| Previous changeset 1:38c9f9a680f0 (2019-09-30) Next changeset 3:1544278c272e (2021-04-27) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8" |
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modified:
macros.xml macros_process.xml stacks_kmerfilter.xml test-data/clonefilter/Removed1_0001.1.1.fq.gz test-data/clonefilter/Removed1_0001.1.1.fq.single.gz test-data/cstacks/catalog.alleles.tsv test-data/cstacks/catalog.snps.tsv test-data/cstacks/catalog.tags.tsv test-data/denovo_map/denovo_map.log test-data/gentest.sh test-data/gstacks/catalog.calls.vcf test-data/gstacks/catalog.fa.gz test-data/gstacks/gstacks.log test-data/gstacks/gstacks.log.distribs test-data/kmerfilter/kfreq.tsv test-data/kmerfilter/kfreqdist.tsv test-data/populations/populations.log test-data/populations/populations.phistats_summary.tsv test-data/refmap/catalog.calls.vcf test-data/refmap/catalog.fa.gz test-data/shortreads/PopA_01.forward.fq.gz test-data/shortreads/PopA_01.reverse.fq.gz test-data/shortreads/process_shortreads.out test-data/sstacks/PopA_01.matches.tsv test-data/sstacks/PopA_02.matches.tsv test-data/tsv2bam/tsv2bam.log test-data/ustacks/PopA_01.alleles.tsv test-data/ustacks/PopA_01.snps.tsv test-data/ustacks/PopA_01.tags.tsv test-data/ustacks/PopA_02.alleles.tsv test-data/ustacks/PopA_02.snps.tsv test-data/ustacks/PopA_02.tags.tsv |
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added:
check_bcfile.py test-data/clonefilter/Discarded1_0001.1.1.fq.gz test-data/clonefilter/Discarded1_0001.1.1.fq.single.gz test-data/clonefilter/Removed1_0001.1.1.fq.single-alt.gz test-data/denovo_map/popmap_cstacks_genotypes.tsv test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz test-data/populations/populations.CP.joinmap.loc test-data/procrad/barcodes-duplicate test-data/procrad/barcodes-duplicate2 test-data/procrad/barcodes-duplicate3 |
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removed:
test-data/stacks_outputs/catalog.calls test-data/stacks_outputs/tsv2bam.log |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf check_bcfile.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/check_bcfile.py Thu Jul 16 07:28:45 2020 -0400 |
| [ |
| @@ -0,0 +1,45 @@ +#!/usr/bin/env python + +import argparse +import sys + +parser = argparse.ArgumentParser() +parser.add_argument('bcfile', help='barcode file') +args = parser.parse_args() + +barcodes = [] + +with open(args.bcfile, "r") as fh: + for line in fh: + if len(line) == 0: + continue + if line.startswith("#"): + continue + barcodes.append(line.split()) + +if len(barcodes) <= 1: + sys.exit("barcode file is empty") + +# check that all lines have the same number of columns +ncol = None +for bc in barcodes: + if ncol is None: + ncol = len(bc) + elif ncol != len(bc): + sys.exit("barcode file has inconsistent number of columns") + +isname = False +for bc in barcodes: + if len(bc[-1].strip("ATCGatcg")) > 0: + isname = True + break + +names = set() +for bc in barcodes: + if isname: + n = bc[-1] + else: + n = '-'.join(bc) + if n in names: + sys.exit("duplicate sample %s in barcode file" % n) + names.add(n) |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf macros.xml --- a/macros.xml Mon Sep 30 14:18:47 2019 -0400 +++ b/macros.xml Thu Jul 16 07:28:45 2020 -0400 |
| [ |
| b'@@ -3,12 +3,14 @@\n <xml name="requirements">\n <requirements>\n <requirement type="package" version="@STACKS_VERSION@">stacks</requirement>\n+ <requirement type="package" version="3.7">python</requirement>\n+ <requirement type="package" version="4.6.0">findutils</requirement>\n <yield/>\n </requirements>\n </xml>\n \n- <token name="@STACKS_VERSION@">2.4</token>\n- <token name="@WRAPPER_VERSION@">1</token>\n+ <token name="@STACKS_VERSION@">2.53</token>\n+ <token name="@WRAPPER_VERSION@">0</token>\n <!-- fix to 18.01 since https://github.com/galaxyproject/galaxy/pull/7032 -->\n <token name="@PROFILE@">18.01</token>\n \n@@ -107,16 +109,11 @@\n <!-- log file handling -->\n <token name="@TEE_APPEND_LOG@"><![CDATA[\n #if $output_log\n- 2>> \'$output_log\' &&\n- #end if\n- ]]></token>\n- <token name="@CAT_LOG_TO_STDERR@"><![CDATA[\n- #if $output_log\n- cat \'$output_log\' 2>&1\n+ 2> \'$output_log\'\n #end if\n ]]></token>\n <xml name="in_log">\n- <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset" />\n+ <param name="add_log" type="boolean" checked="true" truevalue="yes" falsevalue="no" label="Add log output as dataset"/>\n </xml>\n <xml name="out_log">\n <data format="txt" name="output_log" label="${tool.name} on ${on_string} log file">\n@@ -126,19 +123,19 @@\n \n <!-- inputs from previous pipeline steps -->\n <xml name="input_stacks_macro">\n- <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks" />\n+ <param name="input_stacks" format="tabular,txt" type="data_collection" collection_type="list" label="Loci and polymorphism" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or ustacks"/>\n </xml>\n <xml name="input_cat_macro">\n- <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks" />\n+ <param name="input_cat" format="tabular,txt" type="data_collection" collection_type="list" label="Catalog of loci" help="output from a previous Stacks pipeline steps e.g. denovo_map, refmap or cstacks"/>\n </xml>\n <xml name="input_matches_macro">\n- <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks" />\n+ <param name="input_matches" format="tabular,txt" type="data_collection" collection_type="list" label="Matches to the catalog" help="output from previous Stacks pipeline steps e.g. denovo_map, refmap or sstacks"/>\n </xml>\n <xml name="bam_input_macro">\n- <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference" />\n+ <param name="input_bam" format="bam" type="data" multiple="true" optional="false" label="Aligned data" help="either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference"/>\n </xml>\n <xml name="input_aln_macro">\n- <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argument="-P" />\n+ <param name="input_aln" format="vcf,fasta.gz" type="data_collection" collection_type="list" label="Assembled contigs and variant sites" help="output from previous Stacks pipeline steps (e.g. gstacks, denovo_map, or refmap)" argume'..b'ring} Population-level summary statistics" from_work_dir="stacks_outputs/populations.sumstats.tsv"/>\n </xml>\n \n <xml name="populations_output_full">\n <expand macro="populations_output_light"/>\n \n+ <data format="txt" name="out_sql" label="${tool.name} @TOOLADD@ on ${on_string} Genotyping markers" from_work_dir="stacks_outputs/populations.sql.tsv">\n+ <filter>genetic_map_options[\'map_type\'] and genetic_map_options[\'map_format\']</filter>\n+ </data>\n+\n <!