| Next changeset 1:6999173dc0c2 (2017-10-27) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 264fd61d39f252ebb81731bf6cd3349fdb39b306 |
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added:
generate_test_data.sh multiqc.xml readme.rst test-data/aligner_soft_stats.tabular test-data/bamtools.txt test-data/bamtools_stats.tabular test-data/bcftools.txt test-data/bcftools_stats.tabular test-data/bismark.txt test-data/bismark_stats.tabular test-data/bowtie2_1.txt test-data/bowtie2_2.txt test-data/bowtie2_stats.tabular test-data/busco.txt test-data/busco_stats.tabular test-data/cc_ko15.bpc.embedded.tab test-data/cc_ko15.bpc.tab test-data/cc_wt15.bpc.embedded.tab test-data/cc_wt15.bpc.tab test-data/cutadapt.txt test-data/cutadapt_stats.tabular test-data/fastqc_1.txt test-data/fastqc_2.txt test-data/fastqc_stats.tabular test-data/featureCounts.txt test-data/featureCounts_stats.tabular test-data/flexbar.txt test-data/flexbar_stats.tabular test-data/gatk_BaseRecalibrator.txt test-data/gatk_varianteval.txt test-data/gatk_varianteval_stats.tabular test-data/hicup_deduplicator.txt test-data/hicup_filter.txt test-data/hicup_mapper.txt test-data/hicup_truncater.txt test-data/hisat2_1.txt test-data/hisat2_2.txt test-data/hisat2_stats.tabular test-data/htseq.txt test-data/htseq_stats.tabular test-data/kallisto_1.txt test-data/kallisto_2.txt test-data/kallisto_stats.tabular test-data/picard_AlignmentSummaryMetrics_stats.tabular test-data/picard_CollectAlignmentSummaryMetrics.txt test-data/picard_CollectBaseDistributionByCycle.txt test-data/picard_CollectInsertSizeMetrics.txt test-data/picard_CollectRnaSeqMetrics.txt test-data/picard_MarkDuplicates.txt test-data/picard_RnaSeqMetrics_stats.tabular test-data/picard_baseContent_stats.tabular test-data/picard_collectGcBias.txt test-data/picard_dups_stats.tabular test-data/picard_insertSize_stats.tabular test-data/post_aligner_soft_stats.tabular test-data/pre_alignment_soft_log.txt test-data/pre_alignment_soft_stats.tabular test-data/prokka_1.txt test-data/prokka_2.txt test-data/prokka_stats.tabular test-data/quast.tsv test-data/quast_stats.tabular test-data/report_manual_custom_content.html test-data/rsem.txt test-data/rseqc.txt test-data/salmon.txt test-data/samblaster.txt test-data/samblaster_stats.tabular test-data/samtools_flagstat.txt test-data/samtools_flagstat_stats.tabular test-data/samtools_idxstats.txt test-data/samtools_stats.txt test-data/samtools_stats_stats.tabular test-data/snpeff.csv test-data/sortmerna.txt test-data/sortmerna_stats.tabular test-data/star_counts.txt test-data/star_log.txt test-data/star_stats.tabular test-data/tophat.txt test-data/tophat_stats.tabular test-data/trimmomatic.txt test-data/trimmomatic_stats.tabular test-data/vcftools.txt |
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| 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 |
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| b"@@ -0,0 +1,195 @@\n+#!/usr/bin/env bash\n+\n+# 1st test\n+mkdir multiqc_WDir\n+\n+mkdir 'multiqc_WDir/cutadapt_0'\n+cp 'test-data/cutadapt.txt' 'multiqc_WDir/cutadapt_0/cutadapt.txt'\n+sed -i.old 's/You are running/This is/' 'multiqc_WDir/cutadapt_0/cutadapt.txt'\n+\n+mkdir -p 'multiqc_WDir/fastqc_1/data_0/file_0'\n+cp 'test-data/fastqc_1.txt' 'multiqc_WDir/fastqc_1/data_0/file_0/fastqc_data.txt'\n+mkdir 'multiqc_WDir/fastqc_1/data_0/file_1'\n+cp 'test-data/fastqc_2.txt' 'multiqc_WDir/fastqc_1/data_0/file_1/fastqc_data.txt'\n+\n+mkdir 'multiqc_WDir/flexbar_2'\n+cp 'test-data/flexbar.txt' 'multiqc_WDir/flexbar_2/flexbar.txt'\n+\n+mkdir 'multiqc_WDir/sortmerna_3'\n+cp 'test-data/sortmerna.txt' 'multiqc_WDir/sortmerna_3/sortmerna.txt'\n+\n+mkdir 'multiqc_WDir/trimmomatic_4'\n+cp 'test-data/trimmomatic.txt' 'multiqc_WDir/trimmomatic_4/trimmomatic.txt'\n+\n+multiqc multiqc_WDir\n+\n+mv 'multiqc_report.html' 'test-data/pre_alignment_soft_report.html'\n+mv 'multiqc_data/multiqc.log' 'test-data/pre_alignment_soft_log.txt'\n+mv 'multiqc_data/multiqc_cutadapt.txt' 'test-data/cutadapt_stats.tabular'\n+mv 'multiqc_data/multiqc_fastqc.txt' 'test-data/fastqc_stats.tabular'\n+mv 'multiqc_data/multiqc_flexbar.txt' 'test-data/flexbar_stats.tabular'\n+mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/pre_alignment_soft_stats.tabular'\n+mv 'multiqc_data/multiqc_sortmerna.txt' 'test-data/sortmerna_stats.tabular'\n+mv 'multiqc_data/multiqc_trimmomatic.txt' 'test-data/trimmomatic_stats.tabular'\n+\n+rm -rf 'multiqc_WDir'\n+rm -rf 'multiqc_data/'\n+\n+# 2nd test\n+mkdir multiqc_WDir\n+\n+mkdir 'multiqc_WDir/bismark_0'\n+cp 'test-data/bismark.txt' 'multiqc_WDir/bismark_0/bismark_SE_report.txt'\n+\n+mkdir 'multiqc_WDir/bowtie2_1'\n+cp 'test-data/bowtie2_1.txt' 'multiqc_WDir/bowtie2_1/bowtie2_1.txt'\n+cp 'test-data/bowtie2_2.txt' 'multiqc_WDir/bowtie2_1/bowtie2_2.txt'\n+\n+mkdir 'multiqc_WDir/hisat2_3'\n+cp 'test-data/hisat2_1.txt' 'multiqc_WDir/hisat2_3/hisat2_1.txt'\n+cp 'test-data/hisat2_2.txt' 'multiqc_WDir/hisat2_3/hisat2_2.txt'\n+\n+mkdir 'multiqc_WDir/kallisto_4'\n+cp 'test-data/kallisto_1.txt' 'multiqc_WDir/kallisto_4/kallisto_1.txt'\n+cp 'test-data/kallisto_2.txt' 'multiqc_WDir/kallisto_4/kallisto_2.txt'\n+\n+mkdir -p 'multiqc_WDir/salmon_5/fld_0/file_0'\n+cp 'test-data/salmon.txt' 'multiqc_WDir/salmon_5/fld_0/file_0/flenDist.txt'\n+\n+mkdir -p 'multiqc_WDir/star_6/log_0'\n+cp 'test-data/star_log.txt' 'multiqc_WDir/star_6/log_0/star_log_Log.final.out'\n+mkdir 'multiqc_WDir/star_6/genecounts_1'\n+cp 'test-data/star_counts.txt' 'multiqc_WDir/star_6/genecounts_1/star_counts_ReadsPerGene.out.tab'\n+\n+mkdir 'multiqc_WDir/tophat_7'\n+cp 'test-data/tophat.txt' 'multiqc_WDir/tophat_7/tophat_align_summary.txt'\n+\n+multiqc multiqc_WDir\n+\n+mv 'multiqc_report.html' 'test-data/aligner_soft_report.html'\n+mv 'multiqc_data/multiqc_bismark_alignment.txt' 'test-data/bismark_stats.tabular'\n+mv 'multiqc_data/multiqc_bowtie2.txt' 'test-data/bowtie2_stats.tabular'\n+mv 'multiqc_data/multiqc_general_stats.txt' 'test-data/aligner_soft_stats.tabular'\n+mv 'multiqc_data/multiqc_hisat2.txt' 'test-data/hisat2_stats.tabular'\n+mv 'multiqc_data/multiqc_kallisto.txt' 'test-data/kallisto_stats.tabular'\n+mv 'multiqc_data/multiqc_star.txt' 'test-data/star_stats.tabular'\n+mv 'multiqc_data/multiqc_tophat.txt.txt' 'test-data/tophat_stats.tabular'\n+\n+rm -rf 'multiqc_WDir'\n+rm -rf 'multiqc_data/'\n+\n+# 3rd test\n+mkdir multiqc_WDir\n+\n+mkdir 'multiqc_WDir/bamtools_0'\n+cp 'test-data/bamtools.txt' 'multiqc_WDir/bamtools_0/bamtools.txt'\n+\n+mkdir 'multiqc_WDir/bcftools_1'\n+cp 'test-data/bcftools.txt' 'multiqc_WDir/bcftools_1/bcftools.txt'\n+\n+mkdir 'multiqc_WDir/busco_2'\n+cp 'test-data/busco.txt' 'multiqc_WDir/busco_2/short_summary_busco.txt'\n+\n+mkdir 'multiqc_WDir/featureCounts_3'\n+cp 'test-data/featureCounts.txt' 'multiqc_WDir/featureCounts_3/featureCounts.summary'\n+\n+mkdir 'multiqc_WDir/gatk_4'\n+cp 'test-data/gatk_BaseRecalibrator.txt' 'multiqc_WDir/gatk_4/gatk_BaseRecalibrator.txt'\n+cp 'test-data/gatk_varianteval.txt' 'multiqc_WDir/gatk_4/gatk_va"..b't_8/file_0/report.tsv\'\n+\n+#mkdir \'multiqc_WDir/rsem_9\'\n+#cp \'test-data/rsem.txt\' \'multiqc_WDir/rsem_9/rsem.cnt\'\n+\n+mkdir -p \'multiqc_WDir/rseqc_10/read_gc_0\'\n+cp \'test-data/rseqc.txt\' \'multiqc_WDir/rseqc_10/read_gc_0/rseq.GC.xls\'\n+\n+mkdir \'multiqc_WDir/samblaster_11\'\n+cp \'test-data/samblaster.txt\' \'multiqc_WDir/samblaster_11/samblaster.txt\'\n+\n+mkdir -p \'multiqc_WDir/samtools_12/stats_0\'\n+cp \'test-data/samtools_stats.txt\' \'multiqc_WDir/samtools_12/stats_0/samtools_stats.txt\'\n+mkdir \'multiqc_WDir/samtools_12/flagstat_1\'\n+cp \'test-data/samtools_flagstat.txt\' \'multiqc_WDir/samtools_12/flagstat_1/samtools_flagstat.txt\'\n+mkdir \'multiqc_WDir/samtools_12/idxstats_2\'\n+cp \'test-data/samtools_flagstat.txt\' \'multiqc_WDir/samtools_12/idxstats_2/samtools_idxstats_idxstat\'\n+\n+#mkdir \'multiqc_WDir/snpeff_13\'\n+#cp \'test-data/snpeff.csv\' \'multiqc_WDir/snpeff_13/snpeff.txt\'\n+\n+mkdir -p \'multiqc_WDir/vcftools_14/tstv_by_qual_0\'\n+cp \'test-data/vcftools.txt\' \'multiqc_WDir/vcftools_14/tstv_by_qual_0/vcftools.TsTv.qual\'\n+\n+multiqc multiqc_WDir\n+\n+mv \'multiqc_report.html\' \'test-data/post_aligner_soft_report.html\'\n+mv \'multiqc_data/multiqc_bamtools_stats.txt\' \'test-data/bamtools_stats.tabular\'\n+mv \'multiqc_data/multiqc_bcftools_stats.txt\' \'test-data/bcftools_stats.tabular\'\n+mv \'multiqc_data/multiqc_busco.txt\' \'test-data/busco_stats.tabular\'\n+mv \'multiqc_data/multiqc_featureCounts.txt\' \'test-data/featureCounts_stats.tabular\'\n+mv \'multiqc_data/multiqc_gatk_varianteval.txt\' \'test-data/gatk_varianteval_stats.tabular\'\n+mv \'multiqc_data/multiqc_general_stats.txt\' \'test-data/post_aligner_soft_stats.tabular\'\n+mv \'multiqc_data/multiqc_htseq.txt\' \'test-data/htseq_stats.tabular\'\n+mv \'multiqc_data/multiqc_picard_AlignmentSummaryMetrics.txt\' \'test-data/picard_AlignmentSummaryMetrics_stats.tabular\'\n+mv \'multiqc_data/multiqc_picard_RnaSeqMetrics.txt\' \'test-data/picard_RnaSeqMetrics_stats.tabular\'\n+mv \'multiqc_data/multiqc_picard_baseContent.txt\' \'test-data/picard_baseContent_stats.tabular\'\n+mv \'multiqc_data/multiqc_picard_dups.txt\' \'test-data/picard_dups_stats.tabular\'\n+mv \'multiqc_data/multiqc_picard_insertSize.txt\' \'test-data/picard_insertSize_stats.tabular\'\n+mv \'multiqc_data/multiqc_prokka.txt\' \'test-data/prokka_stats.tabular\'\n+mv \'multiqc_data/multiqc_quast.txt\' \'test-data/quast_stats.tabular\'\n+#mv \'multiqc_data/multiqc_rsem.txt\' \'test-data/rsem_stats.tabular\'\n+mv \'multiqc_data/multiqc_rseqc.txt\' \'test-data/rseqc_stats.tabular\'\n+mv \'multiqc_data/multiqc_samblaster.txt\' \'test-data/samblaster_stats.tabular\'\n+mv \'multiqc_data/multiqc_samtools_flagstat.txt\' \'test-data/samtools_flagstat_stats.tabular\'\n+mv \'multiqc_data/multiqc_samtools_stats.txt\' \'test-data/samtools_stats_stats.tabular\'\n+#mv \'multiqc_data/multiqc_snpeff.txt\' \'test-data/snpeff_stats.tabular\'\n+\n+rm -rf \'multiqc_WDir\'\n+rm -rf \'multiqc_data/\'\n+\n+# 4th test\n+mkdir multiqc_WDir\n+\n+mkdir \'multiqc_WDir/custom_content_0\'\n+cp \'test-data/cc_ko15.bpc.tab\' \'multiqc_WDir/custom_content_0/file_0_0.tsv\'\n+cp \'test-data/cc_wt15.bpc.tab\' \'multiqc_WDir/custom_content_0/file_0_1.tsv\'\n+\n+echo "custom_data:" > \'config_file\'\n+echo " section_0:" >> \'config_file\'\n+echo " file_format: \'tsv\'" >> \'config_file\'\n+echo " section_name: \'BPC\'" >> \'config_file\'\n+echo " title: \'Base peak chromatogram\'" >> \'config_file\'\n+echo " description: \'Sum of intensity (Y) of the most intense peaks at each retention time(X)\'" >> \'config_file\'\n+echo " plot_type: \'linegraph\'" >> \'config_file\'\n+echo " pconfig:" >> \'config_file\'\n+echo " id: \'section_0_linegraph\'" >> \'config_file\'\n+echo " ylab: \'Base Peak Intensity\'" >> \'config_file\'\n+echo " xlab: \'Retention Time\'" >> \'config_file\'\n+echo "sp:" >> \'config_file\'\n+echo " section_0:" >> \'config_file\'\n+echo " fn: \'file_0_*\'" >> \'config_file\'\n+\n+multiqc multiqc_WDir -c \'config_file\'\n+\n+mv \'multiqc_report.html\' \'test-data/report_manual_custom_content.html\'\n+\n+rm \'config_file\'\n+rm -rf \'multiqc_WDir\'\n+rm -rf \'multiqc_data/\'\n' |
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| 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 |
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| b'@@ -0,0 +1,994 @@\n+<tool id="multiqc" name="MultiQC" version="@WRAPPER_VERSION@.0">\n+ <description>aggregate results from bioinformatics analyses into a single report</description>\n+ <macros>\n+ <token name="@WRAPPER_VERSION@">1.2</token>\n+ <token name="@LN_FILES@">\n+<![CDATA[\n+#for $file in $repeat.software_cond.input\n+ grep -q "$pattern" $file || die "\'$pattern\' not found in the file" &&\n+ ln -s \'$file\' \'$software_dir/${file.element_identifier}\' &&\n+#end for\n+ ]]></token>\n+ <token name="@LN_2_FILES@">\n+<![CDATA[\n+#for $file in $repeat2.input:\n+ grep -q "$pattern" $file || die "\'$pattern\' not found in the file" &&\n+ ln -s \'$file\' \'$software_dir/${repeat2.type}_${j}_${file.element_identifier}\' &&\n+#end for\n+ ]]></token>\n+ <token name="@LN_3_FILES@">\n+<![CDATA[\n+#for $file in $repeat2.type.input:\n+ grep -q "$pattern" $file || die "\'$pattern\' not found in the file" &&\n+ ln -s \'$file\' \'$repeat_dir/${file.element_identifier}\' &&\n+#end for\n+ ]]></token>\n+ </macros>\n+ <requirements>\n+ <requirement type="package" version="@WRAPPER_VERSION@">multiqc</requirement>\n+ </requirements>\n+ <version_command>mulitqc --version</version_command>\n+ <command detect_errors="aggressive">\n+<![CDATA[\n+die() { echo "$@" 1>&2 ; exit 1; } &&\n+\n+mkdir multiqc_WDir &&\n+\n+#set $configfile="F"\n+\n+#for $i, $repeat in enumerate( $results )\n+ #set software_dir = \'multiqc_WDir/\' + str($repeat.software_cond.software) + \'_\' + str($i)\n+ mkdir $software_dir &&\n+\n+ #if str($repeat.software_cond.software) == "bamtools"\n+ #set $pattern = "Stats for BAM file(s)"\n+ @LN_FILES@\n+ #elif str($repeat.software_cond.software) == "bcftools"\n+ #set $pattern = "This file was produced by bcftools stats"\n+ @LN_FILES@\n+ #elif str($repeat.software_cond.software) == "bismark"\n+ #for $j, $repeat2 in enumerate( $repeat.software_cond.output )\n+ #set file_prefix = $software_dir + \'/\' + str($repeat2.type) + \'_\' + str($j)\n+ #if str($repeat2.type) == "align"\n+ #for $file in $repeat2.input\n+ ln -s \'$file\' \'${file_prefix}_${file.element_identifier}_SE_report.txt\' &&\n+ #end for\n+ #elif str($repeat2.type) == "dedup"\n+ #for $file in $repeat2.input\n+ ln -s \'$file\' \'${file_prefix}_${file.element_identifier}_deduplication_report.txt\' &&\n+ #end for\n+ #elif str($repeat2.type) == "meth_extract"\n+ #for $file in $repeat2.input\n+ ln -s \'$file\' \'${file_prefix}_${file.element_identifier}_splitting_report.txt\' &&\n+ #end for\n+ #elif str($repeat2.type) == "m_bias"\n+ #for $file in $repeat2.input\n+ ln -s \'$file\' \'${file_prefix}_${file.element_identifier}_M-bias.txt\' &&\n+ #end for\n+ #elif str($repeat2.type) == "bam2nuc"\n+ #for $file in $repeat2.input\n+ ln -s \'$file\' \'${file_prefix}_${file.element_identifier}.nucleotide_stats.txt\' &&\n+ #end for\n+ #end if\n+ #end for\n+ #elif str($repeat.software_cond.software) == "bowtie2"\n+ #set $pattern = "reads; of these:"\n+ @LN_FILES@\n+ #elif str($repeat.software_cond.software) == "busco"\n+ ## Searches for files "short_summary_[samplename].txt"\n+ #for $file in $repeat.software_cond.input\n+ ln -s \'$file\' \'$software_dir/short_summary_${file.element_identifier}\' &&\n+ #end for\n+ #elif str($repeat.software_cond.software) == "cutadapt"\n+ #set $pattern = "This is cutadapt"\n+ #for $file in $repeat.software_cond.input\n+ #set file_path = $software_dir + \'/\' + str($file.element_identifier) + \'.txt\'\n+ ln -s \'$file\' \'$file_path\' &&\n+ ## replace header for old cutadapt release\n+ sed -i.old \'s/You are running/This is/\' '..b'r" compare="sim_size" delta="0"/>\n+ <element name="busco" file="busco_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="featureCounts" file="featureCounts_stats.tabular" compare="sim_size" delta="25"/>\n+ <element name="gatk_varianteval" file="gatk_varianteval_stats.tabular" compare="sim_size" delta="20"/>\n+ <element name="general_stats" file="post_aligner_soft_stats.tabular" compare="sim_size" delta="25"/>\n+ <element name="htseq" file="htseq_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="picard_AlignmentSummaryMetrics" file="picard_AlignmentSummaryMetrics_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="picard_RnaSeqMetrics" file="picard_RnaSeqMetrics_stats.tabular" compare="sim_size" delta="40"/>\n+ <element name="picard_baseContent" file="picard_baseContent_stats.tabular" compare="sim_size" delta="50"/>\n+ <element name="picard_dups" file="picard_dups_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="picard_insertSize" file="picard_insertSize_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="prokka" file="prokka_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="quast" file="quast_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="samblaster" file="samblaster_stats.tabular" compare="sim_size" delta="0"/>\n+ <element name="samtools_flagstat">\n+ <assert_contents>\n+ <has_text text="samtools_flagstat" />\n+ <has_text text="mapped_passed" />\n+ <has_text text="20689039" />\n+ </assert_contents>\n+ </element>\n+ <element name="samtools_stats" file="samtools_stats_stats.tabular" compare="sim_size" delta="15"/>\n+ </output_collection>\n+ </test>\n+ <test>\n+ <repeat name="results">\n+ <conditional name="software_cond">\n+ <param name="software" value="custom_content" />\n+ <param name="cc_select" value="manual" />\n+ <param name="plot_type" value="linegraph" />\n+ <param name="section_name" value="BPC" />\n+ <param name="title" value="Base peak chromatogram" />\n+ <param name="description" value="Sum of intensity (Y) of the most intense peaks at each retention time(X)" />\n+ <param name="xlab" value="Retention Time" />\n+ <param name="ylab" value="Base Peak Intensity" />\n+ <param name="input" value="cc_ko15.bpc.tab,cc_wt15.bpc.tab" />\n+ </conditional>\n+ </repeat>\n+ <output name="html_report" file="report_manual_custom_content.html" compare="sim_size"/>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+**What it does**\n+\n+`MultiQC <http://multiqc.info/>`_ 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.\n+\n+**Inputs**\n+\n+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\n+\n+----\n+\n+The first integration of this tool was made by Cyril Monjeaud and Yvan Le Bras (`EnginesOn <http://engineson.fr/>`_ and Rennes GenOuest Bio-informatics Core Facility).\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1093/bioinformatics/btw354</citation>\n+ </citations>\n+</tool>\n' |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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 |
| b |
| 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 |
| b |
| @@ -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%) |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| [ |
| b'@@ -0,0 +1,1177 @@\n+# This file was produced by bcftools stats (1.3.1+htslib-1.3.1) and can be plotted using plot-vcfstats.\n+# The command line was:\tbcftools stats Test1.vcf.gz\n+#\n+# Definition of sets:\n+# ID\t[2]id\t[3]tab-separated file names\n+ID\t0\tTest1.vcf.gz\n+# SN, Summary numbers:\n+# SN\t[2]id\t[3]key\t[4]value\n+SN\t0\tnumber of samples:\t1\n+SN\t0\tnumber of records:\t5522770\n+SN\t0\tnumber of no-ALTs:\t0\n+SN\t0\tnumber of SNPs:\t4474244\n+SN\t0\tnumber of MNPs:\t72330\n+SN\t0\tnumber of indels:\t902934\n+SN\t0\tnumber of others:\t73262\n+SN\t0\tnumber of multiallelic sites:\t0\n+SN\t0\tnumber of multiallelic SNP sites:\t0\n+# TSTV, transitions/transversions:\n+# TSTV\t[2]id\t[3]ts\t[4]tv\t[5]ts/tv\t[6]ts (1st ALT)\t[7]tv (1st ALT)\t[8]ts/tv (1st ALT)\n+TSTV\t0\t2968539\t1505704\t1.97\t2968539\t1505704\t1.97\n+# SiS, Singleton stats:\n+# SiS\t[2]id\t[3]allele count\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n+SiS\t0\t1\t4474243\t2968539\t1505704\t902934\t0\t0\t902934\n+# AF, Stats by non-reference allele frequency:\n+# AF\t[2]id\t[3]allele frequency\t[4]number of SNPs\t[5]number of transitions\t[6]number of transversions\t[7]number of indels\t[8]repeat-consistent\t[9]repeat-inconsistent\t[10]not applicable\n+AF\t0\t0.000000\t4474243\t2968539\t1505704\t902934\t0\t0\t902934\n+# QUAL, Stats by quality:\n+# QUAL\t[2]id\t[3]Quality\t[4]number of SNPs\t[5]number of transitions (1st ALT)\t[6]number of transversions (1st ALT)\t[7]number of indels\n+QUAL\t0\t25\t0\t0\t0\t2\n+QUAL\t0\t26\t0\t0\t0\t14\n+QUAL\t0\t27\t330\t117\t213\t52\n+QUAL\t0\t28\t0\t0\t0\t36\n+QUAL\t0\t29\t698\t273\t425\t136\n+QUAL\t0\t30\t0\t0\t0\t70\n+QUAL\t0\t31\t0\t0\t0\t70\n+QUAL\t0\t32\t1071\t538\t533\t242\n+QUAL\t0\t33\t0\t0\t0\t134\n+QUAL\t0\t34\t2006\t1108\t898\t483\n+QUAL\t0\t35\t0\t0\t0\t169\n+QUAL\t0\t36\t0\t0\t0\t114\n+QUAL\t0\t37\t3117\t1822\t1295\t717\n+QUAL\t0\t38\t0\t0\t0\t203\n+QUAL\t0\t39\t4890\t2607\t2283\t794\n+QUAL\t0\t40\t475\t251\t224\t194\n+QUAL\t0\t41\t0\t0\t0\t100\n+QUAL\t0\t42\t9823\t5611\t4212\t1577\n+QUAL\t0\t43\t0\t0\t0\t44\n+QUAL\t0\t44\t1294\t671\t623\t107\n+QUAL\t0\t45\t575\t308\t267\t113\n+QUAL\t0\t46\t0\t0\t0\t53\n+QUAL\t0\t47\t1220\t724\t496\t137\n+QUAL\t0\t48\t755\t419\t336\t160\n+QUAL\t0\t49\t0\t0\t0\t78\n+QUAL\t0\t50\t2490\t1450\t1040\t280\n+QUAL\t0\t51\t389\t160\t229\t161\n+QUAL\t0\t52\t0\t0\t0\t103\n+QUAL\t0\t53\t1428\t759\t669\t291\n+QUAL\t0\t54\t170\t93\t77\t179\n+QUAL\t0\t55\t1497\t897\t600\t419\n+QUAL\t0\t56\t810\t385\t425\t214\n+QUAL\t0\t57\t0\t0\t0\t186\n+QUAL\t0\t58\t2427\t1436\t991\t501\n+QUAL\t0\t59\t1370\t675\t695\t333\n+QUAL\t0\t60\t180\t97\t83\t185\n+QUAL\t0\t61\t4117\t2446\t1671\t678\n+QUAL\t0\t62\t756\t376\t380\t329\n+QUAL\t0\t63\t3582\t2107\t1475\t672\n+QUAL\t0\t64\t2047\t1062\t985\t355\n+QUAL\t0\t65\t404\t190\t214\t277\n+QUAL\t0\t66\t7220\t4196\t3024\t1273\n+QUAL\t0\t67\t502\t248\t254\t266\n+QUAL\t0\t68\t1707\t962\t745\t230\n+QUAL\t0\t69\t2503\t1319\t1184\t492\n+QUAL\t0\t70\t0\t0\t0\t231\n+QUAL\t0\t71\t3085\t1777\t1308\t644\n+QUAL\t0\t72\t142\t58\t84\t298\n+QUAL\t0\t73\t1880\t1048\t832\t389\n+QUAL\t0\t74\t2127\t1225\t902\t646\n+QUAL\t0\t75\t1181\t691\t490\t404\n+QUAL\t0\t76\t3685\t2138\t1547\t709\n+QUAL\t0\t77\t715\t403\t312\t398\n+QUAL\t0\t78\t3041\t1780\t1261\t641\n+QUAL\t0\t79\t3287\t1867\t1420\t790\n+QUAL\t0\t80\t2149\t1253\t896\t592\n+QUAL\t0\t81\t4668\t2759\t1909\t964\n+QUAL\t0\t82\t1655\t910\t745\t529\n+QUAL\t0\t83\t3422\t2034\t1388\t604\n+QUAL\t0\t84\t5891\t3393\t2498\t1272\n+QUAL\t0\t85\t3175\t1872\t1303\t701\n+QUAL\t0\t86\t1797\t1052\t745\t474\n+QUAL\t0\t87\t2673\t1550\t1123\t627\n+QUAL\t0\t88\t3927\t2334\t1593\t783\n+QUAL\t0\t89\t2503\t1498\t1005\t632\n+QUAL\t0\t90\t4171\t2440\t1731\t884\n+QUAL\t0\t91\t3268\t2019\t1249\t735\n+QUAL\t0\t92\t3328\t1950\t1378\t929\n+QUAL\t0\t93\t4280\t2602\t1678\t764\n+QUAL\t0\t94\t1197\t692\t505\t640\n+QUAL\t0\t95\t7503\t4457\t3046\t1207\n+QUAL\t0\t96\t914\t533\t381\t683\n+QUAL\t0\t97\t7986\t4762\t3224\t1443\n+QUAL\t0\t98\t1750\t1062\t688\t496\n+QUAL\t0\t99\t3108\t1917\t1191\t845\n+QUAL\t0\t100\t3476\t2094\t1382\t734\n+QUAL\t0\t101\t3338\t2007\t1331\t824\n+QUAL\t0\t102\t3860\t2320\t1540\t933\n+QUAL\t0\t103\t3775\t2295\t1480\t840\n+QUAL\t0\t104\t3468\t2115\t1353\t1002\n+QUAL\t0\t105\t4727\t2877\t1850\t1006\n+QUAL\t0\t106\t4536\t2690\t1846\t976\n+QUAL\t0\t107\t3022\t1895\t1127\t874\n+QUAL\t0\t108\t5322\t3178\t2144\t1189\n+QUAL\t0\t109\t3979\t2458\t1521\t957\n+QUAL\t0\t110\t2929\t1739\t1190\t787\n+QUAL\t0\t111\t3070\t1833\t1237\t818\n+QUAL\t0\t112\t5040\t3031\t2009\t1124\n+QUAL\t0\t113\t4212\t2576\t1636\t1001\n+QUAL\t0\t114\t3621\t2186\t1435\t968\n+QUAL\t0\t115\t5099\t2986\t21'..b'000\t762\t0.013797\n+DP\t0\t385\t0\t0.000000\t807\t0.014612\n+DP\t0\t386\t0\t0.000000\t776\t0.014051\n+DP\t0\t387\t0\t0.000000\t762\t0.013797\n+DP\t0\t388\t0\t0.000000\t766\t0.013870\n+DP\t0\t389\t0\t0.000000\t751\t0.013598\n+DP\t0\t390\t0\t0.000000\t789\t0.014286\n+DP\t0\t391\t0\t0.000000\t775\t0.014033\n+DP\t0\t392\t0\t0.000000\t737\t0.013345\n+DP\t0\t393\t0\t0.000000\t688\t0.012458\n+DP\t0\t394\t0\t0.000000\t713\t0.012910\n+DP\t0\t395\t0\t0.000000\t679\t0.012295\n+DP\t0\t396\t0\t0.000000\t754\t0.013653\n+DP\t0\t397\t0\t0.000000\t701\t0.012693\n+DP\t0\t398\t0\t0.000000\t681\t0.012331\n+DP\t0\t399\t0\t0.000000\t703\t0.012729\n+DP\t0\t400\t0\t0.000000\t669\t0.012113\n+DP\t0\t401\t0\t0.000000\t717\t0.012983\n+DP\t0\t402\t0\t0.000000\t703\t0.012729\n+DP\t0\t403\t0\t0.000000\t648\t0.011733\n+DP\t0\t404\t0\t0.000000\t672\t0.012168\n+DP\t0\t405\t0\t0.000000\t664\t0.012023\n+DP\t0\t406\t0\t0.000000\t620\t0.011226\n+DP\t0\t407\t0\t0.000000\t659\t0.011932\n+DP\t0\t408\t0\t0.000000\t635\t0.011498\n+DP\t0\t409\t0\t0.000000\t662\t0.011987\n+DP\t0\t410\t0\t0.000000\t616\t0.011154\n+DP\t0\t411\t0\t0.000000\t635\t0.011498\n+DP\t0\t412\t0\t0.000000\t633\t0.011462\n+DP\t0\t413\t0\t0.000000\t665\t0.012041\n+DP\t0\t414\t0\t0.000000\t609\t0.011027\n+DP\t0\t415\t0\t0.000000\t668\t0.012095\n+DP\t0\t416\t0\t0.000000\t612\t0.011081\n+DP\t0\t417\t0\t0.000000\t631\t0.011425\n+DP\t0\t418\t0\t0.000000\t639\t0.011570\n+DP\t0\t419\t0\t0.000000\t583\t0.010556\n+DP\t0\t420\t0\t0.000000\t625\t0.011317\n+DP\t0\t421\t0\t0.000000\t628\t0.011371\n+DP\t0\t422\t0\t0.000000\t621\t0.011244\n+DP\t0\t423\t0\t0.000000\t577\t0.010448\n+DP\t0\t424\t0\t0.000000\t603\t0.010918\n+DP\t0\t425\t0\t0.000000\t563\t0.010194\n+DP\t0\t426\t0\t0.000000\t550\t0.009959\n+DP\t0\t427\t0\t0.000000\t620\t0.011226\n+DP\t0\t428\t0\t0.000000\t560\t0.010140\n+DP\t0\t429\t0\t0.000000\t569\t0.010303\n+DP\t0\t430\t0\t0.000000\t596\t0.010792\n+DP\t0\t431\t0\t0.000000\t552\t0.009995\n+DP\t0\t432\t0\t0.000000\t609\t0.011027\n+DP\t0\t433\t0\t0.000000\t565\t0.010230\n+DP\t0\t434\t0\t0.000000\t555\t0.010049\n+DP\t0\t435\t0\t0.000000\t576\t0.010430\n+DP\t0\t436\t0\t0.000000\t567\t0.010267\n+DP\t0\t437\t0\t0.000000\t546\t0.009886\n+DP\t0\t438\t0\t0.000000\t582\t0.010538\n+DP\t0\t439\t0\t0.000000\t540\t0.009778\n+DP\t0\t440\t0\t0.000000\t574\t0.010393\n+DP\t0\t441\t0\t0.000000\t559\t0.010122\n+DP\t0\t442\t0\t0.000000\t555\t0.010049\n+DP\t0\t443\t0\t0.000000\t557\t0.010086\n+DP\t0\t444\t0\t0.000000\t562\t0.010176\n+DP\t0\t445\t0\t0.000000\t581\t0.010520\n+DP\t0\t446\t0\t0.000000\t518\t0.009379\n+DP\t0\t447\t0\t0.000000\t548\t0.009923\n+DP\t0\t448\t0\t0.000000\t533\t0.009651\n+DP\t0\t449\t0\t0.000000\t542\t0.009814\n+DP\t0\t450\t0\t0.000000\t488\t0.008836\n+DP\t0\t451\t0\t0.000000\t549\t0.009941\n+DP\t0\t452\t0\t0.000000\t547\t0.009904\n+DP\t0\t453\t0\t0.000000\t575\t0.010411\n+DP\t0\t454\t0\t0.000000\t534\t0.009669\n+DP\t0\t455\t0\t0.000000\t489\t0.008854\n+DP\t0\t456\t0\t0.000000\t505\t0.009144\n+DP\t0\t457\t0\t0.000000\t522\t0.009452\n+DP\t0\t458\t0\t0.000000\t518\t0.009379\n+DP\t0\t459\t0\t0.000000\t517\t0.009361\n+DP\t0\t460\t0\t0.000000\t495\t0.008963\n+DP\t0\t461\t0\t0.000000\t498\t0.009017\n+DP\t0\t462\t0\t0.000000\t556\t0.010067\n+DP\t0\t463\t0\t0.000000\t496\t0.008981\n+DP\t0\t464\t0\t0.000000\t539\t0.009760\n+DP\t0\t465\t0\t0.000000\t507\t0.009180\n+DP\t0\t466\t0\t0.000000\t528\t0.009560\n+DP\t0\t467\t0\t0.000000\t470\t0.008510\n+DP\t0\t468\t0\t0.000000\t467\t0.008456\n+DP\t0\t469\t0\t0.000000\t488\t0.008836\n+DP\t0\t470\t0\t0.000000\t503\t0.009108\n+DP\t0\t471\t0\t0.000000\t492\t0.008909\n+DP\t0\t472\t0\t0.000000\t527\t0.009542\n+DP\t0\t473\t0\t0.000000\t543\t0.009832\n+DP\t0\t474\t0\t0.000000\t492\t0.008909\n+DP\t0\t475\t0\t0.000000\t517\t0.009361\n+DP\t0\t476\t0\t0.000000\t516\t0.009343\n+DP\t0\t477\t0\t0.000000\t484\t0.008764\n+DP\t0\t478\t0\t0.000000\t511\t0.009253\n+DP\t0\t479\t0\t0.000000\t484\t0.008764\n+DP\t0\t480\t0\t0.000000\t519\t0.009397\n+DP\t0\t481\t0\t0.000000\t501\t0.009072\n+DP\t0\t482\t0\t0.000000\t478\t0.008655\n+DP\t0\t483\t0\t0.000000\t491\t0.008890\n+DP\t0\t484\t0\t0.000000\t471\t0.008528\n+DP\t0\t485\t0\t0.000000\t472\t0.008546\n+DP\t0\t486\t0\t0.000000\t510\t0.009234\n+DP\t0\t487\t0\t0.000000\t496\t0.008981\n+DP\t0\t488\t0\t0.000000\t490\t0.008872\n+DP\t0\t489\t0\t0.000000\t501\t0.009072\n+DP\t0\t490\t0\t0.000000\t508\t0.009198\n+DP\t0\t491\t0\t0.000000\t496\t0.008981\n+DP\t0\t492\t0\t0.000000\t475\t0.008601\n+DP\t0\t493\t0\t0.000000\t466\t0.008438\n+DP\t0\t494\t0\t0.000000\t471\t0.008528\n+DP\t0\t495\t0\t0.000000\t480\t0.008691\n+DP\t0\t496\t0\t0.000000\t500\t0.009053\n+DP\t0\t497\t0\t0.000000\t471\t0.008528\n+DP\t0\t498\t0\t0.000000\t496\t0.008981\n+DP\t0\t499\t0\t0.000000\t440\t0.007967\n+DP\t0\t500\t0\t0.000000\t455\t0.008239\n+DP\t0\t>500\t0\t0.000000\t144729\t2.620587\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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% |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b"@@ -0,0 +1,1289 @@\n+# file_format: 'tsv'\n+# section_name: 'BPC'\n+# title: 'Base peak chromatogram'\n+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'\n+# plot_type: 'linegraph'\n+# pconfig:\n+# id: 'bpc_lineplot'\n+# title: 'Base peak chromatogram'\n+# ylab: 'Base Peak Intensity'\n+# xlab: 'Retention Time'\n+Retention Time\tBase Peak