# HG changeset patch
# User iuc
# Date 1739920665 0
# Node ID b7e8663db1ec8a93cef8c429b0830ede6173384e
# Parent  1206c725e45aeddb5499f84633161d9eee86f8a0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/multiqc commit 327834d2ea9b16f0f0264fa4e9b675a2277f2fee

diff -r 1206c725e45a -r b7e8663db1ec bakta_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bakta_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,48 @@
+<macros>
+    <token name="@BAKTA_COMMAND@"><![CDATA[
+        #set $pattern = "Bakta:"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="bakta_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of Bakta" help="It should contain 'Bakta:'"/>
+    </xml>
+    <xml name="bakta_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="bakta"/>
+                    <param name="input" value="bakta.txt"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="Bakta"/>
+                    <has_text text="bakta_txt"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="bakta-Count"/>
+                    <has_text text="bakta-Length"/>
+                    <has_text text="bakta-CDSs"/>
+                    <has_text text="1"/>
+                    <has_text text="1330"/>
+                    <has_text text="2"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="4"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec bamtools_plugin.xml
--- a/bamtools_plugin.xml	Tue Feb 11 10:12:32 2025 +0000
+++ b/bamtools_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@BAMTOOLS_COMMAND@"><![CDATA[
-        #set $pattern = "Stats for BAM file(s)"
+        #set $pattern = "Stats for BAM file\(s\)"
         @LN_FILES@
     ]]></token>
     <xml name="bamtools_form">
diff -r 1206c725e45a -r b7e8663db1ec bbduk_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bbduk_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,44 @@
+<macros>
+    <token name="@BBDUK_COMMAND@"><![CDATA[
+        #set $pattern = "Executing jgi\.BBDuk"
+        @LN_FILES@
+    ]]></token>
+    <xml name="bbduk_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of BBDuk" help="It should contain 'Executing jgi.BBDuk'"/>
+    </xml>
+    <xml name="bbduk_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="bbduk"/>
+                    <param name="input" value="bbduk.txt"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="BBDuk"/>
+                    <has_text text="BBDuk: Filtered Reads"/>
+                    <has_text text="0.0"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="bbduk-Total_Removed_bases_percent"/>
+                    <has_text text="bbduk-Total_Removed_bases"/>
+                    <has_text text="bbduk-Total_Removed_reads_percent"/>
+                    <has_text text="bbduk-Total_Removed_reads"/>
+                    <has_text text="bbduk-Input_reads"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="6"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="2"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec checkm_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/checkm_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,37 @@
+<macros>
+    <token name="@CHECKM_COMMAND@"><![CDATA[
+        #set $pattern = ".*Bin Id(?:\t| {3,})Marker lineage(?:\t| {3,})# genomes(?:\t| {3,})# markers(?:\t| {3,})# marker sets.*"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, 'output_file')
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="checkm_form">
+        <param name="input" type="data" format="tabular" multiple="true" label="Output of Checkm"/>
+    </xml>
+    <xml name="checkm_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="checkm"/>
+                    <param name="input" value="checkm.tabular"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="CheckM"/>
+                    <has_text text="Bin quality"/>
+                    <has_text text="637000110"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec diamond_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/diamond_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,45 @@
+<macros>
+    <token name="@DIAMOND_COMMAND@"><![CDATA[
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, 'diamond.log')
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="diamond_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Log output of DIAMOND"/>
+    </xml>
+    <xml name="diamond_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="diamond"/>
+                    <param name="input" value="diamond.log"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="DIAMOND"/>
+                    <has_text text="Queries aligned"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="Sample"/>
+                    <has_text text="diamond_0"/>
+                    <has_text text="diamond-queries_aligned"/>
+                    <has_text text="1"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="2"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec freyja_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/freyja_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,46 @@
+<macros>
+    <token name="@FREYJA_COMMAND@"><![CDATA[
+        #set $pattern = "summarized\t\["
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + '.tsv')
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="freyja_form">
+        <param name="input" type="data" format="tsv" multiple="true" label="Output of Freyja" help="It should contain 'summarized\t['"/>
+    </xml>
+    <xml name="freyja_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="freyja"/>
+                    <param name="input" value="freyja.tsv"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="Freyja Summary"/>
+                    <has_text text="Top lineage"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="freyja-Top_lineage_freyja"/>
+                    <has_text text="freyja-Top_lineage_freyja_percentage"/>
+                    <has_text text="A"/>
+                    <has_text text="57.89470000000878"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="1"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec gtdbtk_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gtdbtk_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,32 @@
+<macros>
+    <token name="@GTDBTK_COMMAND@"><![CDATA[
+        #set $pattern = "user_genome\tclassification\tclosest_genome_reference\tclosest_genome_reference_radius\tclosest_genome_taxonomy\tclosest_genome_ani"
+        @LN_FILES@
+    ]]></token>
+    <xml name="gtdbtk_form">
+        <param name="input" type="data" format="tsv" multiple="true" label="Output of GTDB-Tk" help="It should contain 'user_genome\tclassification\tclosest_genome_reference\tclosest_genome_reference_radius\tclosest_genome_taxonomy\tclosest_genome_ani'"/>
+    </xml>
+    <xml name="gtdbtk_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="gtdbtk"/>
+                    <param name="input" value="gtdbtk.tsv"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="GTDB-Tk"/>
+                    <has_text text="genome_1_fna_gz"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec kraken_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,43 @@
