Repository 'stacks2_kmerfilter'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/stacks2_kmerfilter

Changeset 2:8a55d29c8fcf (2020-07-16)
Previous changeset 1:38c9f9a680f0 (2019-09-30) Next changeset 3:1544278c272e (2021-04-27)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit f55e2407891a3c1f73f14a77b7ddadcd6f5eb1f8"
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
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
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'
b
diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/clonefilter/Discarded1_0001.1.1.fq.gz
b
Binary file test-data/clonefilter/Discarded1_0001.1.1.fq.gz has changed
b
diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/clonefilter/Discarded1_0001.1.1.fq.single.gz
b
Binary file test-data/clonefilter/Discarded1_0001.1.1.fq.single.gz has changed
b
diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/clonefilter/Removed1_0001.1.1.fq.gz
b
Binary file test-data/clonefilter/Removed1_0001.1.1.fq.gz has changed
b
diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/clonefilter/Removed1_0001.1.1.fq.single-alt.gz
b
Binary file test-data/clonefilter/Removed1_0001.1.1.fq.single-alt.gz has changed
b
diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/clonefilter/Removed1_0001.1.1.fq.single.gz
b
Binary file test-data/clonefilter/Removed1_0001.1.1.fq.single.gz has changed
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -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
b
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
b
@@ -0,0 +1,2 @@
+PopA_01 parent
+PopA_02 progeny
b
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
b
@@ -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
b
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
b
@@ -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">
b
diff -r 38c9f9a680f0 -r 8a55d29c8fcf test-data/gstacks/catalog.fa.gz
b
Binary file test-data/gstacks/catalog.fa.gz has changed
b
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
b
@@ -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'.
 
b
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
b
@@ -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
b
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
b
@@ -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-
b
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
b
@@ -0,0 +1,3 @@
+# KmerFrequency Count
+1 408
+2 136
b
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