Intensity\n+2502.98928676082\t43888\n+2504.55428676082\t43960\n+2506.11928676082\t43392\n+2507.68428676082\t42632\n+2509.24928676082\t42200\n+2510.81428676082\t42288\n+2512.37928676082\t42664\n+2513.94428676082\t42480\n+2515.50928676082\t42320\n+2517.07428676082\t42528\n+2518.63928676082\t43376\n+2520.20428676082\t44240\n+2521.76928676082\t44696\n+2523.33328676082\t44560\n+2524.89828676082\t44112\n+2526.46328676082\t43936\n+2528.02828676082\t43736\n+2529.59328676082\t42912\n+2531.15828676082\t42360\n+2532.72328676082\t43128\n+2534.28828676082\t43880\n+2535.85328676082\t44104\n+2537.41828676082\t44256\n+2538.98328676082\t44664\n+2540.54828676082\t44600\n+2542.11328676082\t44224\n+2543.67828676082\t44120\n+2545.24328676082\t44328\n+2546.80828676082\t44536\n+2548.37328676082\t44872\n+2549.93828676082\t44592\n+2551.50328676082\t43600\n+2553.06828676082\t42872\n+2554.63328676082\t43528\n+2556.19728676082\t44072\n+2557.76228676082\t43360\n+2559.32728676082\t41632\n+2560.89228676082\t40752\n+2562.45728676082\t40472\n+2564.02228676082\t39792\n+2565.58728676082\t39096\n+2567.15228676082\t39696\n+2568.71728676082\t41152\n+2570.28228676082\t41896\n+2571.84728676082\t41568\n+2573.41228676082\t41448\n+2574.97728676082\t42336\n+2576.54228676082\t43432\n+2578.10728676082\t43720\n+2579.67228676082\t43352\n+2581.23728676082\t43528\n+2582.80228676082\t55720\n+2584.36728676082\t74184\n+2585.93228676082\t91992\n+2587.49728676082\t105888\n+2589.06228676082\t114512\n+2590.62628676082\t120272\n+2592.19128676082\t123640\n+2593.75628676082\t122024\n+2595.32128676082\t115504\n+2596.88628676082\t106736\n+2598.45128676082\t97864\n+2600.01628676082\t87640\n+2601.58128676082\t77312\n+2603.14628676082\t67952\n+2604.71128676082\t59464\n+2606.27628676082\t50624\n+2607.84128676082\t43672\n+2609.40628676082\t43920\n+2610.97128676082\t43880\n+2612.53628676082\t44024\n+2614.10128676082\t44192\n+2615.66628676082\t44352\n+2617.23128676082\t44048\n+2618.79628676082\t43312\n+2620.4002803902\t42128\n+2622.00450588418\t41032\n+2623.60789985113\t40696\n+2625.2124745374\t41264\n+2626.81716666296\t42000\n+2628.42193807791\t42792\n+2630.02675063237\t43880\n+2631.63156617644\t45064\n+2633.23634656023\t45872\n+2634.84105363384\t45696\n+2636.44564924738\t44992\n+2638.05009525096\t43776\n+2639.65435349467\t42608\n+2641.25838582864\t41656\n+2642.86215410296\t41328\n+2644.46562016774\t41360\n+2646.06874587309\t41520\n+2647.67149306911\t49200\n+2649.2738236059\t82296\n+2650.87569933359\t127032\n+2652.47708210226\t178368\n+2654.07793376204\t231808\n+2655.67821616301\t285120\n+2657.2778911553\t334464\n+2658.87589905919\t369856\n+2660.47424523347\t387136\n+2662.07186957376\t393344\n+2663.66930678668\t395904\n+2665.26703198027\t395456\n+2666.86491760675\t391936\n+2668.46283611837\t396608\n+2670.06065996733\t419008\n+2671.65826160588\t465280\n+2673.25551348623\t526336\n+2674.85228806062\t586624\n+2676.44845778127\t625472\n+2678.04389510041\t642304\n+2679.63847247027\t651392\n+2681.23206234307\t664256\n+2682.82633158321\t672064\n+2684.41623929172\t664448\n+2686.00135805823\t642048\n+2687.58194841108\t611776\n+2689.1582708786\t577216\n+2690.73058598911\t537408\n+2692.29815313176\t489984\n+2693.86323725773\t437248\n+2695.42509544522\t385536\n+2696.98398822256\t336256\n+2698.54017611806\t287104\n+2700.09391966008\t240512\n+2701.64547937692\t201024\n+2703.19511579694\t166656\n+2704.74308944844\t137088\n+2706.28966085977\t117720\n+2707.83509055926\t98584\n+2709.37963907523\t81576\n+2710.92356693602\t66760\n+2712.46713466996\t53440\n+2714.01060280537\t41984\n+2715.55423187058\t37808\n+2717.09813305014\t37464\n+2718.64227188502\t37832\n+2720.18669043818\t38328\n+2721.73143077261\t38720\n+2723.27653495129\t38992\n+2724.82204503719\t39120\n+2726.36701510869\t38968\n+2727.91346287142\t38728\n+2729.46044270343\t38912\n+2731.00799666769\t38984\n+2732.55616682718\t38640\n+2734.10499524488\t37584\n+2735.654523983"..b'7.39522276304\t3874\n+4228.96022276304\t3507\n+4230.52522276304\t3075\n+4232.09022276304\t2593\n+4233.65522276304\t2285\n+4235.22022276304\t2108\n+4236.78522276304\t1881\n+4238.35022276304\t1616\n+4239.91522276304\t1442\n+4241.47922276304\t1362\n+4243.04422276304\t1309\n+4244.60922276304\t1280\n+4246.17422276304\t1267\n+4247.73922276304\t1302\n+4249.30422276304\t1345\n+4250.86922276304\t1364\n+4252.43422276304\t1310\n+4253.99922276304\t1222\n+4255.56422276304\t1091\n+4257.12922276304\t896\n+4258.69422276304\t698\n+4260.25922276304\t642\n+4261.82422276304\t707\n+4263.38922276304\t711\n+4264.95422276304\t675\n+4266.51922276304\t624\n+4268.08422276304\t486\n+4269.64922276304\t406\n+4271.21422276304\t441\n+4272.77922276304\t464\n+4274.34422276304\t484\n+4275.90822276304\t531\n+4277.47322276304\t545\n+4279.03822276304\t683\n+4280.60322276304\t867\n+4282.16822276304\t954\n+4283.73322276304\t960\n+4285.29822276304\t1196\n+4286.86322276304\t1678\n+4288.42822276304\t2269\n+4289.99322276304\t2618\n+4291.55822276304\t2700\n+4293.12322276304\t2586\n+4294.68822276304\t2367\n+4296.25322276304\t2190\n+4297.81822276304\t2104\n+4299.38322276304\t1989\n+4300.94822276304\t1722\n+4302.51322276304\t1387\n+4304.07822276304\t1111\n+4305.64322276304\t977\n+4307.20822276304\t943\n+4308.77222276304\t927\n+4310.33722276304\t947\n+4311.90222276304\t910\n+4313.46722276304\t909\n+4315.03222276304\t968\n+4316.59722276304\t1005\n+4318.16222276304\t937\n+4319.72722276304\t819\n+4321.29222276304\t739\n+4322.85722276304\t736\n+4324.42222276304\t759\n+4325.98722276304\t721\n+4327.55222276304\t610\n+4329.11722276304\t439\n+4330.68222276304\t276\n+4332.24722276304\t206\n+4333.81222276304\t230\n+4335.37722276304\t309\n+4336.94222276304\t321\n+4338.50722276304\t295\n+4340.07222276304\t322\n+4341.63722276304\t430\n+4343.20122276304\t498\n+4344.76622276304\t504\n+4346.33122276304\t527\n+4347.89622276304\t631\n+4349.46122276304\t720\n+4351.02622276304\t715\n+4352.59122276304\t643\n+4354.15622276304\t654\n+4355.72122276304\t703\n+4357.28622276304\t727\n+4358.85122276304\t720\n+4360.41622276304\t654\n+4361.98122276304\t602\n+4363.54622276304\t658\n+4365.11122276304\t750\n+4366.67622276304\t781\n+4368.24122276304\t811\n+4369.80622276304\t816\n+4371.37122276304\t800\n+4372.93622276304\t770\n+4374.50122276304\t784\n+4376.06522276304\t742\n+4377.63022276304\t654\n+4379.19522276304\t632\n+4380.76022276304\t653\n+4382.32522276304\t726\n+4383.89022276304\t869\n+4385.45522276304\t937\n+4387.02022276304\t847\n+4388.58522276304\t662\n+4390.15022276304\t584\n+4391.71522276304\t671\n+4393.28022276304\t685\n+4394.84522276304\t650\n+4396.41022276304\t741\n+4397.97522276304\t797\n+4399.54022276304\t711\n+4401.10522276304\t678\n+4402.67022276304\t649\n+4404.23522276304\t683\n+4405.80022276304\t767\n+4407.36522276304\t858\n+4408.93022276304\t926\n+4410.49422276304\t1009\n+4412.05922276304\t1090\n+4413.62422276304\t1170\n+4415.18922276304\t1218\n+4416.75422276304\t1313\n+4418.31922276304\t1387\n+4419.88422276304\t1315\n+4421.44922276304\t1110\n+4423.01422276304\t984\n+4424.57922276304\t1065\n+4426.14422276304\t1127\n+4427.70922276304\t1067\n+4429.27422276304\t1116\n+4430.83922276304\t1374\n+4432.40422276304\t1494\n+4433.96922276304\t1375\n+4435.53422276304\t1176\n+4437.09922276304\t1056\n+4438.66422276304\t995\n+4440.22922276304\t973\n+4441.79422276304\t1026\n+4443.35822276304\t1065\n+4444.92322276304\t995\n+4446.48822276304\t836\n+4448.05322276304\t720\n+4449.61822276304\t716\n+4451.18322276304\t777\n+4452.74822276304\t853\n+4454.31322276304\t938\n+4455.87822276304\t1131\n+4457.44322276304\t1266\n+4459.00822276304\t1311\n+4460.57322276304\t1322\n+4462.13822276304\t1407\n+4463.70322276304\t1471\n+4465.26822276304\t1409\n+4466.83322276304\t1342\n+4468.39822276304\t1401\n+4469.96322276304\t1517\n+4471.52822276304\t1433\n+4473.09322276304\t1267\n+4474.65822276304\t1051\n+4476.22322276304\t928\n+4477.78722276304\t850\n+4479.35222276304\t821\n+4480.91722276304\t725\n+4482.48222276304\t682\n+4484.04722276304\t576\n+4485.61222276304\t583\n+4487.17722276304\t672\n+4488.74222276304\t713\n+4490.30722276304\t699\n+4491.87222276304\t667\n+4493.43722276304\t604\n+4495.00222276304\t583\n+4496.56722276304\t627\n+4498.13222276304\t693\n+4499.69722276304\t758\n+4501.26222276304\t771\n+4502.82722276304\t649\n+4504.39222276304\t565\n+4505.95722276304\t722\n' |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/cc_ko15.bpc.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cc_ko15.bpc.tab Tue Oct 24 06:29:59 2017 -0400 |
| b |
| b'@@ -0,0 +1,1278 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|
| b |
| 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 |
| b |
| b"@@ -0,0 +1,1289 @@\n+# file_format: 'tsv'\n+# section_name: 'BPC'\n+# title: 'Base peak chromatogram'\n+# description: 'Sum of intensity (Y) of the most intense peaks at each retention time(X)'\n+# plot_type: 'linegraph'\n+# pconfig:\n+# id: 'bpc_lineplot'\n+# title: 'Base peak chromatogram'\n+# ylab: 'Base Peak Intensity'\n+# xlab: 'Retention Time'\n+Retention Time\tBase Peak Intensity\n+2503.69308488001\t44464\n+2505.25808488001\t44632\n+2506.82308488001\t45232\n+2508.38808488001\t46200\n+2509.95308488001\t46592\n+2511.51808488001\t46376\n+2513.08308488001\t45760\n+2514.64808488001\t45632\n+2516.21308488001\t45152\n+2517.77808488001\t44280\n+2519.34308488001\t43360\n+2520.90708488001\t43768\n+2522.47208488001\t44536\n+2524.03708488001\t45072\n+2525.60208488001\t44528\n+2527.16708488001\t43632\n+2528.73208488001\t42944\n+2530.29708488001\t42520\n+2531.86208488001\t41968\n+2533.42708488001\t41312\n+2534.99208488001\t40832\n+2536.55708488001\t40624\n+2538.12208488001\t40288\n+2539.68708488001\t40144\n+2541.25208488001\t40240\n+2542.81708488001\t40488\n+2544.38208488001\t40624\n+2545.94708488001\t40688\n+2547.51208488001\t41640\n+2549.07708488001\t43840\n+2550.64208488001\t45816\n+2552.20708488001\t45248\n+2553.77208488001\t43200\n+2555.33608488001\t41936\n+2556.90108488001\t42776\n+2558.46608488001\t43472\n+2560.03108488001\t42944\n+2561.59608488001\t41400\n+2563.16108488001\t40752\n+2564.72608488001\t40560\n+2566.29108488001\t40744\n+2567.85608488001\t41488\n+2569.42108488001\t42928\n+2570.98608488001\t44352\n+2572.55108488001\t44968\n+2574.11608488001\t44832\n+2575.68108488001\t43816\n+2577.24608488001\t42704\n+2578.81108488001\t42184\n+2580.37608488001\t42864\n+2581.94108488001\t52312\n+2583.50608488001\t70008\n+2585.07108488001\t87112\n+2586.63608488001\t102376\n+2588.20008488001\t115304\n+2589.76508488001\t125384\n+2591.33008488001\t131136\n+2592.89508488001\t132096\n+2594.46008488001\t128336\n+2596.02508488001\t120840\n+2597.59008488001\t111368\n+2599.15508488001\t102296\n+2600.72008488001\t94400\n+2602.28508488001\t86608\n+2603.85008488001\t77960\n+2605.41508488001\t68544\n+2606.98008488001\t59072\n+2608.54508488001\t50408\n+2610.11008488001\t46216\n+2611.67508488001\t45656\n+2613.24008488001\t44744\n+2614.80508488001\t43880\n+2616.37008488001\t42920\n+2617.93508488001\t41824\n+2619.50008488001\t41520\n+2621.08323664293\t42464\n+2622.66535661694\t43008\n+2624.2484704446\t42256\n+2625.83156900656\t40800\n+2627.41465477536\t40128\n+2628.99773022353\t39824\n+2630.58079782361\t39656\n+2632.16386004811\t39336\n+2633.74691936957\t39456\n+2635.32997826053\t39904\n+2636.9130391935\t41000\n+2638.49610464103\t41752\n+2640.07917707564\t41784\n+2641.66225896986\t41568\n+2643.24535279622\t41952\n+2644.82846102725\t42552\n+2646.41158613548\t43008\n+2647.99473059345\t67248\n+2649.57789687368\t104320\n+2651.1610874487\t148800\n+2652.74430479104\t199872\n+2654.32755137323\t257088\n+2655.90981797773\t312128\n+2657.49313043459\t356928\n+2659.07647954731\t388992\n+2660.65986778842\t406848\n+2662.24329763045\t407360\n+2663.82662043703\t397824\n+2665.40972747004\t395968\n+2666.99268104941\t409600\n+2668.5755434951\t437056\n+2670.15837712702\t475008\n+2671.74124426513\t522112\n+2673.32420722935\t568256\n+2674.90732833963\t610304\n+2676.4906699159\t647616\n+2678.07429427809\t682816\n+2679.65826374615\t705920\n+2681.24264064001\t709568\n+2682.82780937765\t697408\n+2684.41329800875\t682688\n+2685.99992572252\t668928\n+2687.58718990559\t646464\n+2689.17458794457\t615360\n+2690.76060337453\t579584\n+2692.34676200243\t538560\n+2693.9314023906\t485696\n+2695.51423451065\t428096\n+2697.09529149161\t375808\n+2698.67460646253\t329920\n+2700.25221255246\t285888\n+2701.82814289044\t241664\n+2703.4024306055\t199296\n+2704.9751088267\t161472\n+2706.54621068307\t129928\n+2708.11576930366\t107776\n+2709.68381781752\t90320\n+2711.25038935368\t75720\n+2712.81551704119\t62600\n+2714.37923400909\t51632\n+2715.94157338643\t42784\n+2717.50256830224\t43368\n+2719.06225188558\t43000\n+2720.62065726547\t41624\n+2722.17781757098\t39880\n+2723.73277209484\t38296\n+2725.28754238135\t37568\n+2726.84116695942\t37856\n+2728.39367895811\t38736\n+2729.94511150645\t39696\n+2731.49549773349\t40576\n+2733.04487076827\t41336\n+2734.59326373983\t42240\n+2736.14070977"..b'73915089905\t4742\n+4231.30415089905\t3929\n+4232.86915089905\t3246\n+4234.43415089905\t2973\n+4235.99915089905\t2620\n+4237.56415089905\t2296\n+4239.12915089905\t2214\n+4240.69415089905\t2221\n+4242.25815089905\t2112\n+4243.82315089905\t1787\n+4245.38815089905\t1594\n+4246.95315089905\t1593\n+4248.51815089905\t1604\n+4250.08315089905\t1417\n+4251.64815089905\t1264\n+4253.21315089905\t1229\n+4254.77815089905\t1307\n+4256.34315089905\t1303\n+4257.90815089905\t1247\n+4259.47315089905\t1232\n+4261.03815089905\t1225\n+4262.60315089905\t1173\n+4264.16815089905\t1066\n+4265.73315089905\t989\n+4267.29815089905\t884\n+4268.86315089905\t826\n+4270.42815089905\t765\n+4271.99315089905\t819\n+4273.55815089905\t908\n+4275.12215089905\t959\n+4276.68715089905\t933\n+4278.25215089905\t903\n+4279.81715089905\t862\n+4281.38215089905\t785\n+4282.94715089905\t692\n+4284.51215089905\t567\n+4286.07715089905\t405\n+4287.64215089905\t300\n+4289.20715089905\t293\n+4290.77215089905\t344\n+4292.33715089905\t323\n+4293.90215089905\t334\n+4295.46715089905\t343\n+4297.03215089905\t295\n+4298.5971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|
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/cc_wt15.bpc.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cc_wt15.bpc.tab Tue Oct 24 06:29:59 2017 -0400 |
| b |
| b'@@ -0,0 +1,1278 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|
| b |
| 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 |
| b |