+<macros>
+    <token name="@KRAKEN_COMMAND@"><![CDATA[
+        #set $pattern = "^\s{0,2}(\d{1,3}\.\d{1,2})\t(\d+)\t(\d+)\t((\d+)\t(\d+)\t)?([URDKPCOFGS-]\d{0,2})\t(\d+)(\s+)[root|unclassified]"
+        @LN_FILES@
+    ]]></token>
+    <xml name="kraken_form">
+        <param name="input" type="data" format="tabular" multiple="true" label="Output report of Kraken 1 or 2" />
+    </xml>
+    <xml name="kraken_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="kraken"/>
+                    <param name="input" value="kraken_test0_report.tab"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="General Statistics"/>
+                    <has_text text="kraken_test0_report_tab"/>
+                    <has_text text="100.0"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="kraken-pct_top_one"/>
+                    <has_text text="kraken-pct_top_n"/>
+                    <has_text text="100.0"/>
+                    <has_text text="kraken_test0_report_tab"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec macros.xml
--- a/macros.xml	Tue Feb 11 10:12:32 2025 +0000
+++ b/macros.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.27</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@VERSION_SUFFIX@">2</token>
     <xml name="bio_tools">
         <xrefs>
             <xref type="bio.tools">multiqc</xref>
@@ -55,7 +55,7 @@
             #set $file_path += '_' + str($file_paths.count($file_path))
         #end if
         #set $file_paths += [$file_path]
-        grep -q '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
+        grep -Pq '$pattern' $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
         ln -s '$file' '$file_path'  &&
     ]]></token>
     <token name="@CREATE_REPEAT_DIR_1@">
diff -r 1206c725e45a -r b7e8663db1ec megahit_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/megahit_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,44 @@
+<macros>
+    <token name="@MEGAHIT_COMMAND@"><![CDATA[
+        #set $pattern = " - MEGAHIT v"
+        @LN_FILES@
+    ]]></token>
+    <xml name="megahit_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of MEGAHIT" help="It should contain ' - MEGAHIT v'"/>
+    </xml>
+    <xml name="megahit_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="megahit"/>
+                    <param name="input" value="megahit.txt"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="MEGAHIT"/>
+                    <has_text text="NGS read assembler"/>
+                    <has_text text="Metrics and run statistics from MEGAHIT run logs"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="megahit-megahit_contigs"/>
+                    <has_text text="megahit-megahit_avg_contig"/>
+                    <has_text text="megahit-megahit_n50"/>
+                    <has_text text="576"/>
+                    <has_text text="1"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="4"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec metaphlan_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/metaphlan_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,46 @@
+<macros>
+    <token name="@METAPHLAN_COMMAND@"><![CDATA[
+        #set $pattern = "#clade_name\tNCBI_tax_id\trelative_abundance\t"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + '.txt')
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="metaphlan_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of MetaPhlAn" help="It should contain '#clade_name\tNCBI_tax_id\trelative_abundance\t'"/>
+    </xml>
+    <xml name="metaphlan_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="metaphlan"/>
+                    <param name="input" value="metaphlan.txt"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="MetaPhlAn"/>
+                    <has_text text="Top taxa"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="metaphlan-Moraxella_lacunata"/>
+                    <has_text text="metaphlan-Top"/>
+                    <has_text text="22.57968"/>
+                    <has_text text="100.00001000000002"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="3"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="7"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec multiqc.xml
--- a/multiqc.xml	Tue Feb 11 10:12:32 2025 +0000
+++ b/multiqc.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -23,6 +23,19 @@
         <import>star_plugin.xml</import>
         <import>trimmomatic_plugin.xml</import>
         <import>vcftools_plugin.xml</import>
+        <import>kraken_plugin.xml</import>
+        <import>diamond_plugin.xml</import>
+        <import>bakta_plugin.xml</import>
+        <import>freyja_plugin.xml</import>
+        <import>checkm_plugin.xml</import>
+        <import>pairtools_plugin.xml</import>
+        <import>porechop_plugin.xml</import>
+        <import>snippy_plugin.xml</import>
+        <import>metaphlan_plugin.xml</import>
+        <import>bbduk_plugin.xml</import>
+        <import>megahit_plugin.xml</import>
+        <import>nonpareil_plugin.xml</import>
+        <import>gtdbtk_plugin.xml</import>
         <import>sambamba_plugin.xml</import>
     </macros>
     <expand macro="bio_tools"/>
@@ -144,6 +157,32 @@
         @TRIMMOMATIC_COMMAND@
     #elif str($repeat.software_cond.software) == "vcftools"
         @VCFTOOLS_COMMAND@
+    #elif str($repeat.software_cond.software) == "kraken"
+        @KRAKEN_COMMAND@
+    #elif str($repeat.software_cond.software) == "diamond"
+        @DIAMOND_COMMAND@
+    #elif str($repeat.software_cond.software) == "bakta"
+        @BAKTA_COMMAND@
+    #elif str($repeat.software_cond.software) == "freyja"
+        @FREYJA_COMMAND@
+    #elif str($repeat.software_cond.software) == "checkm"
+        @CHECKM_COMMAND@
+    #elif str($repeat.software_cond.software) == "pairtools"
+        @PAIRTOOLS_COMMAND@
+    #elif str($repeat.software_cond.software) == "porechop"
+        @PORECHOP_COMMAND@
+    #elif str($repeat.software_cond.software) == "snippy"
+        @SNIPPY_COMMAND@
+    #elif str($repeat.software_cond.software) == "metaphlan"
+        @METAPHLAN_COMMAND@
+    #elif str($repeat.software_cond.software) == "bbduk"
+        @BBDUK_COMMAND@
+    #elif str($repeat.software_cond.software) == "megahit"
+        @MEGAHIT_COMMAND@
+    #elif str($repeat.software_cond.software) == "nonpareil"
+        @NONPAREIL_COMMAND@
+    #elif str($repeat.software_cond.software) == "gtdbtk"
+        @GTDBTK_COMMAND@
     #elif str($repeat.software_cond.software) == "sambamba"
         @SAMBAMBA_COMMAND@
     #else if str($repeat.software_cond.software) == "custom_content":
@@ -253,6 +292,19 @@
                     <option value="tophat">TopHat2 (TopHat2 is deprecated you should not use it)</option>
                     <option value="trimmomatic">Trimmomatic</option>
                     <option value="vcftools">VCFTools</option>
+                    <option value="kraken">Kraken 1 or 2</option>
+                    <option value="diamond">DIAMOND</option>
+                    <option value="bakta">Bakta</option>
+                    <option value="freyja">Freyja</option>
+                    <option value="checkm">CheckM</option>
