 853 17 +COV [854-854] 854 16 +COV [855-855] 855 18 +COV [856-856] 856 11 +COV [857-857] 857 7 +COV [858-858] 858 6 +COV [859-859] 859 23 +COV [860-860] 860 14 +COV [861-861] 861 10 +COV [862-862] 862 19 +COV [863-863] 863 8 +COV [864-864] 864 14 +COV [865-865] 865 10 +COV [866-866] 866 9 +COV [867-867] 867 11 +COV [868-868] 868 16 +COV [869-869] 869 8 +COV [870-870] 870 9 +COV [871-871] 871 9 +COV [872-872] 872 13 +COV [873-873] 873 6 +COV [874-874] 874 15 +COV [875-875] 875 5 +COV [876-876] 876 6 +COV [877-877] 877 8 +COV [878-878] 878 8 +COV [879-879] 879 14 +COV [880-880] 880 8 +COV [881-881] 881 20 +COV [882-882] 882 15 +COV [883-883] 883 12 +COV [884-884] 884 14 +COV [885-885] 885 14 +COV [886-886] 886 12 +COV [887-887] 887 11 +COV [888-888] 888 13 +COV [889-889] 889 11 +COV [890-890] 890 6 +COV [891-891] 891 11 +COV [892-892] 892 9 +COV [893-893] 893 9 +COV [894-894] 894 12 +COV [895-895] 895 16 +COV [896-896] 896 10 +COV [897-897] 897 8 +COV [898-898] 898 8 +COV [899-899] 899 11 +COV [900-900] 900 7 +COV [901-901] 901 15 +COV [902-902] 902 13 +COV [903-903] 903 17 +COV [904-904] 904 9 +COV [905-905] 905 8 +COV [906-906] 906 13 +COV [907-907] 907 10 +COV [908-908] 908 8 +COV [909-909] 909 13 +COV [910-910] 910 7 +COV [911-911] 911 9 +COV [912-912] 912 8 +COV [913-913] 913 9 +COV [914-914] 914 8 +COV [915-915] 915 9 +COV [916-916] 916 6 +COV [917-917] 917 9 +COV [918-918] 918 7 +COV [919-919] 919 9 +COV [920-920] 920 8 +COV [921-921] 921 13 +COV [922-922] 922 5 +COV [923-923] 923 5 +COV [924-924] 924 5 +COV [925-925] 925 7 +COV [926-926] 926 10 +COV [927-927] 927 6 +COV [928-928] 928 21 +COV [929-929] 929 10 +COV [930-930] 930 10 +COV [931-931] 931 7 +COV [932-932] 932 12 +COV [933-933] 933 14 +COV [934-934] 934 14 +COV [935-935] 935 7 +COV [936-936] 936 12 +COV [937-937] 937 13 +COV [938-938] 938 10 +COV [939-939] 939 12 +COV [940-940] 940 18 +COV [941-941] 941 11 +COV [942-942] 942 10 +COV [943-943] 943 6 +COV [944-944] 944 12 +COV [945-945] 945 12 +COV [946-946] 946 8 +COV [947-947] 947 12 +COV [948-948] 948 10 +COV [949-949] 949 5 +COV [950-950] 950 9 +COV [951-951] 951 16 +COV [952-952] 952 13 +COV [953-953] 953 15 +COV [954-954] 954 15 +COV [955-955] 955 8 +COV [956-956] 956 15 +COV [957-957] 957 18 +COV [958-958] 958 9 +COV [959-959] 959 21 +COV [960-960] 960 14 +COV [961-961] 961 17 +COV [962-962] 962 9 +COV [963-963] 963 14 +COV [964-964] 964 6 +COV [965-965] 965 5 +COV [966-966] 966 13 +COV [967-967] 967 12 +COV [968-968] 968 13 +COV [969-969] 969 10 +COV [970-970] 970 13 +COV [971-971] 971 8 +COV [972-972] 972 13 +COV [973-973] 973 12 +COV [974-974] 974 14 +COV [975-975] 975 9 +COV [976-976] 976 12 +COV [977-977] 977 4 +COV [978-978] 978 14 +COV [979-979] 979 6 +COV [980-980] 980 12 +COV [981-981] 981 5 +COV [982-982] 982 8 +COV [983-983] 983 4 +COV [984-984] 984 9 +COV [985-985] 985 9 +COV [986-986] 986 10 +COV [987-987] 987 8 +COV [988-988] 988 4 +COV [989-989] 989 6 +COV [990-990] 990 3 +COV [991-991] 991 5 +COV [992-992] 992 2 +COV [993-993] 993 6 +COV [994-994] 994 6 +COV [995-995] 995 7 +COV [996-996] 996 14 +COV [997-997] 997 12 +COV [998-998] 998 7 +COV [999-999] 999 8 +COV [1000-1000] 1000 8 +COV [1000<] 1000 5025 +# GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile +GCD 0.0 0.554 0.000 0.000 0.000 0.000 0.000 +GCD 0.5 0.831 0.525 0.525 0.525 0.525 0.525 +GCD 36.0 1.385 0.954 0.954 0.954 1.490 1.490 +GCD 37.0 2.216 2.495 2.495 4.146 6.560 6.560 +GCD 38.0 5.263 0.247 0.454 3.520 5.868 9.883 +GCD 39.0 9.141 0.177 0.303 2.161 8.777 12.812 +GCD 40.0 12.188 0.020 1.192 9.060 22.018 27.371 +GCD 41.0 16.343 0.035 0.550 2.702 11.469 12.908 +GCD 42.0 21.884 0.010 0.172 2.121 5.621 17.094 +GCD 43.0 28.255 0.010 0.328 1.449 4.277 10.166 +GCD 44.0 36.288 0.162 0.394 5.484 15.145 50.490 +GCD 45.0 42.105 0.020 0.131 1.252 7.009 17.811 +GCD 46.0 49.861 0.015 0.121 0.636 1.939 37.506 +GCD 47.0 56.510 0.030 0.141 1.015 4.500 6.338 +GCD 48.0 64.543 0.010 0.091 2.565 7.287 21.872 +GCD 49.0 68.975 0.010 0.333 0.672 10.751 27.129 +GCD 50.0 73.407 0.010 0.121 1.358 3.883 6.615 +GCD 51.0 77.008 0.121 0.576 1.576 4.363 13.923 +GCD 52.0 81.994 0.010 0.086 1.560 4.414 109.383 +GCD 53.0 84.488 0.040 0.071 0.500 3.025 31.234 +GCD 54.0 86.704 0.020 0.313 9.332 39.683 203.959 +GCD 55.0 89.197 0.005 0.051 1.268 5.045 23.578 +GCD 56.0 91.136 0.071 0.192 1.566 9.994 33.315 +GCD 57.0 94.460 0.040 0.348 1.167 5.050 11.660 +GCD 58.0 95.845 0.131 0.131 1.899 2.742 4.929 +GCD 59.0 96.399 3.313 3.313 3.313 3.666 3.666 +GCD 60.0 97.507 0.995 0.995 5.176 6.954 33.234 +GCD 61.0 98.338 1.591 1.591 1.788 4.848 4.848 +GCD 62.0 98.892 3.171 3.171 3.171 7.343 7.343 +GCD 63.0 99.446 0.530 0.530 0.530 6.403 6.403 +GCD 64.0 100.000 1.025 1.025 1.025 4.585 4.585 diff -r 000000000000 -r 3bad335ccea9 test-data/samtools_stats_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/samtools_stats_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample bases_trimmed error_rate insert_size_standard_deviation non-primary_alignments maximum_length reads_MQ0_percent reads_mapped_and_paired sequences average_quality insert_size_average reads_mapped reads_unmapped reads_QC_failed reads_duplicated_percent reads_paired 1st_fragments reads_MQ0 average_length reads_mapped_and_paired_percent bases_mapped total_length bases_mapped_(cigar) bases_duplicated pairs_with_other_orientation mismatches reads_properly_paired inward_oriented_pairs filtered_sequences outward_oriented_pairs reads_unmapped_percent reads_QC_failed_percent reads_properly_paired_percent reads_paired_percent reads_mapped_percent raw_total_sequences pairs_on_different_chromosomes last_fragments is_sorted reads_duplicated +samtools_stats 0.0 0.004248509 1223.0 12111.0 101.0 0.0109064676911 638746.0 641821.0 26.0 719.7 641821.0 0.0 0.0 0.0 641821.0 320981.0 70.0 101.0 99.520894455 64823921.0 64823921.0 64823921.0 0.0 30.0 275405.0 635626.0 317512.0 0.0 1294.0 0.0 0.0 99.0347776093 100.0 100.0 641821.0 0.0 320840.0 1.0 0.0 diff -r 000000000000 -r 3bad335ccea9 test-data/snpeff.