| @@ -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 + |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,2181 @@\n+##FastQC\t0.11.4\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\tpoulet5_1\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t267849\n+Sequences flagged as poor quality\t0\n+Sequence length\t101\n+%GC\t48\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t20.91988023102569\t21.0\t21.0\t21.0\t21.0\t21.0\n+2\t20.71684045861661\t21.0\t20.0\t22.0\t19.0\t23.0\n+3\t20.351574954545285\t21.0\t20.0\t21.0\t18.0\t22.0\n+4\t22.531542025544244\t23.0\t22.0\t24.0\t20.0\t24.0\n+5\t24.673566076408722\t25.0\t24.0\t26.0\t24.0\t26.0\n+6\t25.813099918237516\t26.0\t25.0\t27.0\t25.0\t27.0\n+7\t27.587864804423386\t28.0\t27.0\t29.0\t26.0\t29.0\n+8\t27.598941941168345\t28.0\t27.0\t29.0\t26.0\t29.0\n+9\t27.07115949658203\t28.0\t26.0\t28.0\t26.0\t28.0\n+10-11\t27.129873548155864\t28.0\t26.0\t28.0\t25.5\t28.0\n+12-13\t27.009298149330405\t27.5\t26.0\t28.0\t25.5\t28.0\n+14-15\t27.123565889736383\t28.0\t26.5\t28.0\t26.0\t28.0\n+16-17\t27.086309823818645\t28.0\t26.0\t28.0\t26.0\t28.0\n+18-19\t27.07924614241606\t28.0\t26.0\t28.0\t25.5\t28.0\n+20-21\t27.082520375286073\t28.0\t26.0\t28.0\t26.0\t28.0\n+22-23\t27.054301117420636\t28.0\t26.0\t28.0\t25.0\t28.0\n+24-25\t27.06350966402712\t28.0\t26.0\t28.0\t25.0\t28.0\n+26-27\t27.082996389756914\t28.0\t26.0\t28.0\t26.0\t28.0\n+28-29\t27.065495857740743\t28.0\t26.0\t28.0\t25.5\t28.0\n+30-31\t27.09608772106672\t28.0\t26.0\t28.0\t26.0\t28.0\n+32-33\t27.087097581099798\t28.0\t26.0\t28.0\t26.0\t28.0\n+34-35\t27.098251253504774\t28.0\t26.5\t28.0\t26.0\t28.0\n+36-37\t27.05184077595959\t28.0\t26.0\t28.0\t25.5\t28.0\n+38-39\t27.06521958267531\t28.0\t26.0\t28.0\t26.0\t28.0\n+40-41\t27.072148859992012\t28.0\t26.0\t28.0\t26.0\t28.0\n+42-43\t27.065725464720796\t28.0\t26.0\t28.0\t25.5\t28.0\n+44-45\t27.07168031241483\t28.0\t26.5\t28.0\t25.5\t28.0\n+46-47\t27.048083061725073\t28.0\t26.0\t28.0\t25.5\t28.0\n+48-49\t27.04642354460909\t28.0\t26.0\t28.0\t25.5\t28.0\n+50-51\t27.062865644448927\t28.0\t26.0\t28.0\t25.5\t28.0\n+52-53\t27.01859629866081\t28.0\t26.0\t28.0\t25.0\t28.0\n+54-55\t26.994157155710866\t27.5\t26.0\t28.0\t25.0\t28.0\n+56-57\t27.110127347871376\t28.0\t27.0\t28.0\t26.0\t28.0\n+58-59\t26.995846540401494\t27.5\t26.0\t28.0\t25.0\t28.0\n+60-61\t27.00461640700544\t27.5\t26.0\t28.0\t25.0\t28.0\n+62-63\t26.981614641085088\t27.5\t26.5\t28.0\t25.5\t28.5\n+64-65\t26.98900313236189\t28.0\t26.0\t28.0\t25.0\t28.0\n+66-67\t27.001189102815392\t28.0\t26.0\t28.0\t25.0\t28.0\n+68-69\t26.917739099268616\t27.5\t26.0\t28.0\t25.0\t28.5\n+70-71\t26.98481793846533\t28.0\t27.0\t28.0\t25.0\t29.0\n+72-73\t26.89518908041471\t27.5\t26.5\t28.0\t25.0\t28.5\n+74-75\t26.93677034448514\t28.0\t27.0\t28.0\t25.0\t29.0\n+76-77\t26.87640237596556\t28.0\t26.5\t28.0\t25.0\t29.0\n+78-79\t26.906094478605482\t28.0\t27.0\t28.0\t25.0\t29.0\n+80-81\t26.80463992772047\t28.0\t26.5\t28.0\t25.0\t29.0\n+82-83\t26.717012197170796\t28.0\t26.5\t28.0\t25.0\t29.0\n+84-85\t26.46960974280285\t27.5\t26.5\t28.0\t25.0\t29.0\n+86-87\t26.442842795754324\t27.5\t26.5\t28.0\t25.0\t29.0\n+88-89\t26.34282375517549\t28.0\t26.0\t28.0\t25.0\t29.0\n+90-91\t26.03493946215965\t28.0\t26.0\t28.0\t24.5\t29.0\n+92-93\t25.833215729758187\t28.0\t26.0\t28.0\t24.0\t29.0\n+94-95\t25.503102494315826\t27.5\t26.0\t28.0\t22.5\t29.0\n+96-97\t24.52807178671565\t27.0\t25.5\t27.5\t21.0\t28.0\n+98-99\t23.202399486277717\t26.0\t24.5\t26.5\t10.0\t27.0\n+100-101\t23.72906749698524\t27.0\t26.0\t28.0\t2.0\t29.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1101\t1\t0.017259946109469126\n+1101\t2\t-0.13408255940416325\n+1101\t3\t-0.11853598095770224\n+1101\t4\t0.015421063929771606\n+1101\t5\t-0.06886052494072459\n+1101\t6\t-0.15241701542762698\n+1101\t7\t-0.029853727500473326\n+1101\t8\t0.04533865186875374\n+1101\t9\t0.07102084333114078\n+1101\t10-11\t0.02726717483210095\n+1101\t12-13\t0.05147474989913192\n+1101\t14-15\t-0.006227419450461014\n+1101\t16-17\t0.051879075943595865\n+1101\t18-19\t0.03525737425918152\n+1101\t20-21\t0.012963832365290529\n+1101\t22-23\t0.02506089814612622\n+1101\t24-25\t0.07843149833360386\n+1101\t26-27\t0.02737786083297422\n+1101\t28-29\t0.005161107012540356\n+1101\t30-31\t-0.08720467946375265\n+1101\t32-33\t-0.017197404032327057\n+1101\t34-35\t0.05763469947927646\n+1101\t36-37\t-0.045600552109540615\n+1101\t38-39\t-0.01952943529413176\n+1101\t40-41\t0.007678874836642535\n+1101\t42-43\t-0.00844'..b'433.5\n+55\t9922.0\n+56\t8785.5\n+57\t7997.0\n+58\t6901.0\n+59\t5796.0\n+60\t4967.0\n+61\t4072.5\n+62\t3639.5\n+63\t3267.0\n+64\t2561.5\n+65\t2002.5\n+66\t1561.5\n+67\t1355.5\n+68\t1222.0\n+69\t1019.0\n+70\t803.0\n+71\t568.5\n+72\t371.5\n+73\t235.0\n+74\t164.5\n+75\t110.5\n+76\t70.5\n+77\t56.0\n+78\t39.5\n+79\t27.0\n+80\t18.0\n+81\t17.0\n+82\t15.5\n+83\t12.5\n+84\t6.5\n+85\t1.5\n+86\t0.0\n+87\t0.0\n+88\t0.0\n+89\t0.0\n+90\t0.0\n+91\t0.0\n+92\t0.0\n+93\t0.0\n+94\t0.0\n+95\t0.0\n+96\t0.0\n+97\t0.0\n+98\t0.0\n+99\t0.0\n+100\t0.0\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.029867574640935753\n+2\t0.0\n+3\t0.003733446830116969\n+4\t0.0\n+5\t3.733446830116969E-4\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t0.0\n+84-85\t0.0\n+86-87\t0.0\n+88-89\t0.0\n+90-91\t0.0\n+92-93\t0.0\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.0\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+101\t267849.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\twarn\n+#Total Deduplicated Percentage\t63.69408840068983\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t81.5623716290639\t51.950409087115126\n+2\t9.995611185249079\t12.733226849043577\n+3\t3.1947144335386772\t6.104532706343167\n+4\t1.4905270052149588\t3.797510353351082\n+5\t0.8725392208870194\t2.778779513412342\n+6\t0.55360835935223\t2.115694786796508\n+7\t0.38537193434967776\t1.718213983752925\n+8\t0.314619574221819\t1.603152557845755\n+9\t0.2033036957962869\t1.1654319215012086\n+>10\t1.4223398099582591\t15.850860027094066\n+>50\t0.0049931523680946535\t0.18218821374420768\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\tpass\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\twarn\n+#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n+TTAGTGG\t50\t0.0016122013\t38.00672\t3\n+CCGGGAA\t65\t0.0058204937\t29.246862\t1\n+CTCGCCA\t65\t0.0058204937\t29.246862\t1\n+CCCGCTT\t70\t0.008357804\t27.157803\t1\n+AACAATT\t125\t0.006013185\t19.00336\t2\n+CTGGGAT\t205\t3.3062082E-4\t16.228443\t1\n+AGTTCAA\t195\t0.0044498937\t14.615241\t5\n+GAGTAGT\t125\t0.0014974214\t13.29987\t30-31\n+AAGTTCA\t220\t0.009890434\t12.954418\t4\n+CTGAAAT\t275\t0.003044474\t12.097567\t1\n+CCCAGCT\t405\t3.2130985E-5\t11.734852\t1\n+AGGGTGT\t145\t0.0045575905\t11.465405\t66-67\n+CTGAATT\t335\t0.001024679\t11.349529\t1\n+CTTGAAT\t295\t0.0051441877\t11.277392\t1\n+GAATGTC\t425\t6.555659E-4\t10.058724\t4\n+GGTAGTA\t190\t0.002949709\t9.999902\t52-53\n+CTCTGCC\t390\t0.0036302158\t9.748955\t1\n+CTCCTTT\t535\t5.356131E-4\t8.883393\t1\n+CTTTGCT\t500\t0.0028739348\t8.5547085\t1\n+>>END_MODULE\n' |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,2170 @@\n+##FastQC\t0.11.4\n+>>Basic Statistics\tpass\n+#Measure\tValue\n+Filename\tpoulet5_2\n+File type\tConventional base calls\n+Encoding\tSanger / Illumina 1.9\n+Total Sequences\t267849\n+Sequences flagged as poor quality\t0\n+Sequence length\t101\n+%GC\t48\n+>>END_MODULE\n+>>Per base sequence quality\twarn\n+#Base\tMean\tMedian\tLower Quartile\tUpper Quartile\t10th Percentile\t90th Percentile\n+1\t20.590586487162543\t21.0\t21.0\t21.0\t20.0\t21.0\n+2\t20.458478471078855\t21.0\t19.0\t22.0\t19.0\t22.0\n+3\t20.178608096352797\t21.0\t20.0\t21.0\t18.0\t22.0\n+4\t22.495204387546714\t23.0\t22.0\t24.0\t20.0\t24.0\n+5\t24.59397272343746\t25.0\t24.0\t26.0\t24.0\t26.0\n+6\t25.77560491172265\t26.0\t25.0\t27.0\t25.0\t27.0\n+7\t26.651378201897337\t27.0\t26.0\t28.0\t26.0\t28.0\n+8\t27.54968284369178\t28.0\t27.0\t29.0\t26.0\t29.0\n+9\t27.089005372429988\t28.0\t26.0\t28.0\t26.0\t28.0\n+10-11\t27.058984726469017\t28.0\t26.0\t28.0\t25.5\t28.0\n+12-13\t26.954911162632676\t27.5\t26.0\t28.0\t25.5\t28.0\n+14-15\t27.066410552214123\t28.0\t26.0\t28.0\t26.0\t28.0\n+16-17\t27.04552938409328\t28.0\t26.0\t28.0\t25.5\t28.0\n+18-19\t27.025118630273028\t28.0\t26.0\t28.0\t25.0\t28.0\n+20-21\t27.019042445557012\t28.0\t26.0\t28.0\t25.0\t28.0\n+22-23\t27.010315513591614\t28.0\t26.0\t28.0\t25.0\t28.0\n+24-25\t27.03931879529138\t28.0\t26.0\t28.0\t25.5\t28.0\n+26-27\t26.978450544896567\t28.0\t26.0\t28.0\t25.0\t28.0\n+28-29\t27.003714779595967\t28.0\t26.0\t28.0\t25.0\t28.0\n+30-31\t27.025971722873706\t28.0\t26.0\t28.0\t25.0\t28.0\n+32-33\t27.017791740868923\t28.0\t26.0\t28.0\t25.0\t28.0\n+34-35\t27.00628899118533\t28.0\t26.0\t28.0\t25.0\t28.0\n+36-37\t27.00906294218011\t28.0\t26.0\t28.0\t25.0\t28.0\n+38-39\t27.034922661648913\t28.0\t26.0\t28.0\t25.5\t28.0\n+40-41\t27.005346295860726\t28.0\t26.0\t28.0\t25.0\t28.0\n+42-43\t27.000909094303132\t28.0\t26.0\t28.0\t25.0\t28.0\n+44-45\t27.004913216028434\t28.0\t26.0\t28.0\t25.0\t28.0\n+46-47\t26.979999925331065\t28.0\t26.0\t28.0\t25.0\t28.0\n+48-49\t26.941037674211962\t27.5\t26.0\t28.0\t25.0\t28.0\n+50-51\t26.99995146519121\t27.5\t26.0\t28.0\t25.5\t28.0\n+52-53\t26.95084543903468\t27.5\t26.0\t28.0\t25.0\t28.0\n+54-55\t26.97609847339359\t28.0\t26.0\t28.0\t25.0\t28.0\n+56-57\t26.99262270906369\t27.5\t26.0\t28.0\t25.0\t28.0\n+58-59\t26.942271578389317\t27.0\t26.0\t28.0\t25.0\t28.0\n+60-61\t26.88024222603034\t27.0\t26.0\t28.0\t25.0\t28.0\n+62-63\t26.866450873439888\t27.0\t26.0\t28.0\t25.0\t28.0\n+64-65\t26.947610407356386\t28.0\t26.0\t28.0\t25.0\t28.0\n+66-67\t26.975012040366025\t28.0\t26.5\t28.0\t25.0\t28.5\n+68-69\t26.966286975124042\t28.0\t26.5\t28.0\t25.0\t29.0\n+70-71\t26.917634562757375\t28.0\t26.0\t28.0\t25.0\t29.0\n+72-73\t26.885127441207544\t28.0\t26.0\t28.0\t25.0\t29.0\n+74-75\t26.846286527110426\t28.0\t26.5\t28.0\t25.0\t29.0\n+76-77\t26.769134848366058\t28.0\t26.0\t28.0\t25.0\t29.0\n+78-79\t26.709703975000842\t28.0\t26.5\t28.0\t25.0\t29.0\n+80-81\t26.551336760637525\t27.5\t26.0\t28.0\t25.0\t28.5\n+82-83\t26.42626069165836\t27.5\t26.0\t28.0\t25.0\t28.5\n+84-85\t26.309463541024982\t27.5\t26.0\t28.0\t25.0\t29.0\n+86-87\t26.127226534353312\t27.5\t26.0\t28.0\t25.0\t29.0\n+88-89\t25.91885539987082\t27.5\t26.0\t28.0\t24.0\t29.0\n+90-91\t25.674260497519125\t27.0\t26.0\t28.0\t23.5\t29.0\n+92-93\t25.371903572535274\t27.0\t26.0\t28.0\t22.0\t29.0\n+94-95\t24.758753999454918\t27.0\t26.0\t28.0\t20.5\t28.5\n+96-97\t23.84710415196622\t26.5\t25.0\t27.5\t7.0\t28.0\n+98-99\t22.40618968149965\t25.5\t24.0\t26.5\t2.0\t27.0\n+100-101\t23.009550156991438\t27.0\t25.0\t28.0\t2.0\t29.0\n+>>END_MODULE\n+>>Per tile sequence quality\tpass\n+#Tile\tBase\tMean\n+1101\t1\t-0.1408369887985721\n+1101\t2\t-0.019030947201084558\n+1101\t3\t-0.060059442415557385\n+1101\t4\t0.004085939732711097\n+1101\t5\t-0.018429270835582656\n+1101\t6\t-0.10404524639907464\n+1101\t7\t0.05541229462318498\n+1101\t8\t0.06703529503928962\n+1101\t9\t0.0644374620344621\n+1101\t10-11\t0.06977859906234585\n+1101\t12-13\t0.048103685880093394\n+1101\t14-15\t0.0848396420659725\n+1101\t16-17\t0.030233298636137107\n+1101\t18-19\t0.05253119669850648\n+1101\t20-21\t0.08961672433820667\n+1101\t22-23\t0.014190195653434046\n+1101\t24-25\t-0.013817302849609803\n+1101\t26-27\t0.046003756870838686\n+1101\t28-29\t0.04599618351544166\n+1101\t30-31\t0.04851104267937956\n+1101\t32-33\t0.04656194043190354\n+1101\t34-35\t0.057517795385400916\n+1101\t36-37\t-0.00326392946157128\n+1101\t38-39\t0.0753296536157606\n+1101\t40-41\t0.005995075411309614\n+1101\t42-43\t-0.013913'..b'71.0\n+24\t130.0\n+25\t233.5\n+26\t389.5\n+27\t542.5\n+28\t724.5\n+29\t1063.0\n+30\t1433.0\n+31\t1683.5\n+32\t1996.0\n+33\t2367.5\n+34\t2840.5\n+35\t3318.0\n+36\t3924.5\n+37\t4721.0\n+38\t5510.0\n+39\t6259.0\n+40\t7364.0\n+41\t8736.0\n+42\t9608.5\n+43\t10256.0\n+44\t10928.5\n+45\t11153.5\n+46\t11271.5\n+47\t12042.0\n+48\t12804.5\n+49\t12874.0\n+50\t12482.5\n+51\t11758.0\n+52\t10827.0\n+53\t10433.0\n+54\t10615.0\n+55\t9955.0\n+56\t8760.0\n+57\t7986.5\n+58\t6982.5\n+59\t5802.5\n+60\t4913.5\n+61\t4177.5\n+62\t3751.5\n+63\t3282.0\n+64\t2533.0\n+65\t1954.0\n+66\t1513.0\n+67\t1247.5\n+68\t1102.0\n+69\t957.0\n+70\t777.0\n+71\t535.5\n+72\t361.5\n+73\t253.0\n+74\t157.0\n+75\t99.0\n+76\t60.0\n+77\t46.5\n+78\t37.0\n+79\t21.5\n+80\t13.5\n+81\t16.5\n+82\t19.5\n+83\t14.0\n+84\t6.5\n+85\t3.0\n+86\t0.5\n+87\t0.0\n+88\t0.0\n+89\t0.0\n+90\t0.0\n+91\t0.0\n+92\t0.0\n+93\t0.0\n+94\t0.0\n+95\t0.0\n+96\t0.0\n+97\t0.0\n+98\t0.0\n+99\t0.0\n+100\t0.0\n+>>END_MODULE\n+>>Per base N content\tpass\n+#Base\tN-Count\n+1\t0.11461681768459094\n+2\t0.003733446830116969\n+3\t0.0\n+4\t0.0\n+5\t0.0\n+6\t0.0\n+7\t0.0\n+8\t0.0\n+9\t0.0\n+10-11\t0.0\n+12-13\t0.0\n+14-15\t0.0\n+16-17\t0.0\n+18-19\t0.0\n+20-21\t0.0\n+22-23\t0.0\n+24-25\t0.0\n+26-27\t0.0\n+28-29\t0.0\n+30-31\t0.0\n+32-33\t0.0\n+34-35\t0.0\n+36-37\t0.0\n+38-39\t0.0\n+40-41\t0.0\n+42-43\t0.0\n+44-45\t0.0\n+46-47\t0.0\n+48-49\t0.0\n+50-51\t0.0\n+52-53\t0.0\n+54-55\t0.0\n+56-57\t0.0\n+58-59\t0.0\n+60-61\t0.0\n+62-63\t0.0\n+64-65\t0.0\n+66-67\t0.0\n+68-69\t0.0\n+70-71\t0.0\n+72-73\t0.0\n+74-75\t0.0\n+76-77\t0.0\n+78-79\t0.0\n+80-81\t0.0\n+82-83\t1.8667234150584845E-4\n+84-85\t0.0\n+86-87\t1.8667234150584845E-4\n+88-89\t0.0014933787320467876\n+90-91\t0.0\n+92-93\t0.0011200340490350907\n+94-95\t0.0\n+96-97\t0.0\n+98-99\t0.0\n+100-101\t0.01456044263745618\n+>>END_MODULE\n+>>Sequence Length Distribution\tpass\n+#Length\tCount\n+101\t267849.0\n+>>END_MODULE\n+>>Sequence Duplication Levels\twarn\n+#Total Deduplicated Percentage\t63.826611251945884\n+#Duplication Level\tPercentage of deduplicated\tPercentage of total\n+1\t81.66283073871745\t52.122617512935754\n+2\t9.894108596885154\t12.630148461958491\n+3\t3.18062640137576\t6.090258145748586\n+4\t1.5566170090070461\t3.974143548082379\n+5\t0.8538567368205473\t2.7249391002950074\n+6\t0.5533319107768025\t2.119038045746843\n+7\t0.3960736941041749\t1.7696029190496514\n+8\t0.2698969625036296\t1.3781286803040145\n+9\t0.23212846037984958\t1.3334375701059644\n+>10\t1.3969694370078172\t15.730893862039416\n+>50\t0.0035600524217624095\t0.12679215373389083\n+>100\t0.0\t0.0\n+>500\t0.0\t0.0\n+>1k\t0.0\t0.0\n+>5k\t0.0\t0.0\n+>10k+\t0.0\t0.0\n+>>END_MODULE\n+>>Overrepresented sequences\tpass\n+>>END_MODULE\n+>>Adapter Content\tpass\n+#Position\tIllumina Universal Adapter\tIllumina Small RNA Adapter\tNextera Transposase Sequence\tSOLID Small RNA Adapter\n+1\t0.0\t0.0\t0.0\t0.0\n+2\t0.0\t0.0\t0.0\t0.0\n+3\t0.0\t0.0\t0.0\t0.0\n+4\t0.0\t0.0\t0.0\t0.0\n+5\t0.0\t0.0\t0.0\t0.0\n+6\t0.0\t0.0\t0.0\t0.0\n+7\t0.0\t0.0\t0.0\t0.0\n+8\t0.0\t0.0\t0.0\t0.0\n+9\t0.0\t0.0\t0.0\t0.0\n+10-11\t0.0\t0.0\t0.0\t0.0\n+12-13\t0.0\t0.0\t0.0\t0.0\n+14-15\t0.0\t0.0\t0.0\t0.0\n+16-17\t0.0\t0.0\t0.0\t0.0\n+18-19\t0.0\t0.0\t0.0\t0.0\n+20-21\t0.0\t0.0\t0.0\t0.0\n+22-23\t0.0\t0.0\t0.0\t0.0\n+24-25\t0.0\t0.0\t0.0\t0.0\n+26-27\t0.0\t0.0\t0.0\t0.0\n+28-29\t0.0\t0.0\t0.0\t0.0\n+30-31\t0.0\t0.0\t0.0\t0.0\n+32-33\t0.0\t0.0\t0.0\t0.0\n+34-35\t0.0\t0.0\t0.0\t0.0\n+36-37\t0.0\t0.0\t0.0\t0.0\n+38-39\t0.0\t0.0\t0.0\t0.0\n+40-41\t0.0\t0.0\t0.0\t0.0\n+42-43\t0.0\t0.0\t0.0\t0.0\n+44-45\t0.0\t0.0\t0.0\t0.0\n+46-47\t0.0\t0.0\t0.0\t0.0\n+48-49\t0.0\t0.0\t0.0\t0.0\n+50-51\t0.0\t0.0\t0.0\t0.0\n+52-53\t0.0\t0.0\t0.0\t0.0\n+54-55\t0.0\t0.0\t0.0\t0.0\n+56-57\t0.0\t0.0\t0.0\t0.0\n+58-59\t0.0\t0.0\t0.0\t0.0\n+60-61\t0.0\t0.0\t0.0\t0.0\n+62-63\t0.0\t0.0\t0.0\t0.0\n+64-65\t0.0\t0.0\t0.0\t0.0\n+66-67\t0.0\t0.0\t0.0\t0.0\n+68-69\t0.0\t0.0\t0.0\t0.0\n+70-71\t0.0\t0.0\t0.0\t0.0\n+72-73\t0.0\t0.0\t0.0\t0.0\n+74-75\t0.0\t0.0\t0.0\t0.0\n+76-77\t0.0\t0.0\t0.0\t0.0\n+78-79\t0.0\t0.0\t0.0\t0.0\n+80-81\t0.0\t0.0\t0.0\t0.0\n+82-83\t0.0\t0.0\t0.0\t0.0\n+84-85\t0.0\t0.0\t0.0\t0.0\n+86-87\t0.0\t0.0\t0.0\t0.0\n+88-89\t0.0\t0.0\t0.0\t0.0\n+>>END_MODULE\n+>>Kmer Content\twarn\n+#Sequence\tCount\tPValue\tObs/Exp Max\tMax Obs/Exp Position\n+TACGAGG\t60\t0.0039460836\t31.665857\t9\n+CCCAGAT\t105\t6.861368E-5\t27.157375\t1\n+AATCAAC\t70\t0.008381328\t27.142164\t5\n+CTTGTAT\t120\t0.004739449\t19.802252\t1\n+TCGCTCA\t130\t0.007549489\t18.268764\t2\n+CCCCACT\t195\t0.0044338168\t14.623201\t1\n+TTCAACA\t295\t0.005166332\t11.270898\t2\n+CTTGAAG\t305\t0.006593838\t10.90747\t1\n+>>END_MODULE\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,71 @@ + + ________ __ + / ____/ /__ _ __/ /_ ____ ______ + / /_ / / _ \| |/ / __ \/ __ `/ ___/ + / __/ / / __/> </ /_/ / /_/ / / + /_/ /_/\___/_/|_/_.___/\__._/_/ + +Flexbar - flexible barcode and adapter removal, version 3.0 +Developed with SeqAn, the library for sequence analysis + +Available on github.com/seqan/flexbar + + +Local time: Mon Jun 5 13:20:34 2017 + +Number of threads: 1 +Bundled fragments: 256 + +Target name: result_right +File type: fasta +Reads file: reads.fasta +Adapter file: adapters.fasta + +max-uncalled: 0 +min-read-length: 10 + +adapter-trim-end: RIGHT +adapter-min-overlap: 4 +adapter-error-rate: 0.1 +adapter-match: 1 +adapter-mismatch: -1 +adapter-gap: -6 + +Adapter: Sequence: +ad1 CGTCTT + + +Processing reads ...done. + +Elapsed time: < 1 sec + + +Adapter removal statistics +========================== +Adapter: Overlap removal: Full length: +ad1 11 10 + +Min, max, mean and median overlap: 5 / 6 / 5 / 6 + + +Output file statistics +====================== +Read file: result_right.fasta + written reads 10 + short reads 3 + + +Filtering statistics +==================== +Processed reads 13 + skipped due to uncalled bases 0 + short prior to adapter removal 0 + finally skipped short reads 3 +Discarded reads overall 3 +Remaining reads 10 (76%) + +Processed bases 422 +Remaining bases 231 (54% of input) + + +Flexbar completed adapter removal. |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/flexbar_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/flexbar_stats.tabular Tue Oct 24 06:29:59 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Sample removed_bases_pct remaining_reads short_prior_to_adapter_removal remaining_bases skipped_due_to_uncalled_bases processed_reads processed_bases removed_bases discarded_reads_overall finally_skipped_short_reads +result_right 45.2606635071 10 0 231 0 13 422 191 3 3 |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/gatk_BaseRecalibrator.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gatk_BaseRecalibrator.txt Tue Oct 24 06:29:59 2017 -0400 |