-- log_fst_comp populations.fst_summary.tsv populations.phistats_summary.tsv populations.phistats.tsv-->\n <data format="tabular" name="out_phistats" label="${tool.name} on ${on_string} Phi_st statistics" from_work_dir="stacks_outputs/populations.phistats.tsv">\n <filter>advanced_options[\'log_fst_comp\'] and fstats_conditional[\'fstats\']==\'yes\'</filter>\n@@ -533,6 +533,26 @@\n </data>\n </xml>\n \n+ <!-- fastq output for kmer/clone-filter -->\n+ <xml name="fastq_output_filter">\n+ <data name="clean" format_source="fqinputs" label="${tool.name} on ${on_string}">\n+ <filter>input_type[\'input_type_select\'] == \'single\'</filter>\n+ <yield/>\n+ </data>\n+ <collection name="clean_pair" type="paired" format_source="fqinputs" label="${tool.name} on ${on_string}">\n+ <filter>input_type[\'input_type_select\'] == \'paired\'</filter>\n+ <yield/>\n+ </collection>\n+ <data name="discarded" format_source="fqinputs" label="${tool.name} on ${on_string}: discarded reads">\n+ <filter>capture and input_type[\'input_type_select\'] == \'single\'</filter>\n+ <yield/>\n+ </data>\n+ <collection name="discarded_pair" format_source="fqinputs" type="paired" label="${tool.name} on ${on_string}: discarded reads">\n+ <filter>capture and input_type[\'input_type_select\'] == \'paired\'</filter>\n+ <yield/>\n+ </collection>\n+ </xml>\n+\n <xml name="snp_options_alpha">\n <param argument="--alpha" type="select" label="Chi square significance level required to call a heterozygote or homozygote" >\n <option value="0.1">0.1</option>\n@@ -554,7 +574,7 @@\n </when>\n <when value="bounded">\n <param argument="--bound_low" type="float" value="0.0" min="0.0" max="1.0" label="Lower bound for epsilon, the error rate" help="between 0 and 1.0"/>\n- <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0" />\n+ <param argument="--bound_high" type="float" value="1.0" min="0.0" max="1.0" label="Upper bound for epsilon, the error rate" help="between 0 and 1.0"/>\n <expand macro="snp_options_alpha"/>\n </when>\n <when value="fixed">\n@@ -574,8 +594,8 @@\n "Error: No value was provided for \\-\\-var-alpha and there is no default for this model)"\n \t-->\n <xml name="variant_calling_options_vg" token_varalpha_default="">\n- <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available." />\n- <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes" />\n+ <param argument="--var-alpha" name="var_alpha" type="float" value="@VARALPHA_DEFAULT@" min="0" label="Alpha threshold for discovering SNPs" help="Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available."/>\n+ <param argument="--gt-alpha" name="gt_alpha" type="float" value="0.05" min="0" label="Alpha threshold for calling genotypes"/>\n </xml>\n \n <xml name="barcode_encoding_single" token_type="">\n' |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf macros_process.xml --- a/macros_process.xml Mon Sep 30 14:18:47 2019 -0400 +++ b/macros_process.xml Thu Jul 16 07:28:45 2020 -0400 |
| [ |
| @@ -29,12 +29,12 @@ <xml name="discover_faqgz_output_macro" token_pattern="" token_dir=""> <expand macro="discover_faq_output_macro" pattern="@PATTERN@" dir="@DIR@"/> - <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/" /> - <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/" /> + <discover_datasets pattern="@PATTERN@\.fq\.gz$" ext="fastqsanger.gz" directory="@DIR@/"/> + <discover_datasets pattern="@PATTERN@\.fa\.gz$" ext="fasta.gz" directory="@DIR@/"/> </xml> <xml name="discover_faq_output_macro" token_pattern="" token_dir=""> - <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/" /> - <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/" /> + <discover_datasets pattern="@PATTERN@\.fq$" ext="fastqsanger" directory="@DIR@/"/> + <discover_datasets pattern="@PATTERN@\.fa$" ext="fasta" directory="@DIR@/"/> </xml> <xml name="process_outputs"> @@ -71,17 +71,17 @@ <option value="no" selected="true">No</option> </param> <when value="yes"> - <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1" /> - <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded" /> - <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base" /> + <param name="sliding" type="float" value="0.15" min="0" max="1" argument="-w" label="Set the size of the sliding window as a fraction of the read length, between 0 and 1"/> + <param name="score" type="integer" value="10" min="0" max="40" argument="-s" label="Set the score limit. If the average score within the sliding window drops below this value, the read is discarded"/> + <param name="remove" type="boolean" checked="false" truevalue="-c" falsevalue="" argument="-c" label="Clean data, remove any read with an uncalled base"/> <param name="discard" type="boolean" checked="false" truevalue="-q" falsevalue="" argument="-q" label="Discard reads with low quality scores"/> - <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing" /> + <param argument="--filter-illumina" name="filter_illumina" type="boolean" checked="false" truevalue="--filter-illumina" falsevalue="" label="Discard reads that have been marked by Illumina's chastity/purity filter as failing"/> </when> <when value="no"> <param argument="--len_limit" type="integer" value="" optional="true" label="Minimum sequence length" help="useful if your data has already been trimmed"/> </when> </conditional> - <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" /> + <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/> </xml> <token name="@PROCESS_FILTER@"><![CDATA[ #if $filter_cond.filter_select == 'yes': @@ -104,30 +104,30 @@ ## fix the _R[12]_0 that was added for preparing the input #if $input_type.input_type_select == 'paired': - && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done + && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/_R1_0/.1/; s/_R2_0/.2/;')"; done) #end if ## also remove the gz which is added by procrad (but its uncompressed) - && find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done + && (find stacks_outputs/discarded/ -type f -iname "*.gz.discards" | while read file; do mv "\$file" "\$(echo \$file | sed 's/.gz.discards$/.discards/;')"; done) ## the discard files are named fastq even if the output is fasta #if str($outype).endswith("fasta"): - && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done + && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fa/;')"; done) #else - && find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done + && (find stacks_outputs/discarded/ -type f | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.fastq.discards/.fq/;')"; done) #end if #end if ## prepare paired read output for processing in galaxy #if $input_type.input_type_select == 'paired': && mkdir stacks_outputs/remaining - && find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done - && find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done + && (find stacks_outputs -iregex ".