+                    <option value="pairtools">pairtools</option>
+                    <option value="porechop">Porechop</option>
+                    <option value="snippy">Snippy</option>
+                    <option value="metaphlan">MetaPhlAn</option>
+                    <option value="bbduk">BBDuk</option>
+                    <option value="megahit">MEGAHIT</option>
+                    <option value="nonpareil">Nonpareil</option>
+                    <option value="gtdbtk">GTDB-Tk</option>
                     <!--<option value="verifybamid">VerifyBAMID</option>-->
                     <!--Custom-->
                     <option value="custom_content">Custom Content</option>
@@ -353,6 +405,45 @@
                 <when value="vcftools">
                     <expand macro="vcftools_form"/>
                 </when>
+                <when value="kraken">
+                    <expand macro="kraken_form"/>
+                </when>
+                <when value="diamond">
+                    <expand macro="diamond_form"/>
+                </when>
+                <when value="bakta">
+                    <expand macro="bakta_form"/>
+                </when>
+                <when value="freyja">
+                    <expand macro="freyja_form"/>
+                </when>
+                <when value="checkm">
+                    <expand macro="checkm_form"/>
+                </when>
+                <when value="pairtools">
+                    <expand macro="pairtools_form"/>
+                </when>
+                <when value="porechop">
+                    <expand macro="porechop_form"/>
+                </when>
+                <when value="snippy">
+                    <expand macro="snippy_form"/>
+                </when>
+                <when value="metaphlan">
+                    <expand macro="metaphlan_form"/>
+                </when>
+                <when value="bbduk">
+                    <expand macro="bbduk_form"/>
+                </when>
+                <when value="megahit">
+                    <expand macro="megahit_form"/>
+                </when>
+                <when value="nonpareil">
+                    <expand macro="nonpareil_form"/>
+                </when>
+                <when value="gtdbtk">
+                    <expand macro="gtdbtk_form"/>
+                </when>
                 <when value="sambamba">
                     <expand macro="sambamba_form"/>
                 </when>
@@ -432,6 +523,19 @@
         <expand macro="gatk_test"/>
         <expand macro="bamtools_test"/>
         <expand macro="pycoqc_test"/>
+        <expand macro="kraken_test"/>
+        <expand macro="diamond_test"/>
+        <expand macro="bakta_test"/>
+        <expand macro="freyja_test"/>
+        <expand macro="checkm_test"/>
+        <expand macro="pairtools_test"/>
+        <expand macro="porechop_test"/>
+        <expand macro="snippy_test"/>
+        <expand macro="metaphlan_test"/>
+        <expand macro="bbduk_test"/>
+        <expand macro="megahit_test"/>
+        <expand macro="nonpareil_test"/>
+        <expand macro="gtdbtk_test"/>
         <expand macro="sambamba_test"/>
 
         <!--expand macro="vcftools_test"/> Does not work, did it ever worked? -->
diff -r 1206c725e45a -r b7e8663db1ec nonpareil_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nonpareil_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,52 @@
+<macros>
+    <token name="@NONPAREIL_COMMAND@"><![CDATA[
+        #set $pattern = "LRstar"
+        #for $file in $repeat.software_cond.input
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier) + '.json')
+            ln -s '$file' '$file_path' &&
+        #end for
+    ]]></token>
+    <xml name="nonpareil_form">
+        <param name="input" type="data" format="json" multiple="true" label="JSON object output of Nonpareil" help="It should contain 'LRstar'"/>
+    </xml>
+    <xml name="nonpareil_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="nonpareil"/>
+                    <param name="input" value="nonpareil.json"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="Estimates metagenomic coverage and sequence diversity"/>
+                    <has_text text="Nonpareil"/>
+                    <has_text text="Redundancy levels"/>
+                    <has_text text="21.3"/>
+                    <has_text text="24.3"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="nonpareil-nonpareil_R"/>
+                    <has_text text="nonpareil-nonpareil_LR"/>
+                    <has_text text="nonpareil-nonpareil_kappa"/>
+                    <has_text text="nonpareil-nonpareil_C"/>
+                    <has_text text="nonpareil-nonpareil_diversity"/>
+                    <has_text text="11.9521"/>
+                    <has_text text="0.0005"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="6"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="3"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec pairtools_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pairtools_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,55 @@
+<macros>
+    <token name="@PAIRTOOLS_COMMAND@"><![CDATA[
+        #set $pattern = "total_single_sided_mapped"
+        #set file_paths = []
+        #for $file in $repeat.software_cond.input:
+            @ESCAPE_IDENTIFIER@
+            #set file_path = os.path.join($software_dir, str($identifier))
+            #if $file_path in $file_paths
+                #set $file_path += '_' + str($file_paths.count($file_path))
+            #end if
+            #set $file_paths += [$file_path]
+            grep -Pzq "(?s)(?=.*total_single_sided_mapped\t)(?=.*cis\t)(?=.*trans\t)(?=.*pair_types/)" $file || die "Module '${repeat.software_cond.software}: '$pattern' not found in the file '$identifier'" &&
+            ln -s '$file' '$file_path'  &&
+        #end for
+    ]]></token>
+    <xml name="pairtools_form">
+        <param name="input" type="data" format="tabular" multiple="true" label="Output of Pairtools"/>
+    </xml>
+    <xml name="pairtools_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="pairtools"/>
+                    <param name="input" value="output_dedup_pairs.stats"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="output_dedup_pairs"/>
+                    <has_text text="Pairs by alignment status"/>
+                    <has_text text="Fraction of read pairs by strand orientation"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="pairtools-total"/>
+                    <has_text text="pairtools-frac_unmapped"/>
+                    <has_text text="0.001992"/>
+                    <has_text text="45.88353413654618"/>
+                    <has_text text="pairtools-frac_dups"/>
+                    <has_text text="0.4518072289156626"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="8"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="5"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec picard_plugin.xml
--- a/picard_plugin.xml	Tue Feb 11 10:12:32 2025 +0000
+++ b/picard_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -12,7 +12,7 @@