| b |
| b'@@ -0,0 +1,3040 @@\n+#:GATKReport.v1.1:5\n+#:GATKTable:2:17:%s:%s:;\n+#:GATKTable:Arguments:Recalibration argument collection values used in this run\n+Argument Value \n+binary_tag_name null \n+covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate\n+default_platform null \n+deletions_default_quality 45 \n+force_platform null \n+indels_context_size 3 \n+insertions_default_quality 45 \n+low_quality_tail 2 \n+maximum_cycle_value 500 \n+mismatches_context_size 2 \n+mismatches_default_quality -1 \n+no_standard_covs false \n+quantizing_levels 16 \n+recalibration_report null \n+run_without_dbsnp false \n+solid_nocall_strategy THROW_EXCEPTION \n+solid_recal_mode SET_Q_ZERO \n+\n+#:GATKTable:3:94:%s:%s:%s:;\n+#:GATKTable:Quantized:Quality quantization map\n+QualityScore Count QuantizedScore\n+ 0 0 93\n+ 1 0 93\n+ 2 0 93\n+ 3 0 93\n+ 4 0 93\n+ 5 0 93\n+ 6 0 93\n+ 7 0 93\n+ 8 0 93\n+ 9 0 93\n+ 10 0 93\n+ 11 0 93\n+ 12 0 93\n+ 13 6755595 13\n+ 14 19683376 14\n+ 15 0 93\n+ 16 0 93\n+ 17 0 93\n+ 18 7903490 18\n+ 19 0 93\n+ 20 0 93\n+ 21 0 93\n+ 22 0 93\n+ 23 898722 23\n+ 24 2706118 24\n+ 25 0 93\n+ 26 0 93\n+ 27 70849987 27\n+ 28 736517063 28\n+ 29 0 93\n+ 30 0 93\n+ 31 0 93\n+ 32 0 93\n+ 33 0 93\n+ 34 0 93\n+ 35 0 93\n+ 36 0 93\n+ 37 0 93\n+ 38 0 93\n+ 39 0 93\n+ 40 0 93\n+ 41 0 93\n+ 42 845314351 42\n+ 43 0 43\n+ 44 845314351 44\n+ 45 0 93\n+ '..b'254229 45 57 Cycle D 42.0000 2510968 223.59\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 58 Cycle I 45.0000 2488413 86.95\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 58 Cycle D 42.0000 2488413 206.56\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 59 Cycle I 45.0000 2465198 81.81\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 59 Cycle D 42.0000 2465198 200.27\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 60 Cycle I 45.0000 2441590 70.82\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 60 Cycle D 42.0000 2441590 188.59\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 61 Cycle I 45.0000 2417427 64.29\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 61 Cycle D 43.0000 2417427 174.51\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 62 Cycle I 46.0000 2392135 51.98\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 62 Cycle D 43.0000 2392135 152.99\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 63 Cycle I 46.0000 2365753 41.73\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 63 Cycle D 44.0000 2365753 130.19\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 64 Cycle I 46.0000 2340561 27.21\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 64 Cycle D 44.0000 2340561 96.71\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 65 Cycle I 47.0000 2316184 13.71\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 65 Cycle D 45.0000 2316184 62.39\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 66 Cycle I 47.0000 2291824 4.62\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 66 Cycle D 47.0000 2291824 23.20\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 67 Cycle I 47.0000 2266744 0.83\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 67 Cycle D 47.0000 2266744 7.94\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 68 Cycle I 47.0000 2230794 0.00\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 68 Cycle D 47.0000 2230794 2.10\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 69 Cycle I 47.0000 2151124 0.00\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 69 Cycle D 47.0000 2151124 0.51\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 70 Cycle I 47.0000 1962432 0.00\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 70 Cycle D 47.0000 1962432 0.07\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 71 Cycle I 47.0000 1426764 0.00\n+NB501183:321:HYF5WBGX2:1:PAV10-50254229 45 71 Cycle D 47.0000 1426764 0.07\n+\n' |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/gatk_varianteval.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gatk_varianteval.txt Tue Oct 24 06:29:59 2017 -0400 |
| b |
| b'@@ -0,0 +1,1323 @@\n+#:GATKReport.v1.1:2\n+#:GATKTable:31:657:%s:%s:%s:%s:%s:%s:%d:%d:%d:%d:%.8f:%.8f:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%d:%.2e:%.2f:%.2f:%.2e:%.2f:%.2f:;\n+#:GATKTable:CountVariants:Counts different classes of variants in the sample\n+CountVariants CompRod EvalRod JexlExpression Novelty Sample nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp insertionDeletionRatio\n+CountVariants none eval none all 00O 2675075632 19199310 15505537 3693773 0.00138081 724.00000000 3693773 0 0 0 0 0 0 8703816 1003518 6801721 2690255 17 0 3.75e-04 2665.00 0.37 0.00e+00 0.00 0.00\n+CountVariants none eval none all 00V 2675075632 19199310 14841647 4357663 0.00162899 613.00000000 4357663 0 0 0 0 0 0 7100254 1361571 7741393 2996092 13 0 5.09e-04 1964.00 0.45 0.00e+00 0.00 0.00\n+CountVariants none eval none all 01K 2675075632 19199310 12298798 6900512 0.00257956 387.00000000 6900512 0 0 0 0 0 0 2615821 3642513 9682977 3257999 830 0 1.36e-03 734.00 1.12 0.00e+00 0.00 0.00\n+CountVariants none eval none all 03J 2675075632 19199310 10752303 8447007 0.00315767 316.00000000 8447007 0 0 0 0 0 0 57172 4985840 10695131 3461167 2228 0 1.86e-03 536.00 1.44 0.00e+00 0.00 0.00\n+CountVariants none eval none all 04I 2675075632 19199310 15818704 3380606 0.00126374 791.00000000 3380606 0 0 0 0 0 0 9391683 823349 6427021 2557257 3 0 3.08e-04 3249.00 0.32 0.00e+00 0.00 0.00\n+CountVariants none eval none all 04T 2675075632 19199310 10437209 8762101 0.00327546 305.00000000 8762101 0 0 0 0 0 0 56906 5562564 10380303 3199537 2292 0 2.08e-03 480.00 1.74 0.00e+00 0.00 0.00\n+CountVariants none eval none all 04Z 2675075632 19199310 14053302 5146008 0.00192369 519.00000000 5146008 0 0 0 0 0 0 5384926 1858628 8668376 3287380 409 0 6.95e-04 1439.00 0.57 0.00e+00 0.00 0.00\n+CountVariants none eval none all 07D 2675075632 19199310 10462495 8736815 0.00326601 306.00000000 8736815 0 0 0 0 0 0 53834 5494779 10408661 3242036 1729 0 2.05e-03 486.00 1.69 0.00e+00 0.00 0.00\n+CountVariants none eval none all 0A2 2675075632 19199310 11075482 8123828 0.00303686 329.00000000 8123828 0 0 0 0 '..b' 2.30 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9C5 2599022 1130832 2.30 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9C6 5011378 2232008 2.25 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9D4 5913410 2746199 2.15 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9D8 2236989 971418 2.30 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9E3 1764640 762143 2.32 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9E5 2651943 1164744 2.28 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9E6 1893756 810996 2.34 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9E8 2941139 1283716 2.29 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9F5 2157743 938092 2.30 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9H7 2691226 1163122 2.31 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel 9H9 2916283 1266400 2.30 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel K00 5949627 2779694 2.14 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel N12 2031233 880969 2.31 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel O34 4825075 2155618 2.24 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel O52 2906692 1255997 2.31 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel T84 5152459 2311058 2.23 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel V36 2901332 1280854 2.27 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel X44 1935242 833666 2.32 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel X58 5458129 2484343 2.20 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel Z46 5121173 2296301 2.23 0 0 0.00 0 0 0.00\n+TiTvVariantEvaluator none eval none novel all 13160478 5982016 2.20 0 0 0.00 0 0 0.00\n+\n' |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/gatk_varianteval_stats.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gatk_varianteval_stats.tabular Tue Oct 24 06:29:59 2017 -0400 |
| b |
| @@ -0,0 +1,2 @@ +Sample deletions insertions known_titv snps symbolic novel_titv complex mnps titv_reference mixed nocalls +gatk_varianteval 0 0 0.0 19199310 0 2.2 0 0 none 0 1330372586 |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/hicup_deduplicator.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hicup_deduplicator.txt Tue Oct 24 06:29:59 2017 -0400 |
| b |
| @@ -0,0 +1,7 @@ +File Read_pairs_processed Unique_di-tags Cis_<10kbp_of_uniques Cis_>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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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% |
| b |
| 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 |
| b |
| @@ -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% |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,5 @@ +__no_feature 19 +__ambiguous 0 +__too_low_aQual 0 +__not_aligned 1336 +__alignment_not_unique 0 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| [ |
| b"@@ -0,0 +1,489 @@\n+\n+--------------------------------------------------------------------------------\n+Module:\t\t\tfastqc\n+Run File:\t\tHS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run\n+Job ID:\t\t\tcf_fastq_kallisto_1463255307_fastqc_732\n+Previous Job ID:\tstart_000\n+Date & Time:\t\t20:48, 14-05-2016\n+--------------------------------------------------------------------------------\n+\n+---------- FastQC version information ----------\n+FastQC v0.11.5\n+\n+------- End of FastQC version information ------\n+\n+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz\n+\n+###CF FastQC successfully ran, took 12 minutes\n+\n+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R2.fastq.gz\n+\n+###CF FastQC successfully ran, took 11 minutes, 16 seconds\n+\n+\n+\n+\n+--------------------------------------------------------------------------------\n+Module:\t\t\ttrim_galore\n+Run File:\t\tHS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_fastq_kallisto.run\n+Job ID:\t\t\tcf_fastq_kallisto_1463255307_trim_galore_659\n+Previous Job ID:\tstart_000\n+Date & Time:\t\t20:48, 14-05-2016\n+--------------------------------------------------------------------------------\n+\n+---------- Cutadapt version information ----------\n+1.8.1\n+\n+------- End of Cutadapt version information ------\n+---------- Trim Galore! version information ----------\n+\n+ Quality-/Adapter-/RRBS-Trimming\n+ (powered by Cutadapt)\n+ version 0.4.1\n+\n+ Last update: 20 07 2015\n+\n+\n+------- End of Trim Galore! version information ------\n+\n+###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\n+\n+Path to Cutadapt set as: 'cutadapt' (default)\n+1.8.1\n+Cutadapt seems to be working fine (tested command 'cutadapt --version')\n+\n+\n+AUTO-DETECTING ADAPTER TYPE\n+===========================\n+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 <<)\n+\n+Found perfect matches for the following adapter sequences:\n+Adapter type\tCount\tSequence\tSequences analysed\tPercentage\n+Illumina\t4591\tAGATCGGAAGAGC\t1000000\t0.46\n+Nextera\t4\tCTGTCTCTTATA\t1000000\t0.00\n+smallRNA\t2\tTGGAATTCTCGG\t1000000\t0.00\n+Using Illumina adapter for trimming (count: 4591). Second best hit was Nextera (count: 4)\n+\n+Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz_trimming_report.txt'\n+\n+SUMMARISING RUN PARAMETERS\n+==========================\n+Input filename: HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz\n+Trimming mode: paired-end\n+Trim Galore version: 0.4.1\n+Cutadapt version: 1.8.1\n+Quality Phred score cutoff: 20\n+Quality encoding type selected: ASCII+33\n+Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\n+Maximum trimming error rate: 0.1 (default)\n+Minimum required adapter overlap (stringency): 1 bp\n+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp\n+Running FastQC on the data once trimming has completed\n+Output file(s) will be GZIP compressed\n+\n+Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1_trimmed.fq.gz\n+\n+\n+ >>> 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 <<<\n+10000000 sequences processed\n+20000000 sequences processed\n+30000000 sequences processed\n+40000000 sequences processed\n+50000000 sequences processed\n+60000000 sequences processed\n+This is cutadapt 1.8.1 with Python 2.7.5\n+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM066_CGATGT_L002_R1.fastq.gz\n+Trimming 1 adapter with at most 10.0% errors in single-end mode ...