*\.rem\.[12]\.f[aq]\(\.gz\)?" | while read file; do mv "\$file" stacks_outputs/remaining/; done) + && (find stacks_outputs/ -iregex ".*.f[aq]\(\.gz\)?" | while read file; do mv "\$file" "\$(echo \$file | sed 's/\.1\./.forward./; s/\.2\./.reverse./')"; done) #end if ]]></token> <!-- adapter trimming options --> <xml name="process_adapter"> - <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read" /> - <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read" /> + <param argument="--adapter_1" type="text" value="" optional="true" label="Adaptor sequence that may occur on the first read"/> + <param argument="--adapter_2" type="text" value="" optional="true" label="Adaptor sequence that may occur on the paired-read"/> <param argument="--adapter_mm" type="integer" value="" optional="true" label="Number of mismatches allowed in the adapter sequence"/> </xml> <token name="@PROCESS_ADAPTER@"><![CDATA[ @@ -171,8 +171,8 @@ <!-- advanced options that are shared --> <xml name="common_advanced"> - <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value" /> - <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output" /> + <param name="truncate" type="integer" value="" optional="True" argument="-t" label="Truncate final read length to this value"/> + <param argument="--retain_header" type="boolean" checked="false" truevalue="--retain_header" falsevalue="" label="Retain unmodified FASTQ headers in the output"/> </xml> <token name="@COMMON_ADVANCED@"><![CDATA[ #if str($options_advanced.truncate) @@ -181,3 +181,4 @@ $options_advanced.retain_header ]]></token> </macros> + |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf stacks_kmerfilter.xml --- a/stacks_kmerfilter.xml Mon Sep 30 14:18:47 2019 -0400 +++ b/stacks_kmerfilter.xml Thu Jul 16 07:28:45 2020 -0400 |
| [ |
| b'@@ -7,7 +7,7 @@\n <expand macro="version_cmd"/>\n <command detect_errors="aggressive"><![CDATA[\n @FASTQ_INPUT_FUNCTIONS@\n-\n+trap ">&2 cat \'$output_log\'" err exit &&\n mkdir stacks_inputs stacks_outputs &&\n \n #set ($link_command, $fwd_path, $rev_path, $inputype) = $fastq_input_batch($input_type.fqinputs, $input_type.input_type_select)\n@@ -39,152 +39,156 @@\n --normalize $options_normalization.normalize\n #end if\n #if $options_kmer_char.write_k_freq\n- --read_k_freq $kfreq\n+ --write-k-freq $kfreqdist\n #end if\n+## TODO read_k_freq\n $options_kmer_char.k_dist\n #if $options_kmer_char.k_dist\n- | sed \'s/KmerFrequency/# KmerFrequency/\' > $kfreqdist\n+ > \'$kfreq\'\n #end if\n @TEE_APPEND_LOG@\n-@CAT_LOG_TO_STDERR@\n \n-## move outputs such that Galaxy can find them\n-## if filtering is on then ...filt...fq is created\n-## if normalization is on then ...norm...fq is created\n-## if both are active then both files are created, but only norm is needed\n-#if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="":\n- #if str($options_normalization.normalize)!="":\n- #set infix="norm"\n- #else\n- #set infix="fil"\n- #end if\n- #if $capture:\n+#if $options_kmer_char.k_dist \n+ && sed -i -e \'s/KmerFrequency/# KmerFrequency/\' \'$kfreq\'\n+#elif $options_kmer_char.write_k_freq\n+ && sed -i -e \'s/# Kmer Count/#Kmer\\tCount/; s/ /\\t/\' \'$kfreqdist\';\n+#else\n+ ## move outputs such that Galaxy can find them\n+ ## if filtering is on then ...filt...fq is created\n+ ## if normalization is on then ...norm...fq is created\n+ ## if both are active then both files are created, but only norm is needed\n+ #if str($options_filtering.rare)!="" or str($options_filtering.abundant)!="" or str($options_normalization.normalize)!="":\n+ #if str($options_normalization.normalize)!="":\n+ #set infix="norm"\n+ #else\n+ #set infix="fil"\n+ #end if\n+ #if $capture:\n+ #if $input_type.input_type_select == "single"\n+ && mv stacks_outputs/*.discards.fastq \'$discarded\'\n+ #else\n+ && mv stacks_outputs/*.1.discards.fastq \'$discarded_pair.forward\'\n+ && mv stacks_outputs/*.2.discards.fastq \'$discarded_pair.reverse\'\n+ #end if\n+ #end if\n #if $input_type.input_type_select == "single"\n- && mv stacks_outputs/*.discards.fastq \'$discarded\'\n+ && mv stacks_outputs/*.${infix}.fastq \'$clean\'\n #else\n- && mv stacks_outputs/*.1.discards.fastq \'$discarded_pair.forward\'\n- && mv stacks_outputs/*.2.discards.fastq \'$discarded_pair.reverse\'\n+ && mv stacks_outputs/*.1.${infix}.fastq \'$clean_pair.forward\'\n+ && mv stacks_outputs/*.2.${infix}.fastq \'$clean_pair.reverse\'\n #end if\n #end if\n- #if $input_type.input_type_select == "single"\n- && mv stacks_outputs/*.${infix}.fastq \'$clean\'\n- #else\n- && mv stacks_outputs/*.1.${infix}.fastq \'$clean_pair.forward\'\n- && mv stacks_outputs/*.2.${infix}.fastq \'$clean_pair.reverse\'\n- #end if\n #end if\n-\n ]]></command>\n <inputs>\n <expand macro="fastq_input_bc"/>\n- <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file" />\n+ <param name="capture" type="boolean" checked="false" truevalue="-D" falsevalue="" argument="-D" label="Capture discarded reads to a file"/>\n <section name="options_filtering" title="Filtering options" expanded="False">\n- <param argument="--rare" type="boolean" checked="false" truevalue="--rare" falsevalue="" label="Turn on filtering based on rare k-mers" />\n- <param argument="--abundant" type="boolean" checked="false" truevalue="--abundant" falsevalue="" label="Turn on filtering based on abundant k-mers" />\n- <param argument="--k_len" type="integer" value="15'..b'"/>\n </collection>\n </param>\n </conditional>\n- <param name="capture" value="-D" />\n- <param name="normalize" value="1" />\n+ <param name="capture" value="-D"/>\n+ <param name="normalize" value="1"/>\n <assert_command>\n- <has_text text="--normalize 1" />\n+ <has_text text="--normalize 1"/>\n </assert_command>\n+ <param name="add_log" value="yes"/>\n+ <output name="output_log"><assert_contents><has_text text="8 retained reads."