                 @LN_2_FILES@
             #elif str($repeat2.type) == "hsmetrics"
                 #set $pattern = "picard.analysis.directed.HsMetrics"
-                @   @
+                @LN_2_FILES@
             #elif str($repeat2.type) == "insertsize"
                 #set $pattern = "picard.analysis.InsertSizeMetrics"
                 @LN_2_FILES@
diff -r 1206c725e45a -r b7e8663db1ec porechop_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/porechop_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,44 @@
+<macros>
+    <token name="@PORECHOP_COMMAND@"><![CDATA[
+        #set $pattern = "Looking for known adapter sets"
+        @LN_FILES@
+    ]]></token>
+    <xml name="porechop_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output of Porechop" help="It should contain 'Looking for known adapter sets'"/>
+    </xml>
+    <xml name="porechop_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="porechop"/>
+                    <param name="input" value="porechop.log"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="Porechop"/>
+                    <has_text text="Reads adapter-trimmed read end"/>
+                    <has_text text="Middle split reads"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="porechop-Input_Reads"/>
+                    <has_text text="porechop-Start_Trimmed"/>
+                    <has_text text="porechop-Middle_Split_Percent"/>
+                    <has_text text="44.44444444444444"/>
+                    <has_text text="4e-06"/>
+                    <has_n_lines n="2"/>
+                    <has_n_columns n="8"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="3"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec samtools_plugin.xml
--- a/samtools_plugin.xml	Tue Feb 11 10:12:32 2025 +0000
+++ b/samtools_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -6,7 +6,7 @@
                 #set $pattern = "This file was produced by samtools stats"
                 @LN_3_FILES@
             #elif str($repeat2.type.type) == "flagstat"
-                #set $pattern = "in total (QC-passed reads + QC-failed reads)"
+                #set $pattern = "in total \(QC-passed reads \+ QC-failed reads\)"
                 @LN_3_FILES@
             #elif str($repeat2.type.type) == "idxstats"
                 #for $file in $repeat2.type.input
@@ -15,7 +15,7 @@
                     ln -s '$file' '$file_path' &&
                 #end for
             #elif str($repeat2.type.type) == "rmdup"
-                #set $pattern = "[bam_rmdup"
+                #set $pattern = "\[bam_rmdup"
                 @LN_3_FILES@
             #end if
         #end for
diff -r 1206c725e45a -r b7e8663db1ec snippy_plugin.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snippy_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,42 @@
+<macros>
+    <token name="@SNIPPY_COMMAND@"><![CDATA[
+        #set $pattern = "snippy|ID\tLENGTH\tALIGNED\tUNALIGNED\tVARIANT\tHET\tMASKED\tLOWCOV"
+        @LN_FILES@
+    ]]></token>
+    <xml name="snippy_form">
+        <param name="input" type="data" format="txt" multiple="true" label="Output summary of Snippy" help="It should contain 'snippy' or 'ID\tLENGTH\tALIGNED\tUNALIGNED\tVARIANT\tHET\tMASKED\tLOWCOV'"/>
+    </xml>
+    <xml name="snippy_test">
+        <test expect_num_outputs="3">
+            <repeat name="results">
+                <conditional name="software_cond">
+                    <param name="software" value="snippy"/>
+                    <param name="input" value="snippy.txt"/>
+                </conditional>
+            </repeat>
+            <param name="title" value="Title of the report"/>
+            <param name="comment" value="Commment for the report"/>
+            <param name="flat" value="true"/>
+            <param name="export" value="true"/>
+            <output name="html_report">
+                <assert_contents>
+                    <has_text text="Title of the report"/>
+                    <has_text text="Commment for the report"/>
+                    <has_text text="Snippy-Core Alignment Statistics"/>
+                </assert_contents>
+            </output>
+            <output name="stats">
+                <assert_contents>
+                    <has_text text="snippy-Percent_Het"/>
+                    <has_text text="snippy-HET"/>
+                    <has_text text="700"/>
+                    <has_text text="7.285714285714286"/>
+                    <has_text text="a"/>
+                    <has_n_lines n="5"/>
+                    <has_n_columns n="6"/>
+                </assert_contents>
+            </output>
+            <output_collection name="plots" type="list" count="0"/>
+        </test>
+    </xml>
+</macros>
diff -r 1206c725e45a -r b7e8663db1ec template_plugin.xml
--- a/template_plugin.xml	Tue Feb 11 10:12:32 2025 +0000
+++ b/template_plugin.xml	Tue Feb 18 23:17:45 2025 +0000
@@ -12,7 +12,7 @@
     <token name="@TEMPLATE_COMMAND@"><![CDATA[
         <!--This pattern is used to check the file content in the @CHECK_LN_FILE@ token. The pattern should be included in the file. -->
         #set $pattern = "Trimmomatic"
-        @LN_FILES@f
+        @LN_FILES@
     ]]></token>
     <xml name="TEMPLATE_form">
         <!-- Please add here your input forms specific to your plugin. Keep the name as `input` if you have a single input.
diff -r 1206c725e45a -r b7e8663db1ec test-data/bakta.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bakta.txt	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,30 @@
+Sequence(s):
+Length: 1330
+Count: 1
+GC: 45.2
+N50: 1330
+N ratio: 0.0
+coding density: 79.0
+
+Annotation:
+tRNAs: 0
+tmRNAs: 0
+rRNAs: 0
+ncRNAs: 0
+ncRNA regions: 0
+CRISPR arrays: 0
+CDSs: 2
+pseudogenes: 0
+hypotheticals: 1
+signal peptides: 0
+sORFs: 0
+gaps: 0
+oriCs: 0
+oriVs: 0
+oriTs: 1
+
+Bakta:
+Software: v1.9.4
+Database: v5.0, full
+DOI: 10.1099/mgen.0.000685
+URL: github.com/oschwengers/bakta
diff -r 1206c725e45a -r b7e8663db1ec test-data/bbduk.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/bbduk.txt	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,26 @@
+Executing jgi.BBDuk [in=forward.fastq.gz, out=/data/jwd05e/main/079/061/79061727/outputs/dataset_1abda394-9c76-4c97-9712-e52be8f79694.dat, ref=dataset_5c3ad7b3-f75c-4f5a-a70e-15ae843bc97c.dat.fa, k=27, rcomp=t, maskmiddle=t, minkmerhits=1, minkmerfraction=0.0, mincovfraction=0.0, hammingdistance=0, qhdist=0, editdistance=0, forbidn=f, trimfailures=f, findbestmatch=f, skipr1=f, skipr2=f, t=1]
+Version 39.08
+
+Set threads to 1
+Changed from ASCII-33 to ASCII-64 on input quality B (Q33) for base N at lines 1 and 3, position 0 while prescanning.
+Unspecified format for output /data/jwd05e/main/079/061/79061727/outputs/dataset_1abda394-9c76-4c97-9712-e52be8f79694.dat; defaulting to fastq.
+0.398 seconds.
+Initial:
+Memory: max=3672m, total=270m, free=243m, used=27m
+
+Added 2970 kmers; time: 	0.549 seconds.
+Memory: max=3672m, total=270m, free=238m, used=32m
+
+Input is being processed as unpaired
+Changed from ASCII-33 to ASCII-64 on input ;: 59 -> 28
+Started output streams:	0.052 seconds.