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/snpeff.csv Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,588 @@ + +# Summary table + +Name , Value +Genome , GRCh37.75 +Date , 2016-02-24 19:23 +SnpEff_version , SnpEff 4.1a (build 2015-01-14), by Pablo Cingolani +Command_line_arguments , SnpEff -csvStats -stats /scratch/108820/ANALYSIS/P4107/piper_ngi/07_variant_calls/Sample1.clean.dedup.recal.bam.recalibrated.indel.annotated.vcf.gz.snpEff.summary.csv GRCh37.75 /scratch/108820/ANALYSIS/P4107/piper_ngi/07_variant_calls/Sample1.clean.dedup.recal.bam.recalibrated.indel.vcf.gz +Warnings , 1214759 +Number_of_lines_in_input_file, 917355 +Number_of_variants_before_filter, 972155 +Number_of_not_variants , 0 +Number_of_variants_processed , 972155 +Number_of_known_variants
        (i.e. non-empty ID) , 764271, 78.616167% +Number_of_effects , 5499894 +Genome_total_length ,32036512383 +Genome_effective_length ,3101536026 +Change_rate , 3190 + +# Change rate by chromosome + +Chromosome , Length , Changes , Change_rate +1 , 249250621 , 76982 , 3237 +2 , 243199373 , 77562 , 3135 +3 , 198022430 , 63396 , 3123 +4 , 191154276 , 65298 , 2927 +5 , 180915260 , 56287 , 3214 +6 , 171115067 , 59086 , 2896 +7 , 159138663 , 55505 , 2867 +8 , 146364022 , 44876 , 3261 +9 , 141213431 , 40484 , 3488 +10 , 135534747 , 48468 , 2796 +11 , 135006516 , 45528 , 2965 +12 , 133851895 , 45727 , 2927 +13 , 115169878 , 36006 , 3198 +14 , 107349540 , 30507 , 3518 +15 , 102531392 , 29009 , 3534 +16 , 90354753 , 29320 , 3081 +17 , 81195210 , 30895 , 2628 +18 , 78077248 , 26998 , 2891 +19 , 59128983 , 25980 , 2275 +20 , 63025520 , 20817 , 3027 +21 , 48129895 , 16197 , 2971 +22 , 51304566 , 13805 , 3716 +GL000191.1 , 106433 , 24 , 4434 +GL000192.1 , 547496 , 131 , 4179 +GL000193.1 , 189789 , 133 , 1426 +GL000194.1 , 191469 , 159 , 1204 +GL000195.1 , 182896 , 269 , 679 +GL000197.1 , 37175 , 1 , 37175 +GL000198.1 , 90085 , 146 , 617 +GL000199.1 , 169874 , 54 , 3145 +GL000201.1 , 36148 , 1 , 36148 +GL000202.1 , 40103 , 9 , 4455 +GL000203.1 , 37498 , 78 , 480 +GL000204.1 , 81310 , 15 , 5420 +GL000205.1 , 174588 , 229 , 762 +GL000206.1 , 41001 , 1 , 41001 +GL000208.1 , 92689 , 66 , 1404 +GL000209.1 , 159169 , 4 , 39792 +GL000210.1 , 27682 , 1 , 27682 +GL000211.1 , 166566 , 161 , 1034 +GL000212.1 , 186858 , 123 , 1519 +GL000213.1 , 164239 , 14 , 11731 +GL000214.1 , 137718 , 169 , 814 +GL000215.1 , 172545 , 12 , 14378 +GL000216.1 , 172294 , 636 , 270 +GL000217.1 , 172149 , 227 , 758 +GL000218.1 , 161147 , 141 , 1142 +GL000219.1 , 179198 , 384 , 466 +GL000220.1 , 161802 , 294 , 550 +GL000221.1 , 155397 , 90 , 1726 +GL000222.1 , 186861 , 175 , 1067 +GL000223.1 , 180455 , 2 , 90227 +GL000224.1 , 179693 , 324 , 554 +GL000225.1 , 211173 , 537 , 393 +GL000226.1 , 15008 , 2 , 7504 +GL000227.1 , 128374 , 5 , 25674 +GL000228.1 , 129120 , 65 , 1986 +GL000229.1 , 19913 , 157 , 126 +GL000230.1 , 43691 , 40 , 1092 +GL000231.1 , 27386 , 114 , 240 +GL000232.1 , 40652 , 175 , 232 +GL000233.1 , 45941 , 54 , 850 +GL000234.1 , 40531 , 165 , 245 +GL000235.1 , 34474 , 80 , 430 +GL000236.1 , 41934 , 12 , 3494 +GL000237.1 , 45867 , 50 , 917 +GL000238.1 , 39939 , 3 , 13313 +GL000239.1 , 33824 , 11 , 3074 +GL000240.1 , 41933 , 37 , 1133 +GL000241.1 , 42152 , 138 , 305 +GL000242.1 , 43523 , 4 , 10880 +GL000243.1 , 43341 , 28 , 1547 +GL000244.1 , 39929 , 8 , 4991 +GL000245.1 , 36651 , 12 , 3054 +GL000246.1 , 38154 , 9 , 4239 +GL000247.1 , 36422 , 12 , 3035 +GL000248.1 , 39786 , 6 , 6631 +MT , 16569 , 3 , 5523 +X , 155270560 , 24853 , 6247 +Y , 59373566 , 2769 , 21442 + +# Effects by impact + +Type , Count , Percent +HIGH , 1367 , 0.024855% +LOW , 2178258 , 39.605454% +MODERATE , 3322 , 0.060401% +MODIFIER , 3316947 , 60.30929% + +# Effects by functional class + +Type , Count , Percent + +Missense_Silent_ratio, ? + +# Count by effects + +Type , Count , Percent +3_prime_UTR_variant , 15811 , 0.287478% +5_prime_UTR_truncation+exon_loss_variant , 2 , 0.000036% +5_prime_UTR_variant , 3350 , 0.06091% +TF_binding_site_variant , 986 , 0.017928% +disruptive_inframe_deletion , 408 , 0.007418% +disruptive_inframe_deletion+splice_region_variant , 2 , 0.000036% +disruptive_inframe_insertion , 277 , 0.005036% +downstream_gene_variant , 339790 , 6.178119% +frameshift_variant , 800 , 0.014546% +frameshift_variant+splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018% +frameshift_variant+splice_acceptor_variant+splice_region_variant+intron_variant , 2 , 0.000036% +frameshift_variant+splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant , 6 , 