\n+"..b'strp] running EM for the bootstrap: 9\r[bstrp] running EM for the bootstrap: 10\r[bstrp] running EM for the bootstrap: 11\r[bstrp] running EM for the bootstrap: 12\r[bstrp] running EM for the bootstrap: 13\r[bstrp] running EM for the bootstrap: 14\r[bstrp] running EM for the bootstrap: 15\r[bstrp] running EM for the bootstrap: 16\r[bstrp] running EM for the bootstrap: 17\r[bstrp] running EM for the bootstrap: 18\r[bstrp] running EM for the bootstrap: 19\r[bstrp] running EM for the bootstrap: 20\r[bstrp] running EM for the bootstrap: 21\r[bstrp] running EM for the bootstrap: 22\r[bstrp] running EM for the bootstrap: 23\r[bstrp] running EM for the bootstrap: 24\r[bstrp] running EM for the bootstrap: 25\r[bstrp] running EM for the bootstrap: 26\r[bstrp] running EM for the bootstrap: 27\r[bstrp] running EM for the bootstrap: 28\r[bstrp] running EM for the bootstrap: 29\r[bstrp] running EM for the bootstrap: 30\r[bstrp] running EM for the bootstrap: 31\r[bstrp] running EM for the bootstrap: 32\r[bstrp] running EM for the bootstrap: 33\r[bstrp] running EM for the bootstrap: 34\r[bstrp] running EM for the bootstrap: 35\r[bstrp] running EM for the bootstrap: 36\r[bstrp] running EM for the bootstrap: 37\r[bstrp] running EM for the bootstrap: 38\r[bstrp] running EM for the bootstrap: 39\r[bstrp] running EM for the bootstrap: 40\r[bstrp] running EM for the bootstrap: 41\r[bstrp] running EM for the bootstrap: 42\r[bstrp] running EM for the bootstrap: 43\r[bstrp] running EM for the bootstrap: 44\r[bstrp] running EM for the bootstrap: 45\r[bstrp] running EM for the bootstrap: 46\r[bstrp] running EM for the bootstrap: 47\r[bstrp] running EM for the bootstrap: 48\r[bstrp] running EM for the bootstrap: 49\r[bstrp] running EM for the bootstrap: 50\r[bstrp] running EM for the bootstrap: 51\r[bstrp] running EM for the bootstrap: 52\r[bstrp] running EM for the bootstrap: 53\r[bstrp] running EM for the bootstrap: 54\r[bstrp] running EM for the bootstrap: 55\r[bstrp] running EM for the bootstrap: 56\r[bstrp] running EM for the bootstrap: 57\r[bstrp] running EM for the bootstrap: 58\r[bstrp] running EM for the bootstrap: 59\r[bstrp] running EM for the bootstrap: 60\r[bstrp] running EM for the bootstrap: 61\r[bstrp] running EM for the bootstrap: 62\r[bstrp] running EM for the bootstrap: 63\r[bstrp] running EM for the bootstrap: 64\r[bstrp] running EM for the bootstrap: 65\r[bstrp] running EM for the bootstrap: 66\r[bstrp] running EM for the bootstrap: 67\r[bstrp] running EM for the bootstrap: 68\r[bstrp] running EM for the bootstrap: 69\r[bstrp] running EM for the bootstrap: 70\r[bstrp] running EM for the bootstrap: 71\r[bstrp] running EM for the bootstrap: 72\r[bstrp] running EM for the bootstrap: 73\r[bstrp] running EM for the bootstrap: 74\r[bstrp] running EM for the bootstrap: 75\r[bstrp] running EM for the bootstrap: 76\r[bstrp] running EM for the bootstrap: 77\r[bstrp] running EM for the bootstrap: 78\r[bstrp] running EM for the bootstrap: 79\r[bstrp] running EM for the bootstrap: 80\r[bstrp] running EM for the bootstrap: 81\r[bstrp] running EM for the bootstrap: 82\r[bstrp] running EM for the bootstrap: 83\r[bstrp] running EM for the bootstrap: 84\r[bstrp] running EM for the bootstrap: 85\r[bstrp] running EM for the bootstrap: 86\r[bstrp] running EM for the bootstrap: 87\r[bstrp] running EM for the bootstrap: 88\r[bstrp] running EM for the bootstrap: 89\r[bstrp] running EM for the bootstrap: 90\r[bstrp] running EM for the bootstrap: 91\r[bstrp] running EM for the bootstrap: 92\r[bstrp] running EM for the bootstrap: 93\r[bstrp] running EM for the bootstrap: 94\r[bstrp] running EM for the bootstrap: 95\r[bstrp] running EM for the bootstrap: 96\r[bstrp] running EM for the bootstrap: 97\r[bstrp] running EM for the bootstrap: 98\r[bstrp] running EM for the bootstrap: 99\r[bstrp] running EM for the bootstrap: 100\r\n+\n+###CF kallisto (PE mode) successfully exited, took 2 hours, 30 minutes, 54 seconds..\n+\n+\n+\n+\n+================================================================================\n+\n+\n+\n+\n+\n+###CF Run finished at 01:06 15-05-2016\n' |
| b |
| 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 |
| [ |
| b"@@ -0,0 +1,496 @@\n+\n+--------------------------------------------------------------------------------\n+Module:\t\t\tfastqc\n+Run File:\t\tHS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run\n+Job ID:\t\t\tcf_fastq_kallisto_1463255307_fastqc_792\n+Previous Job ID:\tstart_000\n+Date & Time:\t\t20:48, 14-05-2016\n+--------------------------------------------------------------------------------\n+\n+---------- FastQC version information ----------\n+FastQC v0.11.5\n+\n+------- End of FastQC version information ------\n+\n+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz\n+\n+###CF FastQC successfully ran, took 13 minutes, 29 seconds\n+\n+###CFCMD fastqc -q HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R2.fastq.gz\n+\n+###CF FastQC successfully ran, took 12 minutes, 27 seconds\n+\n+\n+\n+\n+--------------------------------------------------------------------------------\n+Module:\t\t\ttrim_galore\n+Run File:\t\tHS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_fastq_kallisto.run\n+Job ID:\t\t\tcf_fastq_kallisto_1463255307_trim_galore_160\n+Previous Job ID:\tstart_000\n+Date & Time:\t\t20:48, 14-05-2016\n+--------------------------------------------------------------------------------\n+\n+---------- Cutadapt version information ----------\n+1.8.1\n+\n+------- End of Cutadapt version information ------\n+---------- Trim Galore! version information ----------\n+\n+ Quality-/Adapter-/RRBS-Trimming\n+ (powered by Cutadapt)\n+ version 0.4.1\n+\n+ Last update: 20 07 2015\n+\n+\n+------- End of Trim Galore! version information ------\n+\n+###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\n+\n+Path to Cutadapt set as: 'cutadapt' (default)\n+1.8.1\n+Cutadapt seems to be working fine (tested command 'cutadapt --version')\n+\n+\n+AUTO-DETECTING ADAPTER TYPE\n+===========================\n+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 <<)\n+\n+Found perfect matches for the following adapter sequences:\n+Adapter type\tCount\tSequence\tSequences analysed\tPercentage\n+Illumina\t7610\tAGATCGGAAGAGC\t1000000\t0.76\n+Nextera\t8\tCTGTCTCTTATA\t1000000\t0.00\n+smallRNA\t3\tTGGAATTCTCGG\t1000000\t0.00\n+Using Illumina adapter for trimming (count: 7610). Second best hit was Nextera (count: 8)\n+\n+Writing report to 'HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz_trimming_report.txt'\n+\n+SUMMARISING RUN PARAMETERS\n+==========================\n+Input filename: HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz\n+Trimming mode: paired-end\n+Trim Galore version: 0.4.1\n+Cutadapt version: 1.8.1\n+Quality Phred score cutoff: 20\n+Quality encoding type selected: ASCII+33\n+Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)\n+Maximum trimming error rate: 0.1 (default)\n+Minimum required adapter overlap (stringency): 1 bp\n+Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp\n+Running FastQC on the data once trimming has completed\n+Output file(s) will be GZIP compressed\n+\n+Writing final adapter and quality trimmed output to HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1_trimmed.fq.gz\n+\n+\n+ >>> 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 <<< \n+10000000 sequences processed\n+20000000 sequences processed\n+30000000 sequences processed\n+40000000 sequences processed\n+50000000 sequences processed\n+60000000 sequences processed\n+70000000 sequences processed\n+This is cutadapt 1.8.1 with Python 2.7.5\n+Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HS002-PE-R00059_BD0U5YACXX.RHM067_CAGATC_L002_R1.fastq.gz\n+Trimming 1 adapter with at"..b' 12\r[bstrp] running EM for the bootstrap: 13\r[bstrp] running EM for the bootstrap: 14\r[bstrp] running EM for the bootstrap: 15\r[bstrp] running EM for the bootstrap: 16\r[bstrp] running EM for the bootstrap: 17\r[bstrp] running EM for the bootstrap: 18\r[bstrp] running EM for the bootstrap: 19\r[bstrp] running EM for the bootstrap: 20\r[bstrp] running EM for the bootstrap: 21\r[bstrp] running EM for the bootstrap: 22\r[bstrp] running EM for the bootstrap: 23\r[bstrp] running EM for the bootstrap: 24\r[bstrp] running EM for the bootstrap: 25\r[bstrp] running EM for the bootstrap: 26\r[bstrp] running EM for the bootstrap: 27\r[bstrp] running EM for the bootstrap: 28\r[bstrp] running EM for the bootstrap: 29\r[bstrp] running EM for the bootstrap: 30\r[bstrp] running EM for the bootstrap: 31\r[bstrp] running EM for the bootstrap: 32\r[bstrp] running EM for the bootstrap: 33\r[bstrp] running EM for the bootstrap: 34\r[bstrp] running EM for the bootstrap: 35\r[bstrp] running EM for the bootstrap: 36\r[bstrp] running EM for the bootstrap: 37\r[bstrp] running EM for the bootstrap: 38\r[bstrp] running EM for the bootstrap: 39\r[bstrp] running EM for the bootstrap: 40\r[bstrp] running EM for the bootstrap: 41\r[bstrp] running EM for the bootstrap: 42\r[bstrp] running EM for the bootstrap: 43\r[bstrp] running EM for the bootstrap: 44\r[bstrp] running EM for the bootstrap: 45\r[bstrp] running EM for the bootstrap: 46\r[bstrp] running EM for the bootstrap: 47\r[bstrp] running EM for the bootstrap: 48\r[bstrp] running EM for the bootstrap: 49\r[bstrp] running EM for the bootstrap: 50\r[bstrp] running EM for the bootstrap: 51\r[bstrp] running EM for the bootstrap: 52\r[bstrp] running EM for the bootstrap: 53\r[bstrp] running EM for the bootstrap: 54\r[bstrp] running EM for the bootstrap: 55\r[bstrp] running EM for the bootstrap: 56\r[bstrp] running EM for the bootstrap: 57\r[bstrp] running EM for the bootstrap: 58\r[bstrp] running EM for the bootstrap: 59\r[bstrp] running EM for the bootstrap: 60\r[bstrp] running EM for the bootstrap: 61\r[bstrp] running EM for the bootstrap: 62\r[bstrp] running EM for the bootstrap: 63\r[bstrp] running EM for the bootstrap: 64\r[bstrp] running EM for the bootstrap: 65\r[bstrp] running EM for the bootstrap: 66\r[bstrp] running EM for the bootstrap: 67\r[bstrp] running EM for the bootstrap: 68\r[bstrp] running EM for the bootstrap: 69\r[bstrp] running EM for the bootstrap: 70\r[bstrp] running EM for the bootstrap: 71\r[bstrp] running EM for the bootstrap: 72\r[bstrp] running EM for the bootstrap: 73\r[bstrp] running EM for the bootstrap: 74\r[bstrp] running EM for the bootstrap: 75\r[bstrp] running EM for the bootstrap: 76\r[bstrp] running EM for the bootstrap: 77\r[bstrp] running EM for the bootstrap: 78\r[bstrp] running EM for the bootstrap: 79\r[bstrp] running EM for the bootstrap: 80\r[bstrp] running EM for the bootstrap: 81\r[bstrp] running EM for the bootstrap: 82\r[bstrp] running EM for the bootstrap: 83\r[bstrp] running EM for the bootstrap: 84\r[bstrp] running EM for the bootstrap: 85\r[bstrp] running EM for the bootstrap: 86\r[bstrp] running EM for the bootstrap: 87\r[bstrp] running EM for the bootstrap: 88\r[bstrp] running EM for the bootstrap: 89\r[bstrp] running EM for the bootstrap: 90\r[bstrp] running EM for the bootstrap: 91\r[bstrp] running EM for the bootstrap: 92\r[bstrp] running EM for the bootstrap: 93\r[bstrp] running EM for the bootstrap: 94\r[bstrp] running EM for the bootstrap: 95\r[bstrp] running EM for the bootstrap: 96\r[bstrp] running EM for the bootstrap: 97\r[bstrp] running EM for the bootstrap: 98\r[bstrp] running EM for the bootstrap: 99\r[bstrp] running EM for the bootstrap: 100\r\n+\n+###CF kallisto (PE mode) successfully exited, took 2 hours, 44 minutes, 36 seconds..\n+\n+\n+\n+================================================================================\n+\n+\n+\n+\n+\n+###CF Run finished at 01:48 15-05-2016\n+\n+\n+###CF Pipeline fastq_kallisto finished at 01:59 15-05-2016\n+\n+Sending HTML e-mail with sendmail..\n+Sent a pipeline e-mail notification to rsh46@cam.ac.uk\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 + + |
| b |
| 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 |
| b |
| @@ -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 21.589012 20.80903 28.351444 0.000006 +1 35 29.741069 20.846087 21.339816 28.073028 0 +1 36 29.685575 20.657699 21.409349 28.247377 0 +1 37 30.435943 19.845352 21.605325 28.11328 0.0001 +1 38 31.52442 19.566381 20.859275 28.049918 0.000006 +1 39 31.915805 19.322889 20.315213 28.445698 0.000396 +1 40 31.415236 19.831291 20.60081 28.152663 0 +1 41 31.151606 20.007274 19.953602 28.887329 0.000188 +1 42 29.605015 21.700164 21.132809 27.561943 0.000069 +1 43 28.856192 21.690732 21.620633 27.832141 0.000302 +1 44 28.354815 21.89939 21.789262 27.956319 0.000214 +1 45 28.785938 21.376155 22.083299 27.443347 0.311262 +1 46 30.020967 20.974608 20.997153 28.006939 0.000333 +1 47 30.905677 19.834877 21.050285 28.209156 0.000006 +1 48 31.123254 20.025503 20.781792 28.068879 0.000572 +1 49 32.061167 19.135286 20.210972 28.592399 0.000176 +1 50 31.368968 19.831498 20.33522 28.464018 0.000295 +1 51 30.241493 20.530902 21.628272 27.599157 0.000176 +1 52 29.272115 21.228524 22.138875 27.360278 0.000208 +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 + + |
| b |
| 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 +130 923 +131 931 +132 953 +133 1006 +134 1086 +135 1134 +136 1177 +137 1280 +138 1381 +139 1419 +140 1494 +141 1625 +142 1697 +143 1838 +144 1899 +145 1957 +146 2197 +147 2214 +148 2276 +149 2450 +150 2557 +151 2523 +152 2619 +153 2591 +154 2575 +155 2745 +156 2756 +157 2716 +158 2765 +159 2775 +160 2884 +161 2830 +162 2781 +163 2718 +164 2777 +165 2859 +166 2803 +167 2855 +168 2896 +169 2817 +170 2843 +171 2817 +172 2844 +173 2855 +174 2777 +175 2684 +176 2703 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| b |
| 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 + |
| b |
| 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 + |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 + + |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| [ |