+Processing time:   		0.106 seconds.
+
+Input:                  	100 reads 		10000 bases.
+Contaminants:           	0 reads (0.00%) 	0 bases (0.00%)
+Total Removed:          	0 reads (0.00%) 	0 bases (0.00%)
+Result:                 	100 reads (100.00%) 	10000 bases (100.00%)
+
+Time:                         	0.711 seconds.
+Reads Processed:         100 	0.14k reads/sec
+Bases Processed:       10000 	0.01m bases/sec
diff -r 1206c725e45a -r b7e8663db1ec test-data/checkm.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/checkm.tabular	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,2 @@
+Bin Id	Marker lineage	# genomes	# markers	# marker sets	0	1	2	3	4	5+	Completeness	Contamination	Strain heterogeneity
+637000110	f__Enterobacteriaceae (UID5103)	157	1005	324	1005	0	0	0	0	0	0.00	0.00	0.00
diff -r 1206c725e45a -r b7e8663db1ec test-data/diamond.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/diamond.log	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,180 @@
+diamond blastp --quiet --threads 1 --db ./database --query /tmp/tmpxfb7idqd/files/e/4/f/dataset_e4f75201-863d-4397-8ca7-7c0b79593e9d.dat --no-self-hits --outfmt 0 --out /tmp/tmpxfb7idqd/job_working_directory/000/3/outputs/dataset_0fb25f52-9d9b-4592-a709-7e516f37daa1.dat --compress 0 --algo 0 --matrix BLOSUM62 --comp-based-stats 1 --masking 1 --max-target-seqs 25 --evalue 0.001 --id 0 --query-cover 0 --subject-cover 0 --block-size 2.0 --motif-masking 0 --log
+diamond v2.0.15.153
+#CPU threads: 1
+Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
+CPU features detected: ssse3 popcnt sse4.1 avx2
+Runtime dispatch: disabled
+L3 cache size: 8388608
+MAX_SHAPE_LEN=19 SEQ_MASK STRICT_BAND
+Temporary directory: /tmp/tmpxfb7idqd/job_working_directory/000/3/outputs
+#Target sequences to report alignments for: 25
+DP fields: 1
+Opening the database...  [0s]
+Database: ./database.dmnd (type: Diamond database, sequences: 2, letters: 568)
+Block size = 2000000000
+Opening the input file...  [0s]
+Opening the output file...  [0s]
+Loading query sequences...  [0s]
+Sequences = 2, letters = 566, average length = 283
+Masking queries...  [0s]
+Current RSS: 6.8 MB, Peak RSS: 6.8 MB
+Algorithm: Double-indexed
+Shape configuration: 111101110111,111011010010111
+Building query histograms...  [0s]
+Allocating buffers...  [0s]
+Current RSS: 6.9 MB, Peak RSS: 6.9 MB
+Loading reference sequences...  [0s]
+Sequences = 2, letters = 568, average length = 284
+Current RSS: 6.9 MB, Peak RSS: 6.9 MB
+Masking reference...  [0s]
+Masked letters: 0
+Initializing temporary storage... Async_buffer() 2,1
+ [0s]
+Building reference histograms...  [0s]
+Allocating buffers...  [0s]
+Current RSS: 6.9 MB, Peak RSS: 7.0 MB
+Processing query block 1, reference block 1/1, shape 1/2, index chunk 1/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 97875695011120/566 (17292525620339.22%), reference seeds = 0/568 (0.00%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/57 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Processing query block 1, reference block 1/1, shape 1/2, index chunk 2/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 0/568 (0.00%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/57 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Processing query block 1, reference block 1/1, shape 1/2, index chunk 3/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 0/568 (0.00%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/65 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Processing query block 1, reference block 1/1, shape 1/2, index chunk 4/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 129/566 (22.79%), reference seeds = 107/568 (18.84%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/60 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Current RSS: 9.1 MB, Peak RSS: 9.2 MB
+Processing query block 1, reference block 1/1, shape 2/2, index chunk 1/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 97875695011120/566 (17292525620339.22%), reference seeds = 107/568 (18.84%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/58 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Processing query block 1, reference block 1/1, shape 2/2, index chunk 2/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 107/568 (18.84%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/66 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Processing query block 1, reference block 1/1, shape 2/2, index chunk 3/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 2560271741526742528/566 (452344830658435072.00%), reference seeds = 107/568 (18.84%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/46 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Processing query block 1, reference block 1/1, shape 2/2, index chunk 4/4.
+Building reference seed array...  [0s]
+Building query seed array...  [0s]
+Indexed query seeds = 120/566 (21.20%), reference seeds = 102/568 (17.96%)
+Soft masked letters = 0/566 (0.00%), 0/568 (0.00%)
+Computing hash join...  [0s]
+Masking low complexity seeds...  [0s]
+Masked seeds: 0/60 (0.00%)
+Masked positions (query): 0/566 (0.00%)
+Masked positions (target): 0/568 (0.00%)
+Searching alignments...  [0s]
+Deallocating buffers...  [0s]
+Clearing query masking...  [0s]
+Computing alignments... Async_buffer.load() 17(2.37487e-07 GB, 1.4063e-07 GB on disk)
+Loading trace points...  [0s]
+Sorting trace points...  [0s]
+Computing alignments...  [0.01s]
+Deallocating buffers...  [0s]
+Loading trace points...  [0s]
+ [0.011s]
+Deallocating reference...  [0s]
+Loading reference sequences...  [0s]
+Current RSS: 9.6 MB, Peak RSS: 9.6 MB
+Deallocating buffers...  [0s]
+Current RSS: 9.6 MB, Peak RSS: 9.6 MB
+Deallocating queries...  [0s]
+Loading query sequences...  [0s]
+Closing the input file...  [0s]
+Closing the output file...  [0s]
+Cleaning up...  [0s]
+Current RSS: 9.6 MB, Peak RSS: 9.6 MB
+Total time = 0.093s
+Hits (filter stage 0) = 774
+Hits (filter stage 1) = 774 (100 %)
+Hits (filter stage 2) = 774 (100 %)
+Hits (filter stage 3) = 17 (2.19638 %)
+Target hits (stage 0) = 2
+Target hits (stage 1) = 0
+Target hits (stage 2) = 2
+Target hits (stage 3) = 2 (0 (0%) with CBS)
+Target hits (stage 4) = 2
+Target hits (stage 5) = 2
+Swipe realignments    = 0
+Matrix adjusts        = 0
+Extensions (8 bit)    = 0
+Extensions (16 bit)   = 4
+Extensions (32 bit)   = 0
+Hard queries          = 0
+Gapped filter (targets) = 0
+Gapped filter (hits) stage 1 = 0
+Gapped filter (hits) stage 2 = 0
+Time (Load seed hit targets) = 4e-06s (CPU)
+Time (Sort targets by score) = 0s (CPU)
+Time (Gapped filter)         = 0s (CPU)
+Time (Matrix adjust)         = 0s (CPU)
+Time (Chaining)              = 2e-05s (CPU)
+Time (DP target sorting)     = 0s (CPU)
+Time (Smith Waterman)        = 6.9e-05s (CPU)
+Time (Smith Waterman TB)     = 0.0001s (CPU)
+Time (Traceback)             = 8e-06s (CPU)
+Time (Target parallel)       = 0s (wall)
+Time (Load seed hits)        = 0.000495s (wall)
+Time (Sort seed hits)        = 2.4e-05s (wall)
+Time (Extension)             = 0.010185s (wall)
+Temporary disk space used (search): 1.4063e-07 GB
+Reported 2 pairwise alignments, 2 HSPs.