0.000109% +frameshift_variant+splice_donor_variant+splice_region_variant+intron_variant , 3 , 0.000055% +frameshift_variant+splice_region_variant , 77 , 0.0014% +frameshift_variant+start_lost , 8 , 0.000145% +frameshift_variant+start_lost+splice_region_variant , 1 , 0.000018% +frameshift_variant+stop_gained , 21 , 0.000382% +frameshift_variant+stop_lost , 3 , 0.000055% +inframe_deletion , 159 , 0.002891% +inframe_deletion+splice_region_variant , 10 , 0.000182% +inframe_insertion , 266 , 0.004836% +inframe_insertion+splice_region_variant , 2 , 0.000036% +intergenic_region , 461247 , 8.386471% +intragenic_variant , 267 , 0.004855% +intron_variant , 2126738 , 38.668709% +non_coding_exon_variant , 15320 , 0.278551% +sequence_feature , 2174428 , 39.535817% +splice_acceptor_variant+5_prime_UTR_variant+intron_variant , 2 , 0.000036% +splice_acceptor_variant+disruptive_inframe_deletion+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018% +splice_acceptor_variant+inframe_deletion+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018% +splice_acceptor_variant+intron_variant , 224 , 0.004073% +splice_acceptor_variant+splice_donor_variant+intron_variant , 61 , 0.001109% +splice_acceptor_variant+splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 2 , 0.000036% +splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 1 , 0.000018% +splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant , 3 , 0.000055% +splice_acceptor_variant+splice_donor_variant+splice_region_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 5 , 0.000091% +splice_acceptor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 7 , 0.000127% +splice_acceptor_variant+splice_region_variant+intron_variant , 32 , 0.000582% +splice_acceptor_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 5 , 0.000091% +splice_acceptor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 2 , 0.000036% +splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant , 1 , 0.000018% +splice_acceptor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 13 , 0.000236% +splice_donor_variant+5_prime_UTR_variant+intron_variant , 2 , 0.000036% +splice_donor_variant+intron_variant , 41 , 0.000745% +splice_donor_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 1 , 0.000018% +splice_donor_variant+splice_region_variant+5_prime_UTR_variant+intron_variant , 1 , 0.000018% +splice_donor_variant+splice_region_variant+intron_variant , 15 , 0.000273% +splice_donor_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 5 , 0.000091% +splice_donor_variant+splice_region_variant+splice_region_variant+3_prime_UTR_variant+intron_variant , 1 , 0.000018% +splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant , 3 , 0.000055% +splice_donor_variant+splice_region_variant+splice_region_variant+intron_variant+non_coding_exon_variant , 12 , 0.000218% +splice_region_variant , 187 , 0.0034% +splice_region_variant+intron_variant , 4390 , 0.07982% +splice_region_variant+non_coding_exon_variant , 462 , 0.0084% +splice_region_variant+splice_region_variant , 1 , 0.000018% +start_lost+disruptive_inframe_insertion , 1 , 0.000018% +stop_gained+inframe_insertion , 3 , 0.000055% +transcript , 77 , 0.0014% +upstream_gene_variant , 354347 , 6.442797% + +# Count by genomic region + +Type , Count , Percent +DOWNSTREAM , 339790 , 6.178119% +EXON , 17369 , 0.315806% +INTERGENIC , 461247 , 8.386471% +INTRON , 2126738 , 38.668709% +MOTIF , 986 , 0.017928% +NONE , 2174772 , 39.542071% +SPLICE_SITE_ACCEPTOR , 360 , 0.006546% +SPLICE_SITE_DONOR , 81 , 0.001473% +SPLICE_SITE_REGION , 5040 , 0.091638% +TRANSCRIPT , 1 , 0.000018% +UPSTREAM , 354347 , 6.442797% +UTR_3_PRIME , 15811 , 0.287478% +UTR_5_PRIME , 3352 , 0.060947% + +# Quality + +Values , 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,1,1,3,3,1,3,2,2,2,1,1,1,1,1,1,1,4,1,1,4,1,2,3,1,1,1,1,3,1,2,2,3,1,4,3,3,1,2,2,2,2,1,1,3,2,1,1,1,2,2,1,1,2,1,1,4,2,1,3,1,3,1,2,1,2,2,1,1,4,1,3,1,1,1,1,3,4,3,1,3,2,1,1,1,3,1,1,1,2,3,6,2,2,1,2,1,3,2,1,1,1,2,1,1,1,1,2,2,6,2,1,1,2,1,4,1,2,1,2,3,1,1,1,2,1,2,1,1,1,1,2,2,3,1,1,1,5,4,2,2,2,1,3,1,2,3,2,1,2,1,1,2,1,1,1,1,2,4,1,3,2,1,1,3,1,2,1,1,2,2,2,1,3,2,2,1,1,1,1,1,2,1,1,2,4,1,2,1,1,2,1,3,2,1,2,2,1,3,1,1,1,1,1,1,2,1,1,3,2,1,3,2,2,3,3,2,1,3,1,2,1,1,1,2,1,2,1,1,1,1,2,3,1,1,2,1,1,1,4,1,4,2,2,1,2,1,2,1,1,1,1,1,3,3,1,1,1,2,1,2,1,1,3,1,1,1,1,2,2,2,2,1,1,1,3,1,1,2,2,2,1,1,1,2,2,3,2,1,1,2,1,2,1,1,4,1,1,1,1,2,1,2,2,1,2,1,1,1,1,2,2,2,1,1,1,1,1,1,1,2,1,1,1,2,1,2,1,2,2,1,1,1,1,3,1,2,2,2,1,1,1,1,1,1,2,2,1,1,1,2,3,2,2,1,1,2,1,1,1,4,2,1,1,3,1,1,2,5,1,1,2,2,1,1,1,2,1,1,1,3,1,1,1,2,2,1,2,2,2,1,1,1,3,1,1,2,2,2,3,2,1,1,1,1,2,1,1,1,1,1,1,1,1,1,2,3,1,1,2,2,1,1,2,1,1,1,1,1,1,1,1,2,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,2,1,1,2,1,2,1,1,1,1,1,2,1,2,1,2,1,1,1,1,1,2,1,3,2,3,2,1,2,2,1,1,1,1,1,1,1,1,1,1,1,2,1,3,1,1,2,1,1,1,2,1,1,1,1,2,2,2,1,1,1,2,1,2,1,2,1,1,1,1,2,1,1,1,1,1,1,1,2,2,1,1,1,1,2,1,3,1,1,1,1,1,1,2,2,1,3,3,2,1,1,3,2,1,2,1,1,1,2,1,1,2,2,2,1,3,2,1,1,1,1,1,2,2,2,1,1,2,1,2,1,1,1,2,1,2,2,1,1,1,1,1,1,2,2,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,2,1,1,1,1,1,1,2,1,3,3,2,2,1,1,3,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,2,2,2,2,2,1,1,1,2,1,1,1,1,1,2,1,2,1,2,1,1,1,2,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,4,1,1,2,1,1,1,1,1,2,2,1,2,1,1,1,1,1,1,2,1,1,1,1,1,1,2,1,1,1,2,1,1,1,1,1,1,1,1,1,2,1,1,1,2,2,2,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,2,1,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,3,1,1,1,1,2,2,1,1,1,1,1,1,1,1,1,2,2,1,1,1,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,1,1,2,2,1,1,1,1,1,2,1,1,1,1,2,1,1,2,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,2,2,1,3,1,1,1,1,1,1,1,2,1,1,2,1,1,1,2,1,2,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,2,1,1,2,1,1,1,2,2,1,1,2,1,1,1,1,2,1,1,1,1,1,2,2,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,3,1,2,1,1,2,1,1,1,1,1,1,1,1,2,1,1,1,1,2,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,3,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 + +# InDel lengths + +Values , 0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,182,183,184,185,186,187,188,191,193,194,195,196,197,198,199,200,201,202,203,205,209,212,215,219,220,223,226,227,228,229,234,239,240,241,242,247,248,250,257,259,263,264,269,272,273,283,301,310,316,329,333,337,345,349,357,365,371,376,385,415,431,465,468 +Count , 224126,581518,30481,45770,12815,14371,4393,12389,3495,6543,2136,6605,1548,2877,1892,3247,913,1778,721,2174,651,966,487,1226,528,641,389,722,264,539,242,440,216,278,220,311,164,217,137,244,114,153,102,120,97,111,82,140,85,109,64,92,82,103,58,74,53,58,51,79,54,72,36,68,40,63,30,47,26,44,25,50,30,31,33,42,21,26,24,28,26,21,10,28,15,25,22,17,15,25,10,16,17,12,22,33,10,17,15,14,5,10,9,14,6,14,6,9,10,14,8,16,5,6,11,9,8,7,5,4,6,11,9,8,9,5,1,2,8,7,6,4,13,6,10,5,7,3,7,2,4,1,6,1,2,2,1,2,8,3,3,1,3,1,3,3,9,1,1,1,1,2,2,3,6,1,1,4,3,2,3,5,3,2,4,2,4,1,2,1,2,1,1,1,2,2,3,1,1,2,3,2,2,1,1,2,3,2,1,1,2,1,1,1,3,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1 + +# Base changes + +base , A , C , G , T + A , 0 , 0 , 0 , 0 + C , 0 , 0 , 0 , 0 + G , 0 , 0 , 0 , 0 + T , 0 , 0 , 0 , 0 + +# Ts/Tv summary + +Transitions , 0 +Transversions , 0 +Ts_Tv_ratio , 0 + +# Ts/Tv : All variants + +No results available (empty input?) + +# Ts/Tv : Known variants + +No results available (empty input?) + +# Allele frequency + +# Allele frequency : All variants + +Values , 50,100 +Count , 524875,392480 + +# Allele Count + +Values , 1,2 +Count , 524875,392480 + +# Hom/Het table + +Sample_names , Sample1 +Reference , 0 +Het , 524875 +Hom , 392480 +Missing , 0 + + +# Codon change table + +codons , - , AAA , AAC , AAG , AAT , ACA , ACC , ACG , ACT , AGA , AGC , AGG , AGT , ATA , ATC , ATG , ATT , CAA , CAC , CAG , CAT , CCA , CCC , CCG , CCT , CGA , CGC , CGG , CGT , CTA , CTC , CTG , CTT , GAA , GAC , GAG , GAT , GCA , GCC , GCG , GCT , GGA , GGC , GGG , GGT , GTA , GTC , GTG , GTT , TAA , TAC , TAG , TAT , TCA , TCC , TCG , TCT , TGA , TGC , TGG , TGT , TTA , TTC , TTG , TTT + - , 0 , 27 , 16 , 45 , 14 , 22 , 43 , 15 , 7 , 26 , 82 , 21 , 27 , 9 , 15 , 27 , 0 , 32 , 45 , 401 , 17 , 20 , 87 , 51 , 65 , 5 , 14 , 18 , 12 , 18 , 17 , 57 , 12 , 34 , 50 , 123 , 50 , 17 , 59 , 30 , 52 , 37 , 182 , 67 , 47 , 25 , 12 , 34 , 14 , 8 , 5 , 6 , 13 , 22 , 68 , 6 , 26 , 3 , 18 , 21 , 32 , 7 , 38 , 8 , 39 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Position,0,100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500,2600,2700,2800,2900,3000,3100,3200,3300,3400,3500,3600,3700,3800,3900,4000,4100,4200,4300,4400,4500,4600,4700,4800,4900,5000,5100,5200,5300,5400,5500,5600,5700,5800,5900,6000,6100,6200,6300,6400,6500,6600,6700,6800,6900,7000,7100,7200,7300,7400,7500,7600,7700,7800,7900,8000,8100,8200,8300,8400,8500,8600,8700,8800,8900,9000,9100,9200,9300,9400,9500,9600,9700,9800,9900,10000,10100,10200,10300,10400,10500,10600,10700,10800,10900,11000,11100,11200,11300,11400,11500,11600,11700,11800,11900,12000,12100,12200,12300,12400,12500,12600,12700,12800,12900,13000,13100,13200,13300,13400,13500,13600,13700,13800,13900,14000,14100,14200,14300,14400,14500,14600,14700,14800,14900,15000,15100,15200,15300,15400,15500,15600,15700,15800,15900,16000,16100,16200,16300,16400,16500,16600,16700,16800,16900,17000,17100,17200,17300,17400,17500,17600,17700,17800,17900,18000,18100,18200,18300,18400,18500,18600,18700,18800,18900,19000,19100,19200,19300,19400,19500,19600,19700,19800,19900 +GL000229.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,8,0,1,1,0,0,0,0,1,2,1,0,0,0,1,0,0,0,3,2,1,5,1,0,2,2,4,2,0,0,0,0,0,0,2,2,1,3,0,0,2,0,0,0,0,0,1,3,0,0,0,0,0,1,1,2,5,5,4,1,1,2,1,9,4,2,0,0,0,0,0,0,1,1,0,0,2,3,1,0,1,1,0,0,1,0,0,0,0,8,1,0,0,0,1,1,0,0,1,0,2,0,0,0,1,0,0,0,0,0,1,1,0,0,0,0,0,1,0,1,2,0,0,2,2,0,0,1,1,0,2,3,1,3,1,0,0,0,1,1,0,0,0,1,0,0,0,0,0,0,1,0,2,2,5,0,0,0,0,1,0,0,0,0,0,0,0,1,2,2,0,0,0,0,0 + +GL000230.