/></assert_contents></output>\n <output_collection name="clean_pair" type="paired">\n- <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />\n- <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />\n+ <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed1_0001.1.1.fq.gz"/>\n+ <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Removed2_0001.2.2.fq.gz"/>\n </output_collection>\n <output_collection name="discarded_pair" type="paired">\n- <element name="forward" compare="sim_size" file="clonefilter/Removed1_0001.1.1.fq.gz" />\n- <element name="reverse" compare="sim_size" file="clonefilter/Removed2_0001.2.2.fq.gz" />\n+ <element name="forward" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Discarded1_0001.1.1.fq.gz"/>\n+ <element name="reverse" compare="sim_size" delta_frac="0.01" ftype="fastqsanger.gz" file="kmerfilter/Discarded2_0001.2.2.fq.gz"/>\n </output_collection>\n </test>\n <!-- kfreq output -->\n- <test>\n+ <test expect_num_outputs="2">\n <conditional name="input_type">\n- <param name="input_type_select" value="single" />\n- <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />\n+ <param name="input_type_select" value="single"/>\n+ <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>\n </conditional>\n <section name="options_kmer_char">\n- <param name="write_k_freq" value="--write_k_freq" />\n+ <param name="write_k_freq" value="--write_k_freq"/>\n </section>\n- <output name="kfreq" file="kmerfilter/kfreq.tsv"/>\n+ <param name="add_log" value="yes"/>\n+ <output name="output_log"><assert_contents><has_text text="done."/></assert_contents></output>\n+ <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/>\n </test>\n <!-- kfreqdist output -->\n- <test>\n+ <test expect_num_outputs="1">\n <conditional name="input_type">\n- <param name="input_type_select" value="single" />\n- <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz" />\n+ <param name="input_type_select" value="single"/>\n+ <param name="fqinputs" ftype="fastqsanger.gz" value="clonefilter/R1_0001.1.fq.gz"/>\n </conditional>\n <section name="options_kmer_char">\n- <param name="k_dist" value="--k_dist" />\n+ <param name="k_dist" value="--k_dist"/>\n </section>\n- <output name="kfreqdist" file="kmerfilter/kfreqdist.tsv"/>\n+ <param name="add_log" value="no"/>\n+ <assert_stderr><has_text text="Generating kmer distribution..."/></assert_stderr>\n+ <output name="kfreq" file="kmerfilter/kfreq.tsv"/>\n </test>\n </tests>\n <help>\n@@ -196,5 +200,5 @@\n @STACKS_INFOS@\n ]]>\n </help>\n- <expand macro="citation" />\n+ <expand macro="citation"/>\n </tool>\n' |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/cstacks/catalog.alleles.tsv --- a/test-data/cstacks/catalog.alleles.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/cstacks/catalog.alleles.tsv Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -1,3 +1,4 @@ -# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45 +# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 0 1 AC 0 0 0 1 CA 0 0 +# cstacks completed on 2020-03-16 15:39:40 |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/cstacks/catalog.snps.tsv --- a/test-data/cstacks/catalog.snps.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/cstacks/catalog.snps.tsv Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -1,3 +1,4 @@ -# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45 +# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 0 1 33 E 0 A C - - 0 1 88 E 0 A C - - +# cstacks completed on 2020-03-16 15:39:40 |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/cstacks/catalog.tags.tsv --- a/test-data/cstacks/catalog.tags.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/cstacks/catalog.tags.tsv Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -1,4 +1,5 @@ -# cstacks version 2.4; catalog generated on 2019-06-18 10:34:45 +# cstacks version 2.52; catalog generated on 2020-03-16 15:39:40 0 1 consensus 0 1_1,2_1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 0 2 consensus 0 1_2,2_2 AATTCGGCTTGCAACGCAAGTGACGATTCCCACGGACATAACTGATCTAAGTAACTTCCAAATCTGGGAATGGGATTTCATAATTAAGGACTAT 0 0 0 0 3 consensus 0 1_3,2_3 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 0 0 0 +# cstacks completed on 2020-03-16 15:39:40 |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/denovo_map/denovo_map.log --- a/test-data/denovo_map/denovo_map.log Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/denovo_map/denovo_map.log Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -1,5 +1,5 @@ -denovo_map.pl version 2.4 started at 2019-06-18 10:34:45 -/home/berntm/miniconda3/envs/mulled-v1-2b57e7596f85ebb3b321e6c9681e8fd9250523a80d97945c46ac7743359454e7/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired +denovo_map.pl version 2.52 started at 2020-03-16 15:39:40 +/home/berntm/miniconda3/envs/__stacks@2.52/bin/denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired ustacks ========== @@ -110,7 +110,7 @@ cstacks ========== -cstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv +cstacks -M denovo_map/popmap_cstacks.tsv -P stacks_outputs cstacks parameters selected: Loci matched based on sequence identity. @@ -279,8 +279,7 @@ Working on 1 group(s) of populations: defaultgrp: 1 -Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv' -Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' +Raw haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv' Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv' @@ -306,4 +305,4 @@ Populations is done. denovo_map.pl is done. -denovo_map.pl completed at 2019-06-18 10:34:45 +denovo_map.pl completed at 2020-03-16 15:39:40 |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/denovo_map/popmap_cstacks_genotypes.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/denovo_map/popmap_cstacks_genotypes.tsv Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -0,0 +1,2 @@ +PopA_01 parent +PopA_02 progeny |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/gentest.sh --- a/test-data/gentest.sh Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/gentest.sh Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -1,7 +1,11 @@ #!/usr/bin/env bash +eval "$(conda shell.bash hook)" +conda activate __stacks@2.52 + + + mkdir stacks_outputs - denovo_map.pl --samples demultiplexed --popmap denovo_map/popmap_cstacks.tsv -o stacks_outputs --paired && gunzip -c stacks_outputs/catalog.calls > stacks_outputs/catalog.calls.vcf rm stacks_outputs/catalog.calls |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/gstacks/catalog.calls.vcf --- a/test-data/gstacks/catalog.calls.vcf Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/gstacks/catalog.calls.vcf Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20190618 -##source="Stacks v2.4" +##fileDate=20200316 +##source="Stacks v2.52" ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/gstacks/catalog.fa.gz |