+1 queries aligned.
diff -r 1206c725e45a -r b7e8663db1ec test-data/freyja.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/freyja.tsv	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,6 @@
+	variants.tsv
+summarized	[('A', 0.5789470000000878), ('Delta', 0.4188134220012827)]
+lineages	A AY.48 B.1.617.2 A.4 A.2
+abundances	0.57475400 0.37892715 0.03988627 0.00313480 0.00105820
+resid	3.5081238846264213
+coverage	99.73246831421596
diff -r 1206c725e45a -r b7e8663db1ec test-data/gtdbtk.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/gtdbtk.tsv	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,2 @@
+user_genome	classification	closest_genome_reference	closest_genome_reference_radius	closest_genome_taxonomy	closest_genome_ani	closest_genome_af	closest_placement_reference	closest_placement_radius	closest_placement_taxonomy	closest_placement_ani	closest_placement_af	pplacer_taxonomy	classification_method	note	other_related_references(genome_id,species_name,radius,ANI,AF)	msa_percent	translation_table	red_value	warnings
+genome_1_fna_gz	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium	GCF_000024185.1	95.0	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium	100.0	1.0	GCF_000024185.1	95.0	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__Methanobrevibacter ruminantium	100.0	1.0	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter;s__	taxonomic classification defined by topology and ANI	topological placement and ANI have congruent species assignments	N/A	97.56	11	N/A	N/A
diff -r 1206c725e45a -r b7e8663db1ec test-data/kraken_test0_report.tab
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kraken_test0_report.tab	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,1 @@
+100.00	240	240	0	0	U	0	root
diff -r 1206c725e45a -r b7e8663db1ec test-data/megahit.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/megahit.txt	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,143 @@
+2025-02-13 13:23:44 - MEGAHIT v1.2.9
+2025-02-13 13:23:44 - Using megahit_core with POPCNT and BMI2 support
+2025-02-13 13:23:44 - Convert reads to binary library
+2025-02-13 13:23:44 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core buildlib /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib
+2025-02-13 13:23:44 - b'INFO  sequence/io/sequence_lib.cpp  :   75 - Lib 0 (/data/dnb10/galaxy_db/files/c/5/2/dataset_c52c6559-228d-4131-9eec-f5b8d04f08c8.dat): se, 1 reads, 1232 max length'
+2025-02-13 13:23:44 - b'INFO  utils/utils.h                 :  152 - Real: 0.2031\tuser: 0.0028\tsys: 0.0074\tmaxrss: 14696'
+2025-02-13 13:23:44 - Start assembly. Number of CPU threads 10 
+2025-02-13 13:23:44 - k list: 21,29,39,59,79,99,119,141 
+2025-02-13 13:23:44 - Memory used: 83886080
+2025-02-13 13:23:44 - Extract solid (k+1)-mers for k = 21 
+2025-02-13 13:23:44 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core count -k 21 -m 2 --host_mem 83886080 --mem_flag 1 --output_prefix /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 --num_cpu_threads 10 --read_lib_file /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  148 - Preparing data...'
+2025-02-13 13:23:44 - b'INFO  sequence/io/sequence_lib.cpp  :  115 - Before reading, sizeof seq_package: 324'
+2025-02-13 13:23:44 - b'INFO  sequence/io/sequence_lib.cpp  :  117 - After reading, sizeof seq_package: 324'
+2025-02-13 13:23:44 - b'INFO  sorting/kmer_counter.cpp      :   76 - 1 reads, 1232 max read length'
+2025-02-13 13:23:44 - b'INFO  sorting/kmer_counter.cpp      :   82 - 2 words per substring, 2 words per edge'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  153 - Preparing data... Done. Time elapsed: 0.0209'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  156 - Preparing partitions and calculating bucket sizes...'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :   80 - Minimum memory required: 5243336 bytes'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  138 - Lv1 items: 161, Lv2 items: 30'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  139 - Memory of derived class: 5243252, Memory for Lv1+Lv2: 1124'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  165 - Preparing partitions and calculating bucket sizes... Done. Time elapsed: 0.0257'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  172 - Start main loop...'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 0 to 120'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0003'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0022'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 120 to 361'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 361 to 602'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 602 to 843'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0002'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 843 to 1084'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0002'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 1084 to 65536'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0027'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0031'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  204 - Main loop done. Time elapsed: 0.0096'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  207 - Postprocessing...'