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000 +GL000230.1,Count,3,2,2,4,2,0,1,1,1,0,2,2,1,2,2,3,3,2,2,0,3,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 + +GL000231.1, Position,0,100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500,2600,2700,2800,2900,3000,3100,3200,3300,3400,3500,3600,3700,3800,3900,4000,4100,4200,4300,4400,4500,4600,4700,4800,4900,5000,5100,5200,5300,5400,5500,5600,5700,5800,5900,6000,6100,6200,6300,6400,6500,6600,6700,6800,6900,7000,7100,7200,7300,7400,7500,7600,7700,7800,7900,8000,8100,8200,8300,8400,8500,8600,8700,8800,8900,9000,9100,9200,9300,9400,9500,9600,9700,9800,9900,10000,10100,10200,10300,10400,10500,10600,10700,10800,10900,11000,11100,11200,11300,11400,11500,11600,11700,11800,11900,12000,12100,12200,12300,12400,12500,12600,12700,12800,12900,13000,13100,13200,13300,13400,13500,13600,13700,13800,13900,14000,14100,14200,14300,14400,14500,14600,14700,14800,14900,15000,15100,15200,15300,15400,15500,15600,15700,15800,15900,16000,16100,16200,16300,16400,16500,16600,16700,16800,16900,17000,17100,17200,17300,17400,17500,17600,17700,17800,17900,18000,18100,18200,18300,18400,18500,18600,18700,18800,18900,19000,19100,19200,19300,19400,19500,19600,19700,19800,19900,20000,20100,20200,20300,20400,20500,20600,20700,20800,20900,21000,21100,21200,21300,21400,21500,21600,21700,21800,21900,22000,22100,22200,22300,22400,22500,22600,22700,22800,22900,23000,23100,23200,23300,23400,23500,23600,23700,23800,23900,24000,24100,24200,24300,24400,24500,24600,24700,24800,24900,25000,25100,25200,25300,25400,25500,25600,25700,25800,25900,26000,26100,26200,26300,26400,26500,26600,26700,26800,26900,27000,27100,27200,27300 +GL000231.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,0,1,0,0,5,0,0,4,1,0,0,0,0,0,0,1,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,2,0,0,0,0,3,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,1,1,0,0,0,0,0,0,0,0,1,0,0,0,1,1,1,2,0,0,0,0,3,3,1,0,0,1,0,1,0,0,0,1,0,0,1,4,0,0,0,0,0,1,1,0,0,1,2,0,0,1,0,0,0,0,2,1,0,0,0,0,0,0,0,3,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,3,4,1,0,0,0,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0,3,2,2,0,0,0,0,0,0,1,2,1,0,1,0,0,0,0,1,0,1,0,0,1,0,0,0,0,6,1,0,2,1,0,0,0,0,1,0,1,1,2,0,0,0,0,0,1,0,0,0,0,2,0,1,0,0,1,0,0,0,1,2,0,0,1,1,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 + +GL000232.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000 +GL000232.1,Count,5,10,3,7,5,9,6,5,1,2,4,2,0,2,2,6,6,5,5,4,2,5,6,7,5,4,7,2,10,2,4,2,0,7,2,6,2,2,6,5,0 + +GL000233.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000 +GL000233.1,Count,0,4,0,2,0,3,1,4,0,3,3,1,1,4,1,1,3,2,3,1,5,4,3,2,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 + +GL000234.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000 +GL000234.1,Count,0,0,1,4,2,6,7,5,2,1,8,5,4,4,0,2,3,0,1,2,6,4,1,7,10,5,7,5,2,2,4,5,2,2,12,4,7,14,6,3,0 + +GL000235.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000 +GL000235.1,Count,3,5,7,2,1,0,2,0,4,4,0,1,4,6,2,1,4,4,2,0,2,5,0,0,2,2,4,1,0,2,4,0,2,4,0 + +GL000236.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000 +GL000236.1,Count,0,0,2,0,0,0,1,0,0,0,0,0,1,0,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,1,0,0,4,0,0,0,0,0,0,0,1 + +GL000237.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000,44000,45000 +GL000237.1,Count,1,1,2,4,4,2,2,1,0,2,6,12,2,0,2,1,1,4,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0 + +GL000238.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000 +GL000238.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0,0,0 + +GL000239.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000 +GL000239.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,7,0,2,1,0,0,1 + +GL000240.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000 +GL000240.1,Count,0,0,0,0,2,0,0,0,2,0,2,3,1,2,0,1,2,0,3,0,0,0,0,0,0,0,0,0,3,1,0,8,1,0,1,1,1,0,1,2,0,0 + +GL000241.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000 +GL000241.1,Count,5,3,4,5,3,8,4,1,3,9,4,3,8,1,3,5,3,4,2,4,2,2,4,4,1,4,4,2,3,1,3,5,3,5,1,0,1,2,0,2,3,3,1 + +GL000242.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000 +GL000242.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,1,0,0,0,0,0,0,0,0,0,0,1,0 + +GL000243.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000,40000,41000,42000,43000 +GL000243.1,Count,0,0,0,0,1,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,2,7,1,5,3,0,1,0,0,0,0,0,0,1,1,0,0,0,2,0,2,0,0 + +GL000244.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000 +GL000244.1,Count,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0 + +GL000245.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000 +GL000245.1,Count,0,0,0,1,0,0,0,0,1,2,0,0,1,0,0,0,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,0,3,1,0,1,0 + +GL000246.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000 +GL000246.1,Count,0,0,0,0,0,1,1,1,0,0,0,2,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0 + +GL000247.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000 +GL000247.1,Count,1,0,0,0,0,0,0,1,0,0,1,0,1,1,0,0,1,0,0,1,0,3,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0 + +GL000248.1, Position,0,1000,2000,3000,4000,5000,6000,7000,8000,9000,10000,11000,12000,13000,14000,15000,16000,17000,18000,19000,20000,21000,22000,23000,24000,25000,26000,27000,28000,29000,30000,31000,32000,33000,34000,35000,36000,37000,38000,39000 +GL000248.1,Count,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,0,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0 + +MT, Position,0,100,200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500,2600,2700,2800,2900,3000,3100,3200,3300,3400,3500,3600,3700,3800,3900,4000,4100,4200,4300,4400,4500,4600,4700,4800,4900,5000,5100,5200,5300,5400,5500,5600,5700,5800,5900,6000,6100,6200,6300,6400,6500,6600,6700,6800,6900,7000,7100,7200,7300,7400,7500,7600,7700,7800,7900,8000,8100,8200,8300,8400,8500,8600,8700,8800,8900,9000,9100,9200,9300,9400,9500,9600,9700,9800,9900,10000,10100,10200,10300,10400,10500,10600,10700,10800,10900,11000,11100,11200,11300,11400,11500,11600,11700,11800,11900,12000,12100,12200,12300,12400,12500,12600,12700,12800,12900,13000,13100,13200,13300,13400,13500,13600,13700,13800,13900,14000,14100,14200,14300,14400,14500,14600,14700,14800,14900,15000,15100,15200,15300,15400,15500,15600,15700,15800,15900,16000,16100,16200,16300,16400,16500 