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| Binary file test-data/gstacks/catalog.fa.gz has changed |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/gstacks/gstacks.log --- a/test-data/gstacks/gstacks.log Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/gstacks/gstacks.log Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -1,4 +1,4 @@ -gstacks v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11) +gstacks v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) gstacks -P stacks_outputs -M denovo_map/popmap_cstacks.tsv Locus/sample distributions will be written to 'stacks_outputs/gstacks.log.distribs'. |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/gstacks/gstacks.log.distribs --- a/test-data/gstacks/gstacks.log.distribs Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/gstacks/gstacks.log.distribs Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -19,25 +19,25 @@ Num. threads: 1 Parallel time: 0.0 Average thread time spent: - 0.0 reading (3.1%) - 0.0 processing (95.2%) - 0.0 pre-alignments block (72.2%) - 0.0 reformatting fw-reads (0.1%) - 0.0 assembling (22.2%) - 0.0 initializing alignments (5.4%) - 0.0 aligning (42.9%) - 0.0 merging read pairs (1.5%) - 0.0 post-alignments block (21.2%) + 0.0 reading (3.0%) + 0.0 processing (95.7%) + 0.0 pre-alignments block (74.4%) + 0.0 reformatting fw-reads (0.2%) + 0.0 assembling (27.3%) + 0.0 initializing alignments (8.7%) + 0.0 aligning (36.6%) + 0.0 merging read pairs (1.6%) + 0.0 post-alignments block (19.8%) 0.0 filtering reads (0.0%) - 0.0 counting nucleotides (3.5%) - 0.0 genotyping (1.9%) - 0.0 haplotyping (1.0%) + 0.0 counting nucleotides (3.2%) + 0.0 genotyping (1.5%) + 0.0 haplotyping (0.9%) 0.0 computing consensus (0.1%) 0.0 building_fa (0.1%) - 0.0 building_vcf (14.6%) - 0.0 writing_fa (0.1%) - 0.0 writing_vcf (1.3%) - 0.0 clocking (0.2%) -Total time spent writing vcf: 0.0 (1.3%) + 0.0 building_vcf (14.0%) + 0.0 writing_fa (0.0%) + 0.0 writing_vcf (0.9%) + 0.0 clocking (0.1%) +Total time spent writing vcf: 0.0 (0.8%) VCFwrite block size: mean=1.0(n=3); max=1 END clockings |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kmerfilter/Removed1_0001.1.1.fq.single.gz Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -0,0 +1,20 @@ +@K00392:16:HJ2G2BBXX:7:1102:10825:462401 1:N:0:ATCACG +GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC ++ +--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<- +@K00392:16:HJ2G2BBXX:7:1102:10825:46240 1:N:0:ATCACG +GGACATTGGCTGCAGTACTCTGACCCTGGCCACCTCAACCTGTCTCTCTCGCACCGGAAACCTCCGATCCGCAGAAACATGAGCAACCCTACAGTTGACACACACAACAGTTTTCGACCGAAACTACACATTCCTCTGTCCCATTTCCTC ++ +--A-FF-F-<A<-FAF7AAF--F--FF-A<-JJFJFFFF-<<-7--<FFF--77<7-77-<---7-7<-7-AA--<<-7<----<-A-FJFF-7A-F--7FF-<7A-A-<7F7---7-7-77-<7<<A--<J7--<-)-7)-7---7F<- +@K00392:16:HJ2G2BBXX:8:1201:4929:9367 1:N:0:ATCACG +GGATTGAGGATGCAGCAACGTTCTAACATCTAGTGGAAAGCCTTCCCAGAAGAGTGGAGGCTGTTATAGCAGCAAAGGGGGGACCAACTCCATATTATTGCCCATGACTTTTGAATGAGATGTTTGACGAGCAGGGGTCGACATACTTTT ++ +AAAFFJJJJJJJFJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFAJAJFFJFJJFJFJ7FJAJJJAFFJJJJJJAJAFFFFA<JJJAJJFAFJA7<AFAFFA7F7F<-77<F<--7-7-))---)AFF-<A-7FA +@K00392:16:HJ2G2BBXX:7:1104:19268:28727 1:N:0:ATCACG +ATGCCGCGGCCCTTGCAGAGCAAGGGGAACCACTACTTCAACTCAAGGTCTCAAAGCGAGTGACGTAACTGATTGAAACGCTATTAGCGCGCACCACCGCTAACTAGCTATCCATTTCACATCCGTTACATATGTATGTATGTACACACA ++ +AAFFFJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJFJJJFJJJJJJJJJJJJJFFJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJFAFJJJJJJJJ +@K00392:16:HJ2G2BBXX:8:2125:3011:15574 1:N:0:ATCACG +TCAGAAGAAAAACCCACAAAATAGAACCGGAGTCCTATTCCATTATTCCTAGCTGCGGTATTCAGGCGACCGGGCCTGCTTTGAACACTCTAATTTTTTCAAAGTAAACGCTTCGGACCCCGCGGGCCACTCAGTTAAGAGCATCGAGGG ++ +AAFFFJJJJJJJJFJFJFJFJJJJFJJJJJ<J-7FJFAJJJJJJJJAJJFJAJJJJJJJJFJJFAAFAJJJJJFJJJJJFAJJJJJFFJJ<J-FFAJJJF-J<7-7<<A<---AF<7JJJJ-A)77-7--)F-7----<--7A7A<--7- |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/kmerfilter/kfreq.tsv --- a/test-data/kmerfilter/kfreq.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/kmerfilter/kfreq.tsv Thu Jul 16 07:28:45 2020 -0400 |
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| @@ -0,0 +1,3 @@ +# KmerFrequency Count +1 408 +2 136 |
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| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/kmerfilter/kfreqdist.tsv --- a/test-data/kmerfilter/kfreqdist.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/kmerfilter/kfreqdist.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| b'@@ -1,3 +1,545 @@\n-# KmerFrequency\tCount\n-1\t408\n-2\t136\n+#\tKmer\tCount\n+TAAGAGCATCGAGGG\t1\n+CTCAGTTAAGAGCAT\t1\n+ACTCAGTTAAGAGCA\t1\n+CCACTCAGTTAAGAG\t1\n+GCCACTCAGTTAAGA\t1\n+GGCCACTCAGTTAAG\t1\n+GGGCCACTCAGTTAA\t1\n+CCGCGGGCCACTCAG\t1\n+CCCGCGGGCCACTCA\t1\n+CCCCGCGGGCCACTC\t1\n+TTCGGACCCCGCGGG\t1\n+GCTTCGGACCCCGCG\t1\n+CGCTTCGGACCCCGC\t1\n+AACGCTTCGGACCCC\t1\n+GTAAACGCTTCGGAC\t1\n+AGTAAACGCTTCGGA\t1\n+AAGTAAACGCTTCGG\t1\n+AAAGTAAACGCTTCG\t1\n+CAAAGTAAACGCTTC\t1\n+TCAAAGTAAACGCTT\t1\n+TTTTCAAAGTAAACG\t1\n+TTTTTTCAAAGTAAA\t1\n+ATTTTTTCAAAGTAA\t1\n+CTAATTTTTTCAAAG\t1\n+CACTCTAATTTTTTC\t1\n+AACACTCTAATTTTT\t1\n+GAACACTCTAATTTT\t1\n+CTTTGAACACTCTAA\t1\n+GCTTTGAACACTCTA\t1\n+TGCTTTGAACACTCT\t1\n+CTGCTTTGAACACTC\t1\n+TAAACGCTTCGGACC\t1\n+CCTGCTTTGAACACT\t1\n+GCCTGCTTTGAACAC\t1\n+GGGCCTGCTTTGAAC\t1\n+ACCGGGCCTGCTTTG\t1\n+GACCGGGCCTGCTTT\t1\n+ATTCAGGCGACCGGG\t1\n+TATTCAGGCGACCGG\t1\n+GTATTCAGGCGACCG\t1\n+CGGTATTCAGGCGAC\t1\n+ACACTCTAATTTTTT\t1\n+GCGGTATTCAGGCGA\t1\n+TGCGGTATTCAGGCG\t1\n+CTGCGGTATTCAGGC\t1\n+TAGCTGCGGTATTCA\t1\n+CTAGCTGCGGTATTC\t1\n+CCTAGCTGCGGTATT\t1\n+TCCTAGCTGCGGTAT\t1\n+TTCCTAGCTGCGGTA\t1\n+CATTATTCCTAGCTG\t1\n+CCATTATTCCTAGCT\t1\n+ATTCCATTATTCCTA\t1\n+TCCTATTCCATTATT\t1\n+GTCCTATTCCATTAT\t1\n+GAGTCCTATTCCATT\t1\n+GGAGTCCTATTCCAT\t1\n+AACCGGAGTCCTATT\t1\n+GGACCCCGCGGGCCA\t1\n+GAACCGGAGTCCTAT\t1\n+AATAGAACCGGAGTC\t1\n+AAATAGAACCGGAGT\t1\n+AAAATAGAACCGGAG\t1\n+ACAAAATAGAACCGG\t1\n+CCACAAAATAGAACC\t1\n+ACCCACAAAATAGAA\t1\n+AACCCACAAAATAGA\t1\n+AAACCCACAAAATAG\t1\n+AAAACCCACAAAATA\t1\n+AAAAACCCACAAAAT\t1\n+GAAAAACCCACAAAA\t1\n+TTAAGAGCATCGAGG\t1\n+AGAAAAACCCACAAA\t1\n+AAGAAAAACCCACAA\t1\n+TGTTATAGCAGCAAA\t1\n+GTACTCTGACCCTGG\t2\n+GGTCGACATACTTTT\t1\n+AGCAAAGGGGGGACC\t1\n+TAGAACCGGAGTCCT\t1\n+AGGCTGTTATAGCAG\t1\n+AGAACCGGAGTCCTA\t1\n+GAGGCTGTTATAGCA\t1\n+GGAGGCTGTTATAGC\t1\n+AGAAGAGTGGAGGCT\t1\n+CCAGAAGAGTGGAGG\t1\n+TTCCTCTGTCCCATT\t2\n+CCTTCCCAGAAGAGT\t1\n+GCAGCAAAGGGGGGA\t