+2025-02-13 13:23:44 - b'INFO  sorting/kmer_counter.cpp      :  405 - Total number of candidate reads: 1 (1)'
+2025-02-13 13:23:44 - b'INFO  sorting/kmer_counter.cpp      :  407 - Total number of solid edges: 26'
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  210 - Postprocess done. Time elapsed: 0.0595'
+2025-02-13 13:23:44 - b'INFO  utils/utils.h                 :  152 - Real: 0.1204\tuser: 0.3707\tsys: 0.0656\tmaxrss: 30296'
+2025-02-13 13:23:44 - Build graph for k = 21 
+2025-02-13 13:23:44 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core seq2sdbg --host_mem 83886080 --mem_flag 1 --output_prefix /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 --num_cpu_threads 10 -k 21 --kmer_from 0 --input_prefix /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 --need_mercy
+2025-02-13 13:23:44 - b'INFO  sorting/base_engine.cpp       :  148 - Preparing data...'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  369 - Number edges: 26'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  413 - Bases to reserve: 704, number contigs: 0, number multiplicity: 32'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  421 - Before reading, sizeof seq_package: 184, multiplicity vector: 32'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  428 - Read 26 edges.'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  429 - After reading, sizeof seq_package: 184/26/572, multiplicity vector: 26/32'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  440 - Adding mercy edges...'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  191 - Read 1 reads to search for mercy k-mers'
+2025-02-13 13:23:44 - b'INFO  sorting/seq_to_sdbg.cpp       :  355 - Number of reads: 1, Number of mercy edges: 529'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  444 - Done. Time elapsed: 0.2585'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  445 - After adding mercy, sizeof seq_package: 5640/555/12210, multiplicity vector: 555/555'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  506 - Finally, sizeof seq_package: 5640/555/12210, multiplicity vector: 555/555'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  153 - Preparing data... Done. Time elapsed: 0.3852'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  156 - Preparing partitions and calculating bucket sizes...'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :   80 - Minimum memory required: 7022 bytes'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  138 - Lv1 items: 444, Lv2 items: 90'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  139 - Memory of derived class: 6870, Memory for Lv1+Lv2: 2496'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  165 - Preparing partitions and calculating bucket sizes... Done. Time elapsed: 0.0129'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  172 - Start main loop...'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 0 to 167'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0005'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 167 to 355'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0001'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 355 to 543'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 543 to 731'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0001'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 731 to 919'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0002'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  185 - Lv1 scanning from bucket 919 to 65536'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  192 - Lv1 scanning done. Large diff: 0. Time elapsed: 0.0026'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  198 - Lv1 fetching & sorting done. Time elapsed: 0.0024'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  204 - Main loop done. Time elapsed: 0.0066'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  207 - Postprocessing...'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  793 - Number of $ A C G T A- C- G- T-:'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  794 - 0 253 302 302 253 0 0 0 0'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  800 - Total number of edges: 1110'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  801 - Total number of ONEs: 1110'
+2025-02-13 13:23:45 - b'INFO  sorting/seq_to_sdbg.cpp       :  802 - Total number of $v edges: 0'
+2025-02-13 13:23:45 - b'INFO  sorting/base_engine.cpp       :  210 - Postprocess done. Time elapsed: 0.1141'
+2025-02-13 13:23:45 - b'INFO  utils/utils.h                 :  152 - Real: 0.5262\tuser: 0.5163\tsys: 0.3042\tmaxrss: 269456'
+2025-02-13 13:23:45 - Assemble contigs from SdBG for k = 21
+2025-02-13 13:23:45 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core assemble -s /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21 -o /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21 -t 10 --min_standalone 300 --prune_level 2 --merge_len 20 --merge_similar 0.95 --cleaning_rounds 5 --disconnect_ratio 0.1 --low_local_ratio 0.2 --cleaning_rounds 5 --min_depth 2.0 --bubble_level 2 --max_tip_len -1 --careful_bubble
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  129 - Loading succinct de Bruijn graph: /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k21/21Done. Time elapsed: 0.148410'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  133 - Number of Edges: 1110; K value: 21'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  140 - Number of CPU threads: 10'
+2025-02-13 13:23:45 - b'INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 2; Accumulated tips removed: 0; time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 4; Accumulated tips removed: 0; time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 8; Accumulated tips removed: 0; time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 16; Accumulated tips removed: 0; time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  assembly/sdbg_pruning.cpp     :  160 - Removing tips with length less than 32; Accumulated tips removed: 0; time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  assembly/sdbg_pruning.cpp     :  169 - Removing tips with length less than 42; Accumulated tips removed: 0; time elapsed: 0.0000'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  158 - Tips removal done! Time elapsed(sec): 0.002'
+2025-02-13 13:23:45 - b'INFO  assembly/unitig_graph.cpp     :   83 - Graph size without loops: 0, palindrome: 0'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  166 - unitig graph size: 1, time for building: 0.002'
+2025-02-13 13:23:45 - b'INFO  assembly/contig_stat.h        :   40 - Max: 576, Min: 576, N50: 576, number contigs: 1, number isolated: 1, number looped: 1, total size: 576,'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  184 - Graph cleaning round 1'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  200 - Number of bubbles removed: 0, Time elapsed(sec): 0.000'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  210 - Number of complex bubbles removed: 0, Time elapsed(sec): 0.000024'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  221 - Number unitigs disconnected: 0, time: 0.000'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  245 - Unitigs removed in excessive pruning: 0, time: 0.000'