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Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000,60000000,61000000,62000000,63000000,64000000,65000000,66000000,67000000,68000000,69000000,70000000,71000000,72000000,73000000,74000000,75000000,76000000,77000000,78000000,79000000,80000000,81000000,82000000,83000000,84000000,85000000,86000000,87000000,88000000,89000000,90000000,91000000,92000000,93000000,94000000,95000000,96000000,97000000,98000000,99000000,100000000,101000000,102000000,103000000,104000000,105000000,106000000,107000000,108000000,109000000,110000000,111000000,112000000,113000000,114000000,115000000,116000000,117000000,118000000,119000000,120000000,121000000,122000000,123000000,124000000,125000000,126000000,127000000,128000000,129000000,130000000,131000000,132000000,133000000,134000000,135000000,136000000,137000000,138000000,139000000,140000000,141000000,142000000,143000000,144000000,145000000,146000000,147000000,148000000,149000000,150000000,151000000,152000000,153000000,154000000,155000000 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Position,0,1000000,2000000,3000000,4000000,5000000,6000000,7000000,8000000,9000000,10000000,11000000,12000000,13000000,14000000,15000000,16000000,17000000,18000000,19000000,20000000,21000000,22000000,23000000,24000000,25000000,26000000,27000000,28000000,29000000,30000000,31000000,32000000,33000000,34000000,35000000,36000000,37000000,38000000,39000000,40000000,41000000,42000000,43000000,44000000,45000000,46000000,47000000,48000000,49000000,50000000,51000000,52000000,53000000,54000000,55000000,56000000,57000000,58000000,59000000 +Y,Count,0,0,24,47,47,53,44,49,59,277,245,0,0,733,73,51,63,82,69,47,13,53,83,70,23,7,15,20,104,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,258,160 + diff -r 000000000000 -r 3bad335ccea9 test-data/sortmerna.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sortmerna.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,83 @@ + Tue Jan 31 17:04:24 2017 + + Command: /home/lina/sortmerna/sortmerna --ref /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta,/home/lina/sortmerna/index/silva-bac-16s-db:/home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta,/home/lina/sortmerna/index/silva-bac-23s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta,/home/lina/sortmerna/index/silva-arc-16s-db:/home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta,/home/lina/sortmerna/index/silva-arc-23s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta,/home/lina/sortmerna/index/silva-euk-18s-db:/home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta,/home/lina/sortmerna/index/silva-euk-28s:/home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5s-db:/home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta,/home/lina/sortmerna/index/rfam-5.8s-db --reads 25839_merged.fastq --num_alignments 1 --fastx --aligned Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_reads --other Sample_2055324_ribo/sortmerna_out/2055324_ribo_rrna_free_reads.fastq fastq tq --log -v --blast 1 + Process pid = 27736 + Parameters summary: + Index: /home/lina/sortmerna/index/silva-bac-16s-db + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.602725 + Gumbel K = 0.329559 + Minimal SW score based on E-value = 57 + Index: /home/lina/sortmerna/index/silva-bac-23s-db + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.602436 + Gumbel K = 0.335011 + Minimal SW score based on E-value = 57 + Index: /home/lina/sortmerna/index/silva-arc-16s-db + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.596286 + Gumbel K = 0.322254 + Minimal SW score based on E-value = 55 + Index: /home/lina/sortmerna/index/silva-arc-23s-db + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.597507 + Gumbel K = 0.331576 + Minimal SW score based on E-value = 53 + Index: /home/lina/sortmerna/index/silva-euk-18s-db + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.612551 + Gumbel K = 0.339810 + Minimal SW score based on E-value = 56 + Index: /home/lina/sortmerna/index/silva-euk-28s + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.612082 + Gumbel K = 0.345772 + Minimal SW score based on E-value = 56 + Index: /home/lina/sortmerna/index/rfam-5s-db + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.616694 + Gumbel K = 0.342032 + Minimal SW score based on E-value = 54 + Index: /home/lina/sortmerna/index/rfam-5.8s-db + Seed length = 18 + Pass 1 = 18, Pass 2 = 9, Pass 3 = 3 + Gumbel lambda = 0.617555 + Gumbel K = 0.343861 + Minimal SW score based on E-value = 52 + Number of seeds = 2 + Edges = 4 (as integer) + SW match = 2 + SW mismatch = -3 + SW gap open penalty = 5 + SW gap extend penalty = 2 + SW ambiguous nucleotide = -3 + SQ tags are not output + Number of threads = 20 + Reads file = 25839_merged.fastq + + Results: + Total reads = 4443556 + Total reads passing E-value threshold = 48848 (1.10%) + Total reads failing E-value threshold = 4394708 (98.90%) + Minimum read length = 35 + Maximum read length = 76 + Mean read length = 74 + By database: + /home/lina/sortmerna/rRNA_databases/silva-bac-16s-id90.fasta 