| b"@@ -0,0 +1,75 @@\n+[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\n+[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: /Users/bebatut/.multiqc_config.yaml\n+[2017-09-28 17:24:01,554] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml\n+[2017-09-28 17:24:01,554] multiqc [DEBUG ] Command used: /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir\n+[2017-09-28 17:24:02,209] multiqc [DEBUG ] Latest MultiQC version is v1.2\n+[2017-09-28 17:24:02,210] multiqc [INFO ] This is MultiQC v1.2\n+[2017-09-28 17:24:02,210] multiqc [DEBUG ] Command : /Users/bebatut/miniconda3/envs/multiqc2/bin/multiqc multiqc_WDir\n+[2017-09-28 17:24:02,210] multiqc [DEBUG ] Working dir : /Users/bebatut/Documents/post_doc_freiburg/galaxy_projects/tools/tools-iuc/tools/multiqc\n+[2017-09-28 17:24:02,210] multiqc [INFO ] Template : default\n+[2017-09-28 17:24:02,210] multiqc [INFO ] Searching 'multiqc_WDir'\n+[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\n+[2017-09-28 17:24:02,249] multiqc [DEBUG ] Using temporary directory for creating report: /var/folders/rp/scmd2sr56nq9cb0x9d_6_49m000dft/T/tmp7lPIig\n+[2017-09-28 17:24:05,021] multiqc.modules.afterqc.afterqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,098] multiqc.modules.custom_content.custom_content [DEBUG ] No custom content found\n+[2017-09-28 17:24:05,144] multiqc.modules.conpair.conpair [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,235] multiqc.modules.peddy.peddy [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,259] multiqc.modules.methylQA.methylQA [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,306] multiqc.modules.qualimap.QM_BamQC [DEBUG ] Using default Qualimap thresholds: 1, 5, 10, 30, 50\n+[2017-09-28 17:24:05,306] multiqc.modules.qualimap.qualimap [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,315] multiqc.modules.preseq.preseq [DEBUG ] Could not find any preseq data in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,329] multiqc.modules.quast.quast [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,347] multiqc.modules.qorts.qorts [DEBUG ] Could not find any QoRTs data in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,394] multiqc.modules.rna_seqc.rna_seqc [DEBUG ] Could not find any RNA-SeQC data in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,424] multiqc.modules.rseqc.rseqc [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:05,430] multiqc.modules.busco.busco "..b"r',)\n+[2017-09-28 17:24:06,273] multiqc.modules.adapterRemoval.adapterRemoval [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:06,299] multiqc.modules.cutadapt.cutadapt [INFO ] Found 1 reports\n+[2017-09-28 17:24:06,351] multiqc.modules.flexbar.flexbar [INFO ] Found 1 logs\n+[2017-09-28 17:24:06,378] multiqc.modules.trimmomatic.trimmomatic [INFO ] Found 1 logs\n+[2017-09-28 17:24:06,403] multiqc.modules.skewer.skewer [DEBUG ] Could not find any data in ('multiqc_WDir',)\n+[2017-09-28 17:24:06,421] multiqc.modules.sortmerna.sortmerna [INFO ] Found 1 logs\n+[2017-09-28 17:24:06,441] multiqc.modules.biobloomtools.biobloomtools [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:06,448] multiqc.modules.fastq_screen.fastq_screen [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:06,605] multiqc.modules.fastqc.fastqc [INFO ] Found 2 reports\n+[2017-09-28 17:24:06,908] multiqc.modules.clusterflow.clusterflow [DEBUG ] Could not find any reports in ('multiqc_WDir',)\n+[2017-09-28 17:24:06,914] multiqc.modules.bcl2fastq.bcl2fastq [DEBUG ] Could not find any bcl2fastq data in ('multiqc_WDir',)\n+[2017-09-28 17:24:06,923] multiqc [INFO ] Compressing plot data\n+[2017-09-28 17:24:07,121] multiqc [INFO ] Report : multiqc_report.html\n+[2017-09-28 17:24:07,121] multiqc [INFO ] Data : multiqc_data\n+[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'\n+[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'\n+[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'\n+[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'\n+[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'\n+[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'\n+[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'\n+[2017-09-28 17:24:07,952] multiqc [INFO ] MultiQC complete\n" |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,6 @@ +organism: Escherichia coli Sample2 +contigs: 52 +bases: 162997532523 +rRNA: 2 +CDS: 1548 +misc_RNA: 5152 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| [ |
| b'@@ -0,0 +1,4806 @@\n+<!DOCTYPE html>\n+<html lang="en">\n+<head>\n+<!--\n+ __ __ _ _ _ ___ ____\n+ | \\/ |_ _| | |_(_)/ _ \\ / ___|\n+ | |\\/| | | | | | __| | | | | |\n+ | | | | |_| | | |_| | |_| | |___\n+ |_| |_|\\__,_|_|\\__|_|\\__\\_\\\\____|\n+\n+Abandon hope all ye who enter here..\n+http://multiqc.info\n+-->\n+\n+ \n+\n+<meta charset="utf-8">\n+<meta http-equiv="X-UA-Compatible" content="IE=edge">\n+<meta name="viewport" content="width=device-width, initial-scale=1">\n+\n+<meta name="description" content="MultiQC: A modular tool to aggregate results from bioinformatics analyses across many samples into a single report">\n+<meta name="author" content="MultiQC">\n+<title>MultiQC Report</title>\n+\n+<!-- JSON plot data -->\n+<script type="text/javascript">\n+mqc_compressed_plotdata = \'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'..b'-6">\n+ <select id="tableScatter_col1" name="tableScatter_col1" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ <div class="col-sm-6">\n+ <select id="tableScatter_col2" name="tableScatter_col2" class="form-control">\n+ <option value="">Select Column</option>\n+ </select>\n+ </div>\n+ </div>\n+ <div class="hc-plot-wrapper">\n+ <div id="tableScatterPlot" class="hc-plot not_rendered hc-scatter-plot no-handle" style="width:566px; height: 510px;">\n+ <small>Please select two table columns.</small>\n+ </div>\n+ </div>\n+ </form>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+\n+\n+<!-- Regex Help Modal -->\n+<div class="modal fade" id="regex_help_modal" tabindex="-1" role="dialog">\n+ <div class="modal-dialog" role="document">\n+ <div class="modal-content">\n+ <div class="modal-header">\n+ <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">×</span></button>\n+ <h3 class="modal-title">Regex Help</h3>\n+ </div>\n+ <div class="modal-body">\n+ <p>Toolbox search strings can behave as regular expressions (regexes). Click a button below to see an example of it in action. Try modifying them yourself in the text box.</p>\n+ <div class="row">\n+ <div class="col-sm-6 regex_example_buttons">\n+ <button class="btn btn-default" data-example="^samp_1"><code>^</code> (start of string)</button>\n+ <button class="btn btn-default" data-example="samp_1$"><code>$</code> (end of string)</button>\n+ <button class="btn btn-default" data-example="samp_[13]"><code>[]</code> (character choice)</button>\n+ <button class="btn btn-default" data-example="\\d$"><code>\\d</code> (shorthand for <code>[0-9]</code>)</button>\n+ <button class="btn btn-default" data-example="^\\w"><code>\\w</code> (shorthand for <code>[0-9a-zA-Z_]</code>)</button>\n+ <button class="btn btn-default" data-example="._samp"><code>.</code> (any character)</button>\n+ <button class="btn btn-default" data-example="\\."><code>\\.</code> (literal full stop)</button>\n+ <button class="btn btn-default" data-example="(tmp|prepended)_samp"><code>()</code> <code>|</code> (group / separator)</button>\n+ <button class="btn btn-default" data-example="tmpp*_"><code>*</code> (prev char 0 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp+_"><code>+</code> (prev char 1 or more)</button>\n+ <button class="btn btn-default" data-example="tmpp?_"><code>?</code> (prev char 0 or 1)</button>\n+ <button class="btn btn-default" data-example="_1{5}"><code>{}</code> (char num times)</button>\n+ <button class="btn btn-default" data-example="_1{2,5}"><code>{,}</code> (count range)</button>\n+ </div>\n+ <div class="col-sm-6 regex_example_demo">\n+ <input type="text" class="form-control" />\n+<pre>\n+<span>samp_1</span>\n+<span>samp_1_edited</span>\n+<span>samp_2</span>\n+<span>samp_2_edited</span>\n+<span>samp_3</span>\n+<span>samp_3_edited</span>\n+<span>prepended_samp_1</span>\n+<span>tmp_samp_1_edited</span>\n+<span>tmpp_samp_1_edited</span>\n+<span>tmppp_samp_1_edited</span>\n+<span>#samp_1_edited.tmp</span>\n+<span>samp_11</span>\n+<span>samp_11111</span>\n+</pre>\n+ <p>See <a href="https://regex101.com/" target="_blank">regex101.com</a> for a more heavy duty testing suite.</p>\n+ </div>\n+ </div>\n+ </div>\n+ <div class="modal-footer">\n+ <button type="button" class="btn btn-default" data-dismiss="modal">Close</button>\n+ </div>\n+ </div>\n+ </div>\n+</div>\n+\n+</body>\n+</html>\n' |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/rsem.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rsem.txt Tue Oct 24 06:29:59 2017 -0400 |
| b |
| @@ -0,0 +1,57 @@ +2302013 30752387 0 33054400 +30113921 638466 13832652 +65457099 3 +0 2302013 +1 16919735 +2 6224666 +3 3186612 +4 1664884 +5 1091224 +6 555346 +7 358669 +8 245597 +9 98797 +10 65875 +11 83793 +12 46956 +13 26998 +14 45559 +15 33388 +16 11464 +17 7678 +18 12949 +19 22852 +20 16386 +21 6725 +22 16252 +23 3943 +24 3304 +25 18 +26 1 +27 11 +28 27 +29 37 +30 56 +31 115 +32 146 +33 210 +34 18 +35 128 +36 5 +37 47 +38 129 +39 81 +40 1231 +41 284 +42 27 +43 112 +44 6 +45 4 +46 1 +47 1 +48 7 +53 2 +71 24 +73 1 +77 6 +Inf 0 |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/rseqc.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rseqc.txt Tue Oct 24 06:29:59 2017 -0400 |
| b |
| @@ -0,0 +1,53 @@ +GC% read_count +60.78 829481 +27.45 703668 +50.98 2379493 +1.96 261 +7.84 634 +35.29 2846032 +15.69 24491 +84.31 5518 +98.04 16 +17.65 52102 +31.37 1523034 +80.39 13695 +19.61 101270 +92.16 437 +0.00 268 +78.43 21055 +72.55 97109 +64.71 490287 +49.02 3178845 +66.67 337430 +62.75 638616 +43.14 3937851 +25.49 463128 +88.24 1716 +96.08 45 +47.06 2832756 +13.73 10153 +82.35 8743 +52.94 1873671 +58.82 1127263 +94.12 136 +9.80 1544 +74.51 54717 +29.41 1479389 +23.53 295157 +90.20 920 +21.57 178359 +45.10 3299529 +76.47 33755 +3.92 253 +41.18 3524191 +56.86 1272852 +54.90 1460810 +37.25 3180062 +100.00 4 +70.59 209856 +68.63 246416 +86.27 3040 +39.22 3812147 +5.88 382 +11.76 4123 +33.33 2269744 |
| b |
| diff -r 000000000000 -r 3bad335ccea9 test-data/salmon.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/salmon.txt Tue Oct 24 06:29:59 2017 -0400 |
| b |
| b'@@ -0,0 +1,2 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|
| b |
| 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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,2 @@ +Sample n_dups pct_dups n_tot n_nondups +virtual-normal 1 1.28 78 77 |
| b |
| 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 |
| b |
| @@ -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) |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| [ |
| b'@@ -0,0 +1,9736 @@\n+# This file was produced by samtools stats (1.2+htslib-1.2.1) and can be plotted using plot-bamstats\n+# 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\n+# CHK, Checksum\t[2]Read Names\t[3]Sequences\t[4]Qualities\n+# CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)\n+CHK\t7742088d\t2cf80e59\t99341a6a\n+# Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.\n+SN\traw total sequences:\t641821\n+SN\tfiltered sequences:\t0\n+SN\tsequences:\t641821\n+SN\tis sorted:\t1\n+SN\t1st fragments:\t320981\n+SN\tlast fragments:\t320840\n+SN\treads mapped:\t641821\n+SN\treads mapped and paired:\t638746\t# paired-end technology bit set + both mates mapped\n+SN\treads unmapped:\t0\n+SN\treads properly paired:\t635626\t# proper-pair bit set\n+SN\treads paired:\t641821\t# paired-end technology bit set\n+SN\treads duplicated:\t0\t# PCR or optical duplicate bit set\n+SN\treads MQ0:\t70\t# mapped and MQ=0\n+SN\treads QC failed:\t0\n+SN\tnon-primary alignments:\t12111\n+SN\ttotal length:\t64823921\t# ignores clipping\n+SN\tbases mapped:\t64823921\t# ignores clipping\n+SN\tbases mapped (cigar):\t64823921\t# more accurate\n+SN\tbases trimmed:\t0\n+SN\tbases duplicated:\t0\n+SN\tmismatches:\t275405\t# from NM fields\n+SN\terror rate:\t4.248509e-03\t# mismatches / bases mapped (cigar)\n+SN\taverage length:\t101\n+SN\tmaximum length:\t101\n+SN\taverage quality:\t26.0\n+SN\tinsert size average:\t719.7\n+SN\tinsert size standard deviation:\t1223.0\n+SN\tinward oriented pairs:\t317512\n+SN\toutward oriented pairs:\t1294\n+SN\tpairs with other orientation:\t30\n+SN\tpairs on different chromosomes:\t0\n+# First Fragment Qualitites. Use `grep ^FFQ | cut -f 2-` to extract this part.\n+# Columns correspond to qualities and rows to cycles. First column is the cycle number.\n+FFQ\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t113\t0\t0\t0\t0\t320725\t143\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t4\t320810\t71\t91\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t3\t320877\t25\t75\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t5\t320905\t26\t44\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320816\t67\t86\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t8\t320839\t42\t84\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t3\t0\t0\t0\t0\t6\t320867\t57\t47\t1\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t8\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t8\t320845\t59\t64\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t9\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t2\t320851\t46\t78\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t10\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t4\t320836\t57\t77\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t11\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t0\t0\t0\t0\t7\t320849\t46\t67\t5\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t12\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t8\t320812\t80\t78\t2\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t13\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t9\t320826\t56\t82\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t1\t0\t0\t0\t10\t320774\t77\t107\t7\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t15\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t7\t320808\t60\t95\t3\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t16\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t7\t1\t0\t0\t0\t12\t320786\t68\t101\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t17\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t4\t0\t0\t0\t0\t8\t320758\t89\t116\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t18\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t6\t0\t0\t0\t0\t9\t320768\t86\t106\t6\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t19\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t1\t1\t0\t0\t0\t12\t320795\t77\t91\t4\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t20\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t8\t0\t0\t0\t0\t11\t320739\t99\t110\t14\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t5\t0\t0\t0\t0\t16\t320681\t115\t143\t21\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0\n+FFQ\t22\t0\t0\t0\t0\t'..b'92-892]\t892\t9\n+COV\t[893-893]\t893\t9\n+COV\t[894-894]\t894\t12\n+COV\t[895-895]\t895\t16\n+COV\t[896-896]\t896\t10\n+COV\t[897-897]\t897\t8\n+COV\t[898-898]\t898\t8\n+COV\t[899-899]\t899\t11\n+COV\t[900-900]\t900\t7\n+COV\t[901-901]\t901\t15\n+COV\t[902-902]\t902\t13\n+COV\t[903-903]\t903\t17\n+COV\t[904-904]\t904\t9\n+COV\t[905-905]\t905\t8\n+COV\t[906-906]\t906\t13\n+COV\t[907-907]\t907\t10\n+COV\t[908-908]\t908\t8\n+COV\t[909-909]\t909\t13\n+COV\t[910-910]\t910\t7\n+COV\t[911-911]\t911\t9\n+COV\t[912-912]\t912\t8\n+COV\t[913-913]\t913\t9\n+COV\t[914-914]\t914\t8\n+COV\t[915-915]\t915\t9\n+COV\t[916-916]\t916\t6\n+COV\t[917-917]\t917\t9\n+COV\t[918-918]\t918\t7\n+COV\t[919-919]\t919\t9\n+COV\t[920-920]\t920\t8\n+COV\t[921-921]\t921\t13\n+COV\t[922-922]\t922\t5\n+COV\t[923-923]\t923\t5\n+COV\t[924-924]\t924\t5\n+COV\t[925-925]\t925\t7\n+COV\t[926-926]\t926\t10\n+COV\t[927-927]\t927\t6\n+COV\t[928-928]\t928\t21\n+COV\t[929-929]\t929\t10\n+COV\t[930-930]\t930\t10\n+COV\t[931-931]\t931\t7\n+COV\t[932-932]\t932\t12\n+COV\t[933-933]\t933\t14\n+COV\t[934-934]\t934\t14\n+COV\t[935-935]\t935\t7\n+COV\t[936-936]\t936\t12\n+COV\t[937-937]\t937\t13\n+COV\t[938-938]\t938\t10\n+COV\t[939-939]\t939\t12\n+COV\t[940-940]\t940\t18\n+COV\t[941-941]\t941\t11\n+COV\t[942-942]\t942\t10\n+COV\t[943-943]\t943\t6\n+COV\t[944-944]\t944\t12\n+COV\t[945-945]\t945\t12\n+COV\t[946-946]\t946\t8\n+COV\t[947-947]\t947\t12\n+COV\t[948-948]\t948\t10\n+COV\t[949-949]\t949\t5\n+COV\t[950-950]\t950\t9\n+COV\t[951-951]\t951\t16\n+COV\t[952-952]\t952\t13\n+COV\t[953-953]\t953\t15\n+COV\t[954-954]\t954\t15\n+COV\t[955-955]\t955\t8\n+COV\t[956-956]\t956\t15\n+COV\t[957-957]\t957\t18\n+COV\t[958-958]\t958\t9\n+COV\t[959-959]\t959\t21\n+COV\t[960-960]\t960\t14\n+COV\t[961-961]\t961\t17\n+COV\t[962-962]\t962\t9\n+COV\t[963-963]\t963\t14\n+COV\t[964-964]\t964\t6\n+COV\t[965-965]\t965\t5\n+COV\t[966-966]\t966\t13\n+COV\t[967-967]\t967\t12\n+COV\t[968-968]\t968\t13\n+COV\t[969-969]\t969\t10\n+COV\t[970-970]\t970\t13\n+COV\t[971-971]\t971\t8\n+COV\t[972-972]\t972\t13\n+COV\t[973-973]\t973\t12\n+COV\t[974-974]\t974\t14\n+COV\t[975-975]\t975\t9\n+COV\t[976-976]\t976\t12\n+COV\t[977-977]\t977\t4\n+COV\t[978-978]\t978\t14\n+COV\t[979-979]\t979\t6\n+COV\t[980-980]\t980\t12\n+COV\t[981-981]\t981\t5\n+COV\t[982-982]\t982\t8\n+COV\t[983-983]\t983\t4\n+COV\t[984-984]\t984\t9\n+COV\t[985-985]\t985\t9\n+COV\t[986-986]\t986\t10\n+COV\t[987-987]\t987\t8\n+COV\t[988-988]\t988\t4\n+COV\t[989-989]\t989\t6\n+COV\t[990-990]\t990\t3\n+COV\t[991-991]\t991\t5\n+COV\t[992-992]\t992\t2\n+COV\t[993-993]\t993\t6\n+COV\t[994-994]\t994\t6\n+COV\t[995-995]\t995\t7\n+COV\t[996-996]\t996\t14\n+COV\t[997-997]\t997\t12\n+COV\t[998-998]\t998\t7\n+COV\t[999-999]\t999\t8\n+COV\t[1000-1000]\t1000\t8\n+COV\t[1000<]\t1000\t5025\n+# 