1\n+TTTTCGACCGAAACT\t2\n+TCTAACATCTAGTGG\t1\n+AGTGGAGGCTGTTAT\t1\n+AGTTGACACACACAA\t2\n+TCTAGTGGAAAGCCT\t1\n+CTGATTGAAACGCTA\t1\n+CAGTTAAGAGCATCG\t1\n+ACGCTATTAGCGCGC\t1\n+TTGACACACACAACA\t2\n+GAACCACTACTTCAA\t1\n+CACTCAGTTAAGAGC\t1\n+CTAACATCTAGTGGA\t1\n+GCTGCGGTATTCAGG\t1\n+GAGATGTTTGACGAG\t1\n+CGGAGTCCTATTCCA\t1\n+ACCGAAACTACACAT\t2\n+GAAGAGTGGAGGCTG\t1\n+AAGCCTTCCCAGAAG\t1\n+AACCTCCGATCCGCA\t2\n+TGAGCAACCCTACAG\t2\n+ACGTTCTAACATCTA\t1\n+AACGTTCTAACATCT\t1\n+TATTCCTAGCTGCGG\t1\n+ATTATTCCTAGCTGC\t1\n+ATGTTTGACGAGCAG\t1\n+TCTCTCGCACCGGAA\t2\n+ATGAGATGTTTGACG\t1\n+GGCCTGCTTTGAACA\t1\n+AGCCTTCCCAGAAGA\t1\n+TTCCATTATTCCTAG\t1\n+CAACGTTCTAACATC\t1\n+ACTGATTGAAACGCT\t1\n+CTAGTGGAAAGCCTT\t1\n+TGAGATGTTTGACGA\t1\n+TCTGTCCCATTTCCT\t2\n+CCTCTGTCCCATTTC\t2\n+CATTCCTCTGTCCCA\t2\n+TTGAACACTCTAATT\t1\n+GAATGAGATGTTTGA\t1\n+ACACATTCCTCTGTC\t2\n+ATTCCTAGCTGCGGT\t1\n+CTCCATATTATTGCC\t1\n+GACCGAAACTACACA\t2\n+CGACCGAAACTACAC\t2\n+ACTACACATTCCTCT\t2\n+CTGCAGTACTCTGAC\t2\n+TTCTAACATCTAGTG\t1\n+CCGAAACTACACATT\t2\n+ATCCGTTACATATGT\t1\n+TACATATGTATGTAT\t1\n+CAGTACTCTGACCCT\t2\n+GTTCTAACATCTAGT\t1\n+ACAGTTTTCGACCGA\t2\n+TTGACGAGCAGGGGT\t1\n+CTCTGTCCCATTTCC\t2\n+CACAAAATAGAACCG\t1\n+TACTCTGACCCTGGC\t2\n+ATAGCAGCAAAGGGG\t1\n+TGAATGAGATGTTTG\t1\n+AACAGTTTTCGACCG\t2\n+TCGGACCCCGCGGGC\t1\n+ACCCTACAGTTGACA\t2\n+TCTCTCTCGCACCGG\t2\n+GTATGTATGTACACA\t1\n+ACACAACAGTTTTCG\t2\n+ACACACAACAGTTTT\t2\n+TCCCAGAAGAGTGGA\t1\n+ACCACCGCTAACTAG\t1\n+GAGTGGAGGCTGTTA\t1\n+ACACACACAACAGTT\t2\n+AACGCTATTAGCGCG\t1\n+GTAACTGATTGAAAC\t1\n+GTCTCTCTCGCACCG\t2\n+AACATCTAGTGGAAA\t1\n+CTTCCCAGAAGAGTG\t1\n+GTGGAAAGCCTTCCC\t1\n+CTACTTCAACTCAAG\t1\n+CGCGGGCCACTCAGT\t1\n+AACCTGTCTCTCTCG\t2\n+CTCGCACCGGAAACC\t2\n+CGCACCGGAAACCTC\t2\n+TATGTATGTACACAC\t1\n+ATCCATTTCACATCC\t1\n+ACTCTAATTTTTTCA\t1\n+GCTGCAGTACTCTGA\t2\n+ACATGAGCAACCCTA\t2\n+GACCCCGCGGGCCAC\t1\n+AAGAGTGGAGGCTGT\t1\n+CCGGAAACCTCCGAT\t2\n+GCAGCAACGTTCTAA\t1\n+GAAACTACACATTCC\t2\n+CTGACCCTGGCCACC\t2\n+ACCTCAACCTGTCTC\t2\n+AAACTACACATTCCT\t2\n+AGAGTGGAGGCTGTT\t1\n+GCGACCGGGCCTGCT\t1\n+CATCTAGTGGAAAGC\t1\n+CAGAAACATGAGCAA\t2\n+ACTTCAACTCAAGGT\t1\n+CGGGCCACTCAGTTA\t1\n+AGAAACATGAGCAAC\t2\n+CTATTCCATTATTCC\t1\n+TTTTGAATGAGATGT\t1\n+GGCGACCGGGCCTGC\t1\n+ACATCTAGTGGAAAG\t1\n+TAGCAGCAAAGGGGG\t1\n+GGACCAACTCCATAT\t1\n+GACATTGGCTGCAGT\t2\n+CCTATTCCATTATTC\t1\n+CAGTTTTCGACCGAA\t2\n+CAACCCTACAGTTGA\t2\n+TTTGACGAGCAGGGG\t1\n+GACGTAACTGATTGA\t1\n+CAGGCGACCGGGCCT\t1\n+ACTCTGACCCTGGCC\t2\n+CCGGGCCTGCTTTGA\t1\n+AGTGGAAAGCCTTCC\t1\n+TTGAAACGCTATTAG\t1\n+CGTTCTAACATCTAG'..b'GCAGTA\t2\n+CAGTTGACACACACA\t2\n+TCAAGGTCTCAAAGC\t1\n+ATCCGCAGAAACATG\t2\n+CACACAACAGTTTTC\t2\n+GGATGCAGCAACGTT\t1\n+TTCAAAGTAAACGCT\t1\n+AACATGAGCAACCCT\t2\n+GAGTGACGTAACTGA\t1\n+CTGTTATAGCAGCAA\t1\n+TAACATCTAGTGGAA\t1\n+CTCTCGCACCGGAAA\t2\n+CGCAGAAACATGAGC\t2\n+GGATTGAGGATGCAG\t1\n+TCCTCTGTCCCATTT\t2\n+GGTATTCAGGCGACC\t1\n+ATGAGCAACCCTACA\t2\n+TGGAAAGCCTTCCCA\t1\n+AGGCGACCGGGCCTG\t1\n+ACCTCCGATCCGCAG\t2\n+TCCATTATTCCTAGC\t1\n+ACTACTTCAACTCAA\t1\n+GAGCAACCCTACAGT\t2\n+GCAACCCTACAGTTG\t2\n+AGCTGCGGTATTCAG\t1\n+ACTAGCTATCCATTT\t1\n+AGAAGAAAAACCCAC\t1\n+CCCTACAGTTGACAC\t2\n+CTACAGTTGACACAC\t2\n+CAAGGGGAACCACTA\t1\n+AGGATGCAGCAACGT\t1\n+TTATAGCAGCAAAGG\t1\n+GTTAAGAGCATCGAG\t1\n+TATAGCAGCAAAGGG\t1\n+GCAAAGGGGGGACCA\t1\n+CAAAGGGGGGACCAA\t1\n+ACCCCGCGGGCCACT\t1\n+GACCAACTCCATATT\t1\n+ACATATGTATGTATG\t1\n+AAGGGGGGACCAACT\t1\n+ACATTCCTCTGTCCC\t2\n+GCACCACCGCTAACT\t1\n+CCGCAGAAACATGAG\t2\n+AGGGGGGACCAACTC\t1\n+GGGGGGACCAACTCC\t1\n+GGGGGACCAACTCCA\t1\n+GCACCGGAAACCTCC\t2\n+GGGGACCAACTCCAT\t1\n+GCAGTACTCTGACCC\t2\n+ACCAACTCCATATTA\t1\n+CCAACTCCATATTAT\t1\n+ACATCCGTTACATAT\t1\n+TATTGCCCATGACTT\t1\n+CAACTCCATATTATT\t1\n+CTCAAGGTCTCAAAG\t1\n+CTATTAGCGCGCACC\t1\n+AACTCCATATTATTG\t1\n+ATTGAGGATGCAGCA\t1\n+CATATTATTGCCCAT\t1\n+GGGAACCACTACTTC\t1\n+ATATTATTGCCCATG\t1\n+TATTATTGCCCATGA\t1\n+TCTAATTTTTTCAAA\t1\n+TTTCGACCGAAACTA\t2\n+ATTATTGCCCATGAC\t1\n+ACTCCATATTATTGC\t1\n+CCGCTAACTAGCTAT\t1\n+TTATTGCCCATGACT\t1\n+CAACAGTTTTCGACC\t2\n+ATTGCCCATGACTTT\t1\n+TTGCCCATGACTTTT\t1\n+TGAGGATGCAGCAAC\t1\n+TGCCCATGACTTTTG\t1\n+CGCACCACCGCTAAC\t1\n+CCCATGACTTTTGAA\t1\n+TTCACATCCGTTACA\t1\n+CCATGACTTTTGAAT\t1\n+ATGACTTTTGAATGA\t1\n+ATGCAGCAACGTTCT\t1\n+GCGCACCACCGCTAA\t1\n+ACTTTTGAATGAGAT\t1\n+CATGACTTTTGAATG\t1\n+TTTGAATGAGATGTT\t1\n+AATTTTTTCAAAGTA\t1\n+ATGTATGTACACACA\t1\n+TCCGCAGAAACATGA\t2\n+TTGAATGAGATGTTT\t1\n+GATGTTTGACGAGCA\t1\n+TCACATCCGTTACAT\t1\n+ACGAGCAGGGGTCGA\t1\n+GAAGAAAAACCCACA\t1\n+CCCAGAAGAGTGGAG\t1\n+CGAGCAGGGGTCGAC\t1\n+GAGCAGGGGTCGACA\t1\n+GCAGAGCAAGGGGAA\t1\n+GTTGACACACACAAC\t2\n+GCAGGGGTCGACATA\t1\n+CGGACCCCGCGGGCC\t1\n+GATTGAAACGCTATT\t1\n+CAGGGGTCGACATAC\t1\n+ATTGAAACGCTATTA\t1\n+CAGCAACGTTCTAAC\t1\n+CAGAGCAAGGGGAAC\t1\n+AATGAGATGTTTGAC\t1\n+AGGGGTCGACATACT\t1\n+CTCCGATCCGCAGAA\t2\n+GGGGTCGACATACTT\t1\n+CAACCTGTCTCTCTC\t2\n+GGGTCGACATACTTT\t1\n+CAAAATAGAACCGGA\t1\n+TACACATTCCTCTGT\t2\n+AACTCAAGGTCTCAA\t1\n+TGCCGCGGCCCTTGC\t1\n+GCCGCGGCCCTTGCA\t1\n+CGCGGCCCTTGCAGA\t1\n+GCGGCCCTTGCAGAG\t1\n+CGGCCCTTGCAGAGC\t1\n+TTTCAAAGTAAACGC\t1\n+GCCTTCCCAGAAGAG\t1\n+TTTCACATCCGTTAC\t1\n+CCCTTGCAGAGCAAG\t1\n+CGGGCCTGCTTTGAA\t1\n+CTTGCAGAGCAAGGG\t1\n+TTGCAGAGCAAGGGG\t1\n+AAAGGGGGGACCAAC\t1\n+CCTTGCAGAGCAAGG\t1\n+TGCAGAGCAAGGGGA\t1\n+AGAGCAAGGGGAACC\t1\n+CCGGAGTCCTATTCC\t1\n+GCAAGGGGAACCACT\t1\n+TCCGTTACATATGTA\t1\n+AGGGGAACCACTACT\t1\n+CCTCCGATCCGCAGA\t2\n+CCTGGCCACCTCAAC\t2\n+CACTACTTCAACTCA\t1\n+TTCCCAGAAGAGTGG\t1\n+TTCAACTCAAGGTCT\t1\n+CAACTCAAGGTCTCA\t1\n+ACTCAAGGTCTCAAA\t1\n+GGTCTCAAAGCGAGT\t1\n+ACGCTTCGGACCCCG\t1\n+ATTGGCTGCAGTACT\t2\n+CAAGGTCTCAAAGCG\t1\n+GCTATCCATTTCACA\t1\n+GGGACCAACTCCATA\t1\n+TATCCATTTCACATC\t1\n+AACTACACATTCCTC\t2\n+AGGTCTCAAAGCGAG\t1\n+GATGCAGCAACGTTC\t1\n+GTCTCAAAGCGAGTG\t1\n+TGAACACTCTAATTT\t1\n+TGTATGTATGTACAC\t1\n+TCTCAAAGCGAGTGA\t1\n+TCAAAGCGAGTGACG\t1\n+AAGCGAGTGACGTAA\t1\n+CACCGCTAACTAGCT\t1\n+AGCGAGTGACGTAAC\t1\n+TTCAGGCGACCGGGC\t1\n+CACCACCGCTAACTA\t1\n+GCGAGTGACGTAACT\t1\n+AGTGACGTAACTGAT\t1\n+GTGACGTAACTGATT\t1\n+TATGTATGTATGTAC\t1\n+TGACGTAACTGATTG\t1\n+ACGTAACTGATTGAA\t1\n+CTCAACCTGTCTCTC\t2\n+CGTAACTGATTGAAA\t1\n+TAGTGGAAAGCCTTC\t1\n+TAACTGATTGAAACG\t1\n+GGAAAGCCTTCCCAG\t1\n+AACTGATTGAAACGC\t1\n+AGCAGCAAAGGGGGG\t1\n+TGAAACGCTATTAGC\t1\n+GAAACGCTATTAGCG\t1\n+CGCTATTAGCGCGCA\t1\n+GCTATTAGCGCGCAC\t1\n+AAAGCGAGTGACGTA\t1\n+TATTAGCGCGCACCA\t1\n+TCAGGCGACCGGGCC\t1\n+ATTAGCGCGCACCAC\t1\n+GCGCGCACCACCGCT\t1\n+ACCGGAGTCCTATTC\t1\n+CGCGCACCACCGCTA\t1\n+CCACCGCTAACTAGC\t1\n+GAAAGCCTTCCCAGA\t1\n+CGCTAACTAGCTATC\t1\n+CTAACTAGCTATCCA\t1\n+TAACTAGCTATCCAT\t1\n+GACACACACAACAGT\t2\n+CTAGCTATCCATTTC\t1\n+GCCCTTGCAGAGCAA\t1\n+TAGCTATCCATTTCA\t1\n+TGACGAGCAGGGGTC\t1\n+CTATCCATTTCACAT\t1\n+TCCATTTCACATCCG\t1\n+GTTTGACGAGCAGGG\t1\n+CATTTCACATCCGTT\t1\n+AGTTAAGAGCATCGA\t1\n+CACATCCGTTACATA\t1\n+ATGTATGTATGTACA\t1\n+CTACACATTCCTCTG\t2\n+CATCCGTTACATATG\t1\n+CCGTTACATATGTAT\t1\n+CGAGTGACGTAACTG\t1\n+CGTTACATATGTATG\t1\n+CCATTTCACATCCGT\t1\n+GTTACATATGTATGT\t1\n+TTACATATGTATGTA\t1\n+CGAAACTACACATTC\t2\n+CATATGTATGTATGT\t1\n+ATATGTATGTATGTA\t1\n' |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/populations/populations.CP.joinmap.