0.59% + /home/lina/sortmerna/rRNA_databases/silva-bac-23s-id98.fasta 0.24% + /home/lina/sortmerna/rRNA_databases/silva-arc-16s-id95.fasta 0.00% + /home/lina/sortmerna/rRNA_databases/silva-arc-23s-id98.fasta 0.00% + /home/lina/sortmerna/rRNA_databases/silva-euk-18s-id95.fasta 0.25% + /home/lina/sortmerna/rRNA_databases/silva-euk-28s-id98.fasta 0.01% + /home/lina/sortmerna/rRNA_databases/rfam-5s-database-id98.fasta 0.00% + /home/lina/sortmerna/rRNA_databases/rfam-5.8s-database-id98.fasta 0.00% + + Tue Jan 31 17:08:40 2017 + diff -r 000000000000 -r 3bad335ccea9 test-data/sortmerna_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sortmerna_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample silva-arc-16s-id95_count silva-euk-28s-id98_pct non_rRNA silva-bac-23s-id98_pct silva-euk-18s-id95_pct silva-bac-23s-id98_count rRNA_pct silva-arc-23s-id98_count rfam-5s-database-id98_pct silva-arc-16s-id95_pct rfam-5s-database-id98_count non_rRNA_pct silva-euk-28s-id98_count rfam-5.8s-database-id98_pct rRNA silva-bac-16s-id90_pct silva-euk-18s-id95_count silva-bac-16s-id90_count total rfam-5.8s-database-id98_count silva-arc-23s-id98_pct +25839_merged 0.0 0.01 4394708 0.24 0.25 10664.5344 1.09929975002 0.0 0.0 0.0 0.0 98.90070025 444.3556 0.0 48848 0.59 11108.89 26216.9804 4443556 0.0 0.0 diff -r 000000000000 -r 3bad335ccea9 test-data/star_counts.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/star_counts.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,5 @@ +N_unmapped 0 0 0 +N_multimapping 1 1 1 +N_noFeature 0 51 48 +N_ambiguous 0 0 0 +GENE1 99 48 51 diff -r 000000000000 -r 3bad335ccea9 test-data/star_log.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/star_log.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,34 @@ + Started job on | Mar 01 15:53:05 + Started mapping on | Mar 01 15:53:08 + Finished on | Mar 01 15:53:08 + Mapping speed, Million of reads per hour | inf + + Number of input reads | 100 + Average input read length | 75 + UNIQUE READS: + Uniquely mapped reads number | 89 + Uniquely mapped reads % | 89.00% + Average mapped length | 74.80 + Number of splices: Total | 47 + Number of splices: Annotated (sjdb) | 0 + Number of splices: GT/AG | 47 + Number of splices: GC/AG | 0 + Number of splices: AT/AC | 0 + Number of splices: Non-canonical | 0 + Mismatch rate per base, % | 1.73% + Deletion rate per base | 0.00% + Deletion average length | 0.00 + Insertion rate per base | 0.00% + Insertion average length | 0.00 + MULTI-MAPPING READS: + Number of reads mapped to multiple loci | 1 + % of reads mapped to multiple loci | 1.00% + Number of reads mapped to too many loci | 0 + % of reads mapped to too many loci | 0.00% + UNMAPPED READS: + % of reads unmapped: too many mismatches | 0.00% + % of reads unmapped: too short | 10.00% + % of reads unmapped: other | 0.00% + CHIMERIC READS: + Number of chimeric reads | 0 + % of chimeric reads | 0.00% diff -r 000000000000 -r 3bad335ccea9 test-data/star_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/star_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample uniquely_mapped_percent num_splices num_GCAG_splices insertion_length deletion_length unmapped_tooshort_percent avg_mapped_read_length deletion_rate mismatch_rate avg_input_read_length num_ATAC_splices num_annotated_splices num_GTAG_splices uniquely_mapped multimapped_toomany unmapped_mismatches unmapped_mismatches_percent total_reads unmapped_other insertion_rate unmapped_other_percent multimapped_percent multimapped num_noncanonical_splices unmapped_tooshort multimapped_toomany_percent +star_log 89.0 47.0 0.0 0.0 0.0 10.0 74.8 0.0 1.73 75.0 0.0 0.0 47.0 89.0 0.0 0 0.0 100.0 0 0.0 0.0 1.0 1.0 0.0 10 0.0 diff -r 000000000000 -r 3bad335ccea9 test-data/tophat.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,14 @@ +Left reads: + Input : 316390 + Mapped : 314921 (99.5% of input) + of these: 5715 ( 1.8%) have multiple alignments (0 have >20) +Right reads: + Input : 316390 + Mapped : 314789 (99.5% of input) + of these: 5707 ( 1.8%) have multiple alignments (0 have >20) +99.5% overall read mapping rate. + +Aligned pairs: 313405 + of these: 5638 ( 1.8%) have multiple alignments + 34 ( 0.0%) are discordant alignments +99.0% concordant pair alignment rate. diff -r 000000000000 -r 3bad335ccea9 test-data/tophat_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tophat_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample unaligned_total aligned_total aligned_not_multimapped_discordant overall_aligned_percent aligned_multimap aligned_discordant total_reads concordant_aligned_percent +tophat_align 2985.0 313405.0 307733.0 99.5 5638.0 34.0 316390.0 99.0 diff -r 000000000000 -r 3bad335ccea9 test-data/trimmomatic.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,6 @@ +TrimmomaticSE: Started with arguments: -threads 52 -phred64 -trimlog C2.log.txt C2.fastq.gz C2.Processed ILLUMINACLIP:./Trimmomatic-0.32/TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 CROP:24 MINLEN:21 +Using Long Clipping Sequence: 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA' +Using Long Clipping Sequence: 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC' +ILLUMINACLIP: Using 0 prefix pairs, 2 forward/reverse sequences, 0 forward only sequences, 0 reverse only sequences +Input Reads: 39733090 Surviving: 32590558 (82.02%) Dropped: 7142532 (17.98%) +TrimmomaticSE: Completed successfully \ No newline at end of file diff -r 000000000000 -r 3bad335ccea9 test-data/trimmomatic_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_stats.tabular Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,2 @@ +Sample input_reads surviving_pct dropped surviving dropped_pct +C2 39733090.0 82.02 7142532.0 32590558.0 17.98 diff -r 000000000000 -r 3bad335ccea9 test-data/vcftools.