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\n+GCD\t0.0\t0.554\t0.000\t0.000\t0.000\t0.000\t0.000\n+GCD\t0.5\t0.831\t0.525\t0.525\t0.525\t0.525\t0.525\n+GCD\t36.0\t1.385\t0.954\t0.954\t0.954\t1.490\t1.490\n+GCD\t37.0\t2.216\t2.495\t2.495\t4.146\t6.560\t6.560\n+GCD\t38.0\t5.263\t0.247\t0.454\t3.520\t5.868\t9.883\n+GCD\t39.0\t9.141\t0.177\t0.303\t2.161\t8.777\t12.812\n+GCD\t40.0\t12.188\t0.020\t1.192\t9.060\t22.018\t27.371\n+GCD\t41.0\t16.343\t0.035\t0.550\t2.702\t11.469\t12.908\n+GCD\t42.0\t21.884\t0.010\t0.172\t2.121\t5.621\t17.094\n+GCD\t43.0\t28.255\t0.010\t0.328\t1.449\t4.277\t10.166\n+GCD\t44.0\t36.288\t0.162\t0.394\t5.484\t15.145\t50.490\n+GCD\t45.0\t42.105\t0.020\t0.131\t1.252\t7.009\t17.811\n+GCD\t46.0\t49.861\t0.015\t0.121\t0.636\t1.939\t37.506\n+GCD\t47.0\t56.510\t0.030\t0.141\t1.015\t4.500\t6.338\n+GCD\t48.0\t64.543\t0.010\t0.091\t2.565\t7.287\t21.872\n+GCD\t49.0\t68.975\t0.010\t0.333\t0.672\t10.751\t27.129\n+GCD\t50.0\t73.407\t0.010\t0.121\t1.358\t3.883\t6.615\n+GCD\t51.0\t77.008\t0.121\t0.576\t1.576\t4.363\t13.923\n+GCD\t52.0\t81.994\t0.010\t0.086\t1.560\t4.414\t109.383\n+GCD\t53.0\t84.488\t0.040\t0.071\t0.500\t3.025\t31.234\n+GCD\t54.0\t86.704\t0.020\t0.313\t9.332\t39.683\t203.959\n+GCD\t55.0\t89.197\t0.005\t0.051\t1.268\t5.045\t23.578\n+GCD\t56.0\t91.136\t0.071\t0.192\t1.566\t9.994\t33.315\n+GCD\t57.0\t94.460\t0.040\t0.348\t1.167\t5.050\t11.660\n+GCD\t58.0\t95.845\t0.131\t0.131\t1.899\t2.742\t4.929\n+GCD\t59.0\t96.399\t3.313\t3.313\t3.313\t3.666\t3.666\n+GCD\t60.0\t97.507\t0.995\t0.995\t5.176\t6.954\t33.234\n+GCD\t61.0\t98.338\t1.591\t1.591\t1.788\t4.848\t4.848\n+GCD\t62.0\t98.892\t3.171\t3.171\t3.171\t7.343\t7.343\n+GCD\t63.0\t99.446\t0.530\t0.530\t0.530\t6.403\t6.403\n+GCD\t64.0\t100.000\t1.025\t1.025\t1.025\t4.585\t4.585\n' |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,588 @@\n+\n+# Summary table \n+\n+Name , Value\n+Genome , GRCh37.75 \n+Date , 2016-02-24 19:23\n+SnpEff_version , SnpEff 4.1a (build 2015-01-14), by Pablo Cingolani\n+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 \n+Warnings , 1214759 \n+Number_of_lines_in_input_file, 917355\n+Number_of_variants_before_filter, 972155\n+Number_of_not_variants , 0\n+Number_of_variants_processed , 972155\n+Number_of_known_variants <br>(i.e. non-empty ID) , 764271, 78.616167% \n+Number_of_effects , 5499894 \n+Genome_total_length ,32036512383 \n+Genome_effective_length ,3101536026 \n+Change_rate , 3190 \n+\n+# Change rate by chromosome\n+\n+Chromosome , Length , Changes , Change_rate \n+1 , 249250621 , 76982 , 3237\n+2 , 243199373 , 77562 , 3135\n+3 , 198022430 , 63396 , 3123\n+4 , 191154276 , 65298 , 2927\n+5 , 180915260 , 56287 , 3214\n+6 , 171115067 , 59086 , 2896\n+7 , 159138663 , 55505 , 2867\n+8 , 146364022 , 44876 , 3261\n+9 , 141213431 , 40484 , 3488\n+10 , 135534747 , 48468 , 2796\n+11 , 135006516 , 45528 , 2965\n+12 , 133851895 , 45727 , 2927\n+13 , 115169878 , 36006 , 3198\n+14 , 107349540 , 30507 , 3518\n+15 , 102531392 , 29009 , 3534\n+16 , 90354753 , 29320 , 3081\n+17 , 81195210 , 30895 , 2628\n+18 , 78077248 , 26998 , 2891\n+19 , 59128983 , 25980 , 2275\n+20 , 63025520 , 20817 , 3027\n+21 , 48129895 , 16197 , 2971\n+22 , 51304566 , 13805 , 3716\n+GL000191.1 , 106433 , 24 , 4434\n+GL000192.1 , 547496 , 131 , 4179\n+GL000193.1 , 189789 , 133 , 1426\n+GL000194.1 , 191469 , 159 , 1204\n+GL000195.1 , 182896 , 269 , 679\n+GL000197.1 , 37175 , 1 , 37175\n+GL000198.1 , 90085 , 146 , 617\n+GL000199.1 , 169874 , 54 , 3145\n+GL000201.1 , 36148 , 1 , 36148\n+GL000202.1 , 40103 , 9 , 4455\n+GL000203.1 , 37498 , 78 , 480\n+GL000204.1 , 81310 , 15 , 5420\n+GL000205.1 , 174588 , 229 , 762\n+GL000206.1 , 41001 , 1 , 41001\n+GL000208.1 , 92689 , 66 , 1404\n+GL000209.1 , 159169 , 4 , 39792\n+GL000210.1 , 27682 , 1 , 27682\n+GL000211.1 , 166566 , 161 , 1034\n+GL000212.1 , 186858 , 123 , 1519\n+GL000213.1 , 164239 , 14 , 11731\n+GL000214.1 , 137718 , 169 , 814\n+GL000215.1 , 172545 , 12 , 14378\n+GL000216.1 , 172294 , 636 , 270\n+GL000217.1 , 172149 , 227 , 758\n+GL000218.1 , 161147 , 141 , 1142\n+GL000219.1 , 179198 , 384 , 466\n+GL000220.1 , 161802 , 294 , 550\n+GL000221.1 , 155397 , 90 , 1726\n+GL000222.1 , 186861 , 175 , 1067\n+GL000223.1 , 180455 , 2 , 90227\n+GL000224.1 , 179693 , 324 , 554\n+GL000225.1 , 211173 , 537 , 393\n+GL000226.1 , 15008 , 2 , 7504\n+GL000227.1 , 128374 , 5 , 25674\n+GL000228.1 , 129120 , 65 , 1986\n+GL000229.1 , 19913 , 157 , 126\n+GL000230.1 , 43691 , 40 , 1092\n+GL000231.1 , 27386 , 114 , 240\n+GL000232.1 , 40652 , 175 , 232\n+GL000233.1 , 45941 , 54 , 850\n+GL000234.1 , 40531 , 165 , 245\n+GL000235.1 , 34474 , 80 , 430\n+GL000236.1 , 41934 , 12 , 3494\n+GL000237.1 , 45867 , 50 , 917\n+GL000238.1 , 39939 , 3 , 13313\n+GL000239.1 , 33824 , 11 , 3074\n+GL000240.1 , 41933 , 37 , 1133\n+GL000241.1 , 42152 , 138 , 305\n+GL000242.1 , 43523 , 4 , 10880\n+GL000243.1 , 43341 , 28 , 1547\n+GL000244.1 , 39929 , 8 , 4991\n+GL000245.1 , 36651 , 12 , 3054\n+GL000246.1 , 38154 , 9 , 4239\n+GL000247.1 , 36422 , 12 , 3035\n+GL000248.1 , 39786 , 6 , 6631\n+MT , 16569 , 3 , 5523\n+X , 155270560 , 24853 , 6247\n+Y , 59373566 , 2769 , 21442\n+\n+# Effects by impact\n+\n+Type , Count , Percent \n+HIGH , 1367 , 0.024855% \n+LOW , 2178258 , 39.605454% \n+MODERATE , 3322 , 0.060401% \n+MODIFIER , 3316947 , 60.30929% \n+\n+# Effects by functional class\n+\n+Type , Count , Percent \n+\n+Missense_Silent_ratio, ?\n+\n+# Count by effects\n+\n+Type , Count , Percent \n+3_prime_UTR_variant , 15811 , 0.287478% \n+5_prime_UTR_truncation+exon_loss_variant , 2 , 0.000036% \n+5_prime_UTR_variant , 3350 , 0.06091% \n+TF_binding_site_variant , 986 , 0.017928% \n+disruptive_inframe_deletion , 408 , 0.00741'..b'+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\n+MT,Count,0,0,0,2,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0\n+\n+X, 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\n+X,Count,1053,986,644,282,170,296,159,83,204,207,64,72,234,178,111,238,97,119,153,70,71,87,166,242,165,92,22,90,69,194,145,154,158,158,111,198,95,68,162,139,256,108,105,124,176,126,222,219,192,89,133,97,73,196,112,145,223,103,34,0,0,33,38,48,62,98,95,178,143,166,145,146,103,145,139,143,141,145,162,168,131,68,147,159,127,170,263,174,242,119,147,167,161,154,109,167,172,147,83,207,210,77,170,177,187,65,140,70,112,86,98,100,181,143,159,163,119,136,315,179,92,204,186,195,215,159,133,186,185,116,106,118,170,96,144,191,165,135,158,205,134,222,128,283,189,146,140,146,148,145,251,129,140,137,113,205\n+\n+Y, 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\n+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\n+\n' |
| b |
| 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 |
| b |
| @@ -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 + |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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% |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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. |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -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 |
| b |
| 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 |
| b |
| @@ -0,0 +1,2 @@ +Sample input_reads surviving_pct dropped surviving dropped_pct +C2 39733090.0 82.02 7142532.0 32590558.0 17.98 |
| b |
| 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 |
| b |
| b'@@ -0,0 +1,1000 @@\n+QUAL_THRESHOLD\tN_Ts_LT_QUAL_THRESHOLD\tN_Tv_LT_QUAL_THRESHOLD\tTs/Tv_LT_QUAL_THRESHOLD\tN_Ts_GT_QUAL_THRESHOLD\tN_Tv_GT_QUAL_THRESHOLD\tTs/Tv_GT_QUAL_THRESHOLD\n+3.01037\t0\t0\t-nan\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01039\t1\t0\tinf\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01041\t2\t0\tinf\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01042\t3\t0\tinf\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01046\t3\t1\t3\t1.5337e+07\t6.70583e+06\t2.28711\n+3.0105\t4\t1\t4\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01051\t4\t2\t2\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01056\t4\t3\t1.33333\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01058\t6\t3\t2\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01061\t7\t3\t2.33333\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01064\t8\t3\t2.66667\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01067\t9\t3\t3\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01069\t10\t3\t3.33333\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01071\t11\t3\t3.66667\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01087\t12\t3\t4\t1.5337e+07\t6.70583e+06\t2.28711\n+3.0109\t14\t3\t4.66667\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01094\t14\t4\t3.5\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01105\t15\t4\t3.75\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01108\t16\t5\t3.2\t1.5337e+07\t6.70583e+06\t2.28711\n+3.0111\t17\t6\t2.83333\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01113\t18\t6\t3\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01114\t19\t6\t3.16667\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01117\t20\t6\t3.33333\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01119\t21\t6\t3.5\t1.5337e+07\t6.70583e+06\t2.28711\n+3.0112\t23\t6\t3.83333\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01127\t23\t7\t3.28571\t1.5337e+07\t6.70583e+06\t2.28711\n+3.01129\t24\t8\t3\t1.5337e+07\t6.70582e+06\t2.28711\n+3.0113\t25\t9\t2.77778\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01131\t26\t9\t2.88889\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01133\t27\t9\t3\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01134\t28\t10\t2.8\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01135\t31\t10\t3.1\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01136\t35\t11\t3.18182\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01137\t37\t14\t2.64286\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01138\t40\t16\t2.5\t1.5337e+07\t6.70582e+06\t2.28711\n+3.01139\t46\t17\t2.70588\t1.53369e+07\t6.70581e+06\t2.28711\n+3.0114\t51\t20\t2.55\t1.53369e+07\t6.70581e+06\t2.28711\n+3.01141\t53\t23\t2.30435\t1.53369e+07\t6.70581e+06\t2.28711\n+3.01142\t59\t26\t2.26923\t1.53369e+07\t6.70581e+06\t2.28711\n+3.01143\t62\t28\t2.21429\t1.53369e+07\t6.7058e+06\t2.28711\n+3.01144\t66\t31\t2.12903\t1.53369e+07\t6.7058e+06\t2.28711\n+3.01145\t70\t32\t2.1875\t1.53369e+07\t6.7058e+06\t2.28711\n+3.01146\t73\t35\t2.08571\t1.53369e+07\t6.7058e+06\t2.28711\n+3.01147\t77\t35\t2.2\t1.53369e+07\t6.7058e+06\t2.28711\n+3.01148\t77\t36\t2.13889\t1.53369e+07\t6.7058e+06\t2.28711\n+3.01149\t81\t38\t2.13158\t1.53369e+07\t6.70579e+06\t2.28711\n+3.0115\t81\t41\t1.97561\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01151\t83\t42\t1.97619\t1.53369e+07\t6.70579e+06\t2.28712\n+3.01152\t83\t44\t1.88636\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01153\t84\t44\t1.90909\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01154\t86\t44\t1.95455\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01158\t88\t45\t1.95556\t1.53369e+07\t6.70579e+06\t2.28712\n+3.01159\t88\t47\t1.87234\t1.53369e+07\t6.70579e+06\t2.28712\n+3.0116\t89\t47\t1.89362\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01161\t90\t47\t1.91489\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01165\t91\t47\t1.93617\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01166\t93\t47\t1.97872\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01167\t93\t48\t1.9375\t1.53369e+07\t6.70579e+06\t2.28711\n+3.01171\t94\t48\t1.95833\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01172\t97\t49\t1.97959\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01173\t97\t50\t1.94\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01174\t99\t50\t1.98\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01179\t100\t50\t2\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01182\t100\t51\t1.96078\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01184\t102\t51\t2\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01188\t103\t51\t2.01961\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01193\t104\t51\t2.03922\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01194\t105\t52\t2.01923\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01195\t105\t53\t1.98113\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01198\t106\t53\t2\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01199\t107\t53\t2.01887\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01203\t108\t53\t2.03774\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01205\t109\t53\t2.0566\t1.53369e+07\t6.70578e+06\t2.28711\n+3.01207\t110\t54\t2.0'..b'1022\t2.70841\t1.53342e+07\t6.70481e+06\t2.28705\n+3.0295\t2769\t1022\t2.70939\t1.53342e+07\t6.70481e+06\t2.28705\n+3.02951\t2770\t1022\t2.71037\t1.53342e+07\t6.70481e+06\t2.28705\n+3.02952\t2772\t1022\t2.71233\t1.53342e+07\t6.70481e+06\t2.28705\n+3.02953\t2773\t1022\t2.71331\t1.53342e+07\t6.70481e+06\t2.28705\n+3.02957\t2774\t1022\t2.71429\t1.53342e+07\t6.70481e+06\t2.28705\n+3.02958\t2774\t1023\t2.71163\t1.53342e+07\t6.70481e+06\t2.28705\n+3.02962\t2774\t1024\t2.70898\t1.53342e+07\t6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|