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/populations/populations.CP.joinmap.loc Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -0,0 +1,13 @@ +# Stacks v2.52; JoinMap; March 17, 2020 +# Parent: PopA_01 +name = populations.20200317 +popt = CP +nloc = 3 +nind = 1 + +1 <lmxll> lm +2 <lmxll> -- +3 <lmxll> lm + +individual names: +PopA_02 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/populations/populations.log --- a/test-data/populations/populations.log Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/populations/populations.log Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ -populations v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11) +populations v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) populations -P stacks_outputs -M denovo_map/popmap_cstacks.tsv Locus/sample distributions will be written to 'stacks_outputs/populations.log.distribs'. populations parameters selected: @@ -20,8 +20,7 @@ Working on 1 group(s) of populations: defaultgrp: 1 -Genotyping markers will be written to 'stacks_outputs/populations.markers.tsv' -Raw Genotypes/Haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' +Raw haplotypes will be written to 'stacks_outputs/populations.haplotypes.tsv' Population-level summary statistics will be written to 'stacks_outputs/populations.sumstats.tsv' Population-level haplotype summary statistics will be written to 'stacks_outputs/populations.hapstats.tsv' |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/populations/populations.phistats_summary.tsv --- a/test-data/populations/populations.phistats_summary.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/populations/populations.phistats_summary.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -3,3 +3,6 @@ # Fst' Means 1 + +# Dxy Means + 1 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/procrad/barcodes-duplicate --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/barcodes-duplicate Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -0,0 +1,41 @@ +ATGGGG PopA_01 +GGGTAA PopA_02 +AGGAAA PopA_03 +TTTAAG PopA_04 +GGTGTG PopA_05 +TGATGT PopA_06 +GGTTGT PopA_07 +ATAAGT PopA_08 +AAGATA PopA_09 +TGTGAG PopA_10 +ATAGTT PopA_11 +GGAAGG PopA_12 +TTTGTG PopA_13 +TTAAAT PopA_14 +AATAAG PopA_15 +AAGAGG PopA_16 +TAGTGT PopA_17 +TGGAAG PopA_18 +GGGTTG PopA_19 +CATCAT PopA_20 +GGAGAG PopB_20 +GTTTTA PopB_01 +TGATAA PopB_02 +GTTGAT PopB_03 +AGATTA PopB_04 +GTATAG PopB_05 +TTGGGA PopB_06 +ATATAT PopB_07 +GATGAG PopB_08 +GGGAAT PopB_09 +AGTAAT PopB_10 +GGGATA PopB_11 +GAGAAG PopB_12 +AGTAGA PopB_13 +AAGGAT PopB_14 +AGGGTA PopB_15 +TGTTTT PopB_16 +ATGATG PopB_17 +GAGTTA PopB_18 +ATGTAG PopB_19 +AAAAAA PopA_01 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/procrad/barcodes-duplicate2 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/barcodes-duplicate2 Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -0,0 +1,41 @@ +ATGGGG +GGGTAA +AGGAAA +TTTAAG +GGTGTG +TGATGT +GGTTGT +ATAAGT +AAGATA +TGTGAG +ATAGTT +GGAAGG +TTTGTG +TTAAAT +AATAAG +AAGAGG +TAGTGT +TGGAAG +GGGTTG +CATCAT +GGAGAG +GTTTTA +TGATAA +GTTGAT +AGATTA +GTATAG +TTGGGA +ATATAT +GATGAG +GGGAAT +AGTAAT +GGGATA +GAGAAG +AGTAGA +AAGGAT +AGGGTA +TGTTTT +ATGATG +GAGTTA +ATGTAG +ATGGGG |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/procrad/barcodes-duplicate3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/procrad/barcodes-duplicate3 Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -0,0 +1,41 @@ +ATGGGG AAAAAA +GGGTAA AAAAAA +AGGAAA AAAAAA +TTTAAG AAAAAA +GGTGTG AAAAAA +TGATGT AAAAAA +GGTTGT AAAAAA +ATAAGT AAAAAA +AAGATA AAAAAA +TGTGAG AAAAAA +ATAGTT AAAAAA +GGAAGG AAAAAA +TTTGTG AAAAAA +TTAAAT AAAAAA +AATAAG AAAAAA +AAGAGG AAAAAA +TAGTGT AAAAAA +TGGAAG AAAAAA +GGGTTG AAAAAA +CATCAT AAAAAA +GGAGAG AAAAAA +GTTTTA AAAAAA +TGATAA AAAAAA +GTTGAT AAAAAA +AGATTA AAAAAA +GTATAG AAAAAA +TTGGGA AAAAAA +ATATAT AAAAAA +GATGAG AAAAAA +GGGAAT AAAAAA +AGTAAT AAAAAA +GGGATA AAAAAA +GAGAAG AAAAAA +AGTAGA AAAAAA +AAGGAT AAAAAA +AGGGTA AAAAAA +TGTTTT AAAAAA +ATGATG AAAAAA +GAGTTA AAAAAA +ATGTAG AAAAAA +ATGGGG AAAAAA |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/refmap/catalog.calls.vcf --- a/test-data/refmap/catalog.calls.vcf Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/refmap/catalog.calls.vcf Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,6 +1,6 @@ ##fileformat=VCFv4.2 -##fileDate=20190617 -##source="Stacks v2.4" +##fileDate=20200709 +##source="Stacks v2.53" ##INFO=<ID=AD,Number=R,Type=Integer,Description="Total Depth for Each Allele"> ##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency"> ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/refmap/catalog.fa.gz |
| b |
| Binary file test-data/refmap/catalog.fa.gz has changed |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/shortreads/PopA_01.forward.fq.gz |
| b |
| Binary file test-data/shortreads/PopA_01.forward.fq.gz has changed |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/shortreads/PopA_01.reverse.fq.gz |
| b |
| Binary file test-data/shortreads/PopA_01.reverse.fq.gz has changed |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/shortreads/process_shortreads.out --- a/test-data/shortreads/process_shortreads.out Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/shortreads/process_shortreads.out Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,5 +1,5 @@ -process_shortreads v2.2, executed 2018-12-03 21:27:19 -process_shortreads -p stacks_inputs/ -i fastq -b /tmp/tmpiZT6X4/files/000/dataset_2.dat --inline_null -o stacks_outputs +process_shortreads v2.53, executed 2020-07-10 13:51:53 (zlib-1.2.11) +process_shortreads -p stacks_inputs/ -i fastq -b /tmp/tmpidt4mij_/files/7/7/8/dataset_778705df-5f0c-4210-9ad6-4c43e8aacd52.dat --inline_null -o stacks_outputs File Retained Reads Low Quality Ambiguous Barcodes Trimmed Reads Orphaned paired-end reads Total R1.fastq 7000 0 0 0 0 7000 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/sstacks/PopA_01.matches.tsv --- a/test-data/sstacks/PopA_01.matches.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/sstacks/PopA_01.matches.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,5 +1,6 @@ -# sstacks version 2.4; generated on 2019-06-18 10:34:45 +# sstacks version 2.52; generated on 2020-03-16 15:39:40 1 1 1 AC 9 94M 1 1 1 CA 9 94M 2 1 2 consensus 28 94M 3 1 3 consensus 20 94M +# sstacks completed on 2020-03-16 15:39:40 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/sstacks/PopA_02.matches.tsv --- a/test-data/sstacks/PopA_02.matches.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/sstacks/PopA_02.matches.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,5 +1,6 @@ -# sstacks version 2.4; generated on 2019-06-18 10:34:45 +# sstacks version 2.52; generated on 2020-03-16 15:39:40 1 2 1 AC 6 94M 1 2 1 CA 6 94M 2 2 2 consensus 28 94M 3 2 3 consensus 20 94M +# sstacks completed on 2020-03-16 15:39:40 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/stacks_outputs/catalog.calls |