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vcftools.txt Tue Oct 24 06:29:59 2017 -0400 @@ -0,0 +1,1000 @@ +QUAL_THRESHOLD N_Ts_LT_QUAL_THRESHOLD N_Tv_LT_QUAL_THRESHOLD Ts/Tv_LT_QUAL_THRESHOLD N_Ts_GT_QUAL_THRESHOLD N_Tv_GT_QUAL_THRESHOLD Ts/Tv_GT_QUAL_THRESHOLD +3.01037 0 0 -nan 1.5337e+07 6.70583e+06 2.28711 +3.01039 1 0 inf 1.5337e+07 6.70583e+06 2.28711 +3.01041 2 0 inf 1.5337e+07 6.70583e+06 2.28711 +3.01042 3 0 inf 1.5337e+07 6.70583e+06 2.28711 +3.01046 3 1 3 1.5337e+07 6.70583e+06 2.28711 +3.0105 4 1 4 1.5337e+07 6.70583e+06 2.28711 +3.01051 4 2 2 1.5337e+07 6.70583e+06 2.28711 +3.01056 4 3 1.33333 1.5337e+07 6.70583e+06 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6.70518e+06 2.28706 +3.0183 1836 656 2.79878 1.53351e+07 6.70518e+06 2.28706 +3.01831 1851 657 2.81735 1.53351e+07 6.70516e+06 2.28706 +3.01832 1911 679 2.81443 1.5335e+07 6.70514e+06 2.28706 +3.01833 1947 690 2.82174 1.5335e+07 6.70514e+06 2.28706 +3.01834 1957 692 2.82803 1.5335e+07 6.70514e+06 2.28706 +3.01835 1966 695 2.82878 1.5335e+07 6.70514e+06 2.28706 +3.01836 1970 695 2.83453 1.5335e+07 6.70514e+06 2.28706 +3.01837 1974 697 2.83214 1.5335e+07 6.70514e+06 2.28706 +3.01838 1976 698 2.83095 1.5335e+07 6.70514e+06 2.28706 +3.01839 1977 698 2.83238 1.5335e+07 6.70514e+06 2.28706 +3.01842 1978 699 2.82976 1.5335e+07 6.70513e+06 2.28706 +3.01843 1979 700 2.82714 1.5335e+07 6.70513e+06 2.28706 +3.01844 1980 700 2.82857 1.5335e+07 6.70513e+06 2.28706 +3.01846 1982 700 2.83143 1.5335e+07 6.70513e+06 2.28706 +3.01848 1983 700 2.83286 1.5335e+07 6.70513e+06 2.28705 +3.01849 1986 700 2.83714 1.5335e+07 6.70513e+06 2.28705 +3.01853 1987 700 2.83857 1.5335e+07 6.70513e+06 2.28706 +3.01854 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6.70513e+06 2.28705 +3.01901 2007 707 2.83876 1.5335e+07 6.70513e+06 2.28705 +3.01902 2008 707 2.84017 1.5335e+07 6.70513e+06 2.28705 +3.01905 2009 707 2.84158 1.5335e+07 6.70513e+06 2.28705 +3.01907 2009 708 2.83757 1.5335e+07 6.70512e+06 2.28705 +3.01909 2010 709 2.83498 1.5335e+07 6.70512e+06 2.28705 +3.0191 2010 710 2.83099 1.5335e+07 6.70512e+06 2.28705 +3.01914 2012 711 2.82982 1.5335e+07 6.70512e+06 2.28706 +3.01915 2012 713 2.82188 1.5335e+07 6.70512e+06 2.28706 +3.01917 2013 713 2.82328 1.5335e+07 6.70512e+06 2.28706 +3.01921 2013 714 2.81933 1.5335e+07 6.70512e+06 2.28706 +3.01922 2013 715 2.81538 1.5335e+07 6.70512e+06 2.28706 +3.01926 2015 715 2.81818 1.5335e+07 6.70512e+06 2.28706 +3.0193 2015 716 2.81425 1.5335e+07 6.70512e+06 2.28706 +3.01932 2016 718 2.8078 1.5335e+07 6.70512e+06 2.28706 +3.01934 2017 718 2.80919 1.5335e+07 6.70512e+06 2.28706 +3.01935 2018 719 2.80668 1.5335e+07 6.70511e+06 2.28706 +3.01941 2018 720 2.80278 1.5335e+07 6.70511e+06 2.28706 +3.01942 2018 721 2.79889 1.5335e+07 6.70511e+06 2.28706 +3.01943 2020 721 2.80166 1.5335e+07 6.70511e+06 2.28706 +3.01944 2021 721 2.80305 1.5335e+07 6.70511e+06 2.28706 +3.01951 2021 722 2.79917 1.5335e+07 6.70511e+06 2.28706 +3.01952 2021 723 2.7953 1.5335e+07 6.70511e+06 2.28706 +3.01954 2023 725 2.79034 1.5335e+07 6.70511e+06 2.28706 +3.01955 2026 725 2.79448 1.5335e+07 6.70511e+06 2.28706 +3.01956 2027 725 2.79586 1.5335e+07 6.70511e+06 2.28706 +3.01958 2028 726 2.79339 1.5335e+07 6.70511e+06 2.28706 +3.01959 2028 727 2.78955 1.5335e+07 6.70511e+06 2.28706 +3.01961 2028 728 2.78571 1.5335e+07 6.7051e+06 2.28706 +3.01962 2028 729 2.78189 1.5335e+07 6.7051e+06 2.28706 +3.01963 2029 729 2.78326 1.5335e+07 6.7051e+06 2.28706 +3.01965 2031 730 2.78219 1.5335e+07 6.7051e+06 2.28706 +3.01966 2033 731 2.78112 1.5335e+07 6.7051e+06 2.28706 +3.01967 2033 732 2.77732 1.5335e+07 6.7051e+06 2.28706 +3.01969 2035 732 2.78005 1.5335e+07 6.7051e+06 2.28706 +3.01975 2035 733 2.77626 1.5335e+07 6.7051e+06 2.28706 +3.01976 2037 733 2.77899 1.5335e+07 6.7051e+06 2.28706 +3.01978 2038 733 2.78035 1.5335e+07 6.7051e+06 2.28706 +3.01979 2038 734 2.77657 1.5335e+07 6.7051e+06 2.28706 +3.0198 2039 734 2.77793 1.5335e+07 6.7051e+06 2.28706 +3.01985 2041 734 2.78065 1.5335e+07 6.7051e+06 2.28706 +3.0199 2042 734 2.78202 1.5335e+07 6.7051e+06 2.28706 +3.01994 2043 734 2.78338 1.5335e+07 6.7051e+06 2.28706 +3.01995 2044 734 2.78474 1.5335e+07 6.7051e+06 2.28706 +3.01997 2045 734 2.7861 1.5335e+07 6.7051e+06 2.28706 +3.01998 2046 734 2.78747 1.53349e+07 6.7051e+06 2.28706 +3.01999 2047 734 2.78883 1.53349e+07 6.7051e+06 2.28706 +3.02001 2049 734 2.79155 1.53349e+07 6.7051e+06 2.28706 +3.02009 2050 734 2.79292 1.53349e+07 6.7051e+06 2.28706 +3.02015 2051 735 2.79048 1.53349e+07 6.7051e+06 2.28706 +3.02016 2052 735 2.79184 1.53349e+07 6.7051e+06 2.28706 +3.02017 2054 735 2.79456 1.53349e+07 6.7051e+06 2.28706 +3.02019 2055 735 2.79592 1.53349e+07 6.7051e+06 2.28706 +3.02022 2056 735 2.79728 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