| b |
| Binary file test-data/stacks_outputs/catalog.calls has changed |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/stacks_outputs/tsv2bam.log --- a/test-data/stacks_outputs/tsv2bam.log Mon Sep 30 14:18:47 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,17 +0,0 @@ -tsv2bam v2.4, executed 2019-06-18 10:34:45 (zlib-1.2.11) -tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ -Configuration for this run: - Stacks directory: 'stacks_outputs/' - Population map: 'denovo_map/popmap_cstacks.tsv' - Num. samples: 2 - Paired-end reads directory: 'demultiplexed/' - -Paired-end reads files found, e.g. 'demultiplexed/PopA_01.2.fq'. -Loading the catalog... -Processing sample 'PopA_01'... -Processing sample 'PopA_02'... - -Sample 'PopA_01': matched 3 sample loci to 3 catalog loci; found a paired-end read for 66 (100.0%) of the assembled forward reads; wrote 132 records. -Sample 'PopA_02': matched 3 sample loci to 3 catalog loci; found a paired-end read for 60 (100.0%) of the assembled forward reads; wrote 120 records. - -tsv2bam is done. |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/tsv2bam/tsv2bam.log --- a/test-data/tsv2bam/tsv2bam.log Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/tsv2bam/tsv2bam.log Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ -tsv2bam v2.4, executed 2019-06-17 21:22:16 (zlib-1.2.11) +tsv2bam v2.52, executed 2020-03-16 15:39:40 (zlib-1.2.11) tsv2bam -P stacks_outputs -M denovo_map/popmap_cstacks.tsv -R demultiplexed/ Configuration for this run: Stacks directory: 'stacks_outputs/' |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/ustacks/PopA_01.alleles.tsv --- a/test-data/ustacks/PopA_01.alleles.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/ustacks/PopA_01.alleles.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,3 +1,4 @@ -# ustacks version 2.4; generated on 2019-06-18 10:34:45 +# ustacks version 2.52; generated on 2020-03-16 15:39:40 1 1 AC 50.00 9 1 1 CA 50.00 9 +# ustacks completed on 2020-03-16 15:39:40 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/ustacks/PopA_01.snps.tsv --- a/test-data/ustacks/PopA_01.snps.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/ustacks/PopA_01.snps.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ -# ustacks version 2.4; generated on 2019-06-18 10:34:45 +# ustacks version 2.52; generated on 2020-03-16 15:39:40 1 1 0 O 24.95 A - 1 1 1 O 24.95 A - 1 1 2 O 24.95 T - @@ -281,3 +281,4 @@ 1 3 91 O 27.73 A - 1 3 92 O 27.73 G - 1 3 93 O 27.73 A - +# ustacks completed on 2020-03-16 15:39:40 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/ustacks/PopA_01.tags.tsv --- a/test-data/ustacks/PopA_01.tags.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/ustacks/PopA_01.tags.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ -# ustacks version 2.4; generated on 2019-06-18 10:34:45 +# ustacks version 2.52; generated on 2020-03-16 15:39:40 1 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 1 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO 1 1 primary 0 lane1_fakedata7_0 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC @@ -71,3 +71,4 @@ 1 3 primary 0 lane1_fakedata2_19 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 1 3 secondary lane1_fakedata2_5 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTAAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 1 3 secondary lane1_fakedata2_17 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCCAGA +# ustacks completed on 2020-03-16 15:39:40 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/ustacks/PopA_02.alleles.tsv --- a/test-data/ustacks/PopA_02.alleles.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/ustacks/PopA_02.alleles.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,3 +1,4 @@ -# ustacks version 2.4; generated on 2019-06-18 10:34:45 +# ustacks version 2.52; generated on 2020-03-16 15:39:40 2 1 AC 50.00 6 2 1 CA 50.00 6 +# ustacks completed on 2020-03-16 15:39:40 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/ustacks/PopA_02.snps.tsv --- a/test-data/ustacks/PopA_02.snps.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/ustacks/PopA_02.snps.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ -# ustacks version 2.4; generated on 2019-06-18 10:34:45 +# ustacks version 2.52; generated on 2020-03-16 15:39:40 2 1 0 O 16.64 A - 2 1 1 O 16.64 A - 2 1 2 O 16.64 T - @@ -281,3 +281,4 @@ 2 3 91 O 27.73 A - 2 3 92 O 27.73 G - 2 3 93 O 27.73 A - +# ustacks completed on 2020-03-16 15:39:40 |
| b |
| diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/ustacks/PopA_02.tags.tsv --- a/test-data/ustacks/PopA_02.tags.tsv Mon Sep 30 14:18:47 2019 -0400 +++ b/test-data/ustacks/PopA_02.tags.tsv Thu Jul 16 07:28:45 2020 -0400 |
| b |
| @@ -1,4 +1,4 @@ -# ustacks version 2.4; generated on 2019-06-18 10:34:45 +# ustacks version 2.52; generated on 2020-03-16 15:39:40 2 1 consensus AATTCGTTTGCTGCTTCAGGAATCTCTCGTATAATCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC 0 0 0 2 1 model OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOEOOOOO 2 1 primary 0 lane1_fakedata7_7 1:N:0:/1 AATTCGTTTGCTGCTTCAGGAATCTCTCGTATACTCTGAGTATGTGCGTACGTACGCTATTTAGATGGATAACCGACGCTGCCAGACGAGAGAC @@ -65,3 +65,4 @@ 2 3 primary 0 lane1_fakedata2_18 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 2 3 primary 0 lane1_fakedata2_19 1:N:0:/1 AATTCTCTACACCACAGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA 2 3 secondary lane1_fakedata2_1 1:N:0:/1 AATTCTCTACACCACTGCATCAATTCTAAAAATGACTACCAGAGAGACAACTCCGCAGTTAAACACTCTGACTGCCACGCCAGCTACCTCTAGA +# ustacks completed on 2020-03-16 15:39:40 |