+2025-02-13 13:23:45 - b'INFO  assembly/contig_stat.h        :   40 - Max: 576, Min: 576, N50: 576, number contigs: 1, number isolated: 1, number looped: 1, total size: 576,'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  267 - Time to output: 0.000192'
+2025-02-13 13:23:45 - b'INFO  main_assemble.cpp             :  286 - Number of local low depth unitigs removed: 0, complex bubbles removed: 0, time: 0.000034'
+2025-02-13 13:23:45 - b'INFO  assembly/contig_stat.h        :   40 - Max: 576, Min: 576, N50: 576, number contigs: 1, number isolated: 1, number looped: 1, total size: 576,'
+2025-02-13 13:23:45 - b'INFO  utils/utils.h                 :  152 - Real: 0.1675\tuser: 0.2808\tsys: 0.0330\tmaxrss: 22464'
+2025-02-13 13:23:45 - Local assembly for k = 21
+2025-02-13 13:23:45 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core local -c /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.contigs.fa -l /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib -t 10 -o /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.local.fa --kmax 29
+2025-02-13 13:23:45 - b'INFO  localasm/hash_mapper.cpp      :   99 - Number of contigs: 0, index size: 0'
+2025-02-13 13:23:45 - b'INFO  localasm/local_assemble.cpp   :  315 - Hash mapper construction time elapsed: 0.003884'
+2025-02-13 13:23:45 - b'INFO  sequence/io/sequence_lib.cpp  :  115 - Before reading, sizeof seq_package: 324'
+2025-02-13 13:23:45 - b'INFO  sequence/io/sequence_lib.cpp  :  117 - After reading, sizeof seq_package: 324'
+2025-02-13 13:23:45 - b'INFO  localasm/local_assemble.cpp   :  324 - Read lib time elapsed: 0.001268'
+2025-02-13 13:23:45 - b'INFO  localasm/local_assemble.cpp   :  330 - Insert size estimation time elapsed: 0.000001'
+2025-02-13 13:23:45 - b'INFO  localasm/local_assemble.cpp   :  218 - Lib 0: total 1 reads, aligned 0, added 0 reads to local assembly'
+2025-02-13 13:23:45 - b'INFO  localasm/local_assemble.cpp   :  338 - Mapping time elapsed: 0.000047'
+2025-02-13 13:23:45 - b'INFO  localasm/local_assemble.cpp   :  232 - Minimum number of reads to do local assembly: 0'
+2025-02-13 13:23:45 - b'INFO  localasm/local_assemble.cpp   :  346 - Local assembly time elapsed: 0.004100'
+2025-02-13 13:23:45 - b'INFO  utils/utils.h                 :  152 - Real: 0.0094\tuser: 0.0553\tsys: 0.0074\tmaxrss: 14696'
+2025-02-13 13:23:45 - Extract iterative edges from k = 21 to 29 
+2025-02-13 13:23:45 - command /usr/local/tools/_conda/envs/__megahit@1.2.9/bin/megahit_core iterate -c /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.contigs.fa -b /data/jwd02f/main/079/102/79102477/working/megahit_out/intermediate_contigs/k21.bubble_seq.fa -t 10 -k 21 -s 8 -o /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/k29/29 -r /data/jwd02f/main/079/102/79102477/working/megahit_out/tmp/reads.lib.bin
+2025-02-13 13:23:45 - b'INFO  main_iterate.cpp              :  190 - Selected kmer type size for k: 8'
+2025-02-13 13:23:45 - b'INFO  main_iterate.cpp              :  123 - Selected kmer type size for next k: 8'
+2025-02-13 13:23:45 - b'INFO  main_iterate.cpp              :  138 - Processed: 1, aligned: 0. Iterative edges: 0'
+2025-02-13 13:23:45 - b'INFO  main_iterate.cpp              :  142 - Total: 1, aligned: 0. Iterative edges: 0'
+2025-02-13 13:23:45 - b'INFO  utils/utils.h                 :  152 - Real: 0.0136\tuser: 0.0433\tsys: 0.0101\tmaxrss: 14696'
+2025-02-13 13:23:45 - Merging to output final contigs 
+2025-02-13 13:23:45 - 1 contigs, total 576 bp, min 576 bp, max 576 bp, avg 576 bp, N50 576 bp
+2025-02-13 13:23:45 - ALL DONE. Time elapsed: 1.490756 seconds 
diff -r 1206c725e45a -r b7e8663db1ec test-data/metaphlan.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/metaphlan.txt	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,31 @@
+#custom_db
+#mpa_v21_CHOCOPhlAnxxx_2
+#/home/bebatut/miniconda3/envs/mulled-v1-b4915a464cf72db4053ec566c65e3f5f431691323f08f9b6b1c9ecfc4f8b9c88/bin/metaphlan in --input_type fasta --read_min_len 70 --bowtie2db ref_db/ --index custom_db --bt2_ps very-sensitive --min_mapq_val 5 -t rel_ab --tax_lev a --min_cu_len 2000 --add_viruses --stat_q 0.2 --perc_nonzero 0.33 --avoid_disqm --sample_id_key SampleID --sample_id Metaphlan_Analysis -o /tmp/tmptu3575j7/files/000/dataset_19.dat --bowtie2out bowtie2out -s /tmp/tmptu3575j7/files/000/dataset_21.dat --biom /tmp/tmptu3575j7/files/000/dataset_22.dat --nproc 1
+#SampleID	Metaphlan_Analysis
+#clade_name	NCBI_tax_id	relative_abundance	additional_species
+k__Bacteria	2	100.0	
+k__Bacteria|p__Proteobacteria	2|1224	52.20019	
+k__Bacteria|p__Actinobacteria	2|201174	34.37371	
+k__Bacteria|p__Firmicutes	2|1239	13.4261	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria	2|1224|1236	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria	2|201174|1760	34.37371	
+k__Bacteria|p__Firmicutes|c__Bacilli	2|1239|91061	13.4261	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales	2|1224|1236|72274	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales	2|201174|1760|85007	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales	2|1239|91061|186826	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales	2|201174|1760|85009	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae	2|1224|1236|72274|468	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae	2|201174|1760|85007|1653	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae	2|1239|91061|186826|186828	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae	2|201174|1760|85009|31957	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella	2|1224|1236|72274|468|475	52.20019	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium	2|201174|1760|85007|1653|1716	24.7409	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum	2|1239|91061|186826|186828|29393	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium	2|201174|1760|85009|31957|1912216	9.63281	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_lacunata	2|1224|1236|72274|468|475|477	22.57968	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_pseudodiphtheriticum	2|201174|1760|85007|1653|1716|37637	18.75365	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_nonliquefaciens	2|1224|1236|72274|468|475|478	15.88652	
+k__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Pseudomonadales|f__Moraxellaceae|g__Moraxella|s__Moraxella_equi	2|1224|1236|72274|468|475|60442	13.73399	
+k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Dolosigranulum|s__Dolosigranulum_pigrum	2|1239|91061|186826|186828|29393|29394	13.4261	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Propionibacteriales|f__Propionibacteriaceae|g__Cutibacterium|s__Cutibacterium_acnes	2|201174|1760|85009|31957|1912216|1747	9.63281	
+k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_accolens	2|201174|1760|85007|1653|1716|38284	5.98726	
diff -r 1206c725e45a -r b7e8663db1ec test-data/nonpareil.json
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/nonpareil.json	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,2194 @@
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+}
+
diff -r 1206c725e45a -r b7e8663db1ec test-data/output_dedup_pairs.stats
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/output_dedup_pairs.stats	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,438 @@
+total	1992
+total_unmapped	914
+total_single_sided_mapped	287
+total_mapped	791
+total_dups	9
+total_nodups	782
+cis	597
+trans	185
+pair_types/NN	853
+pair_types/UU	782
+pair_types/NU	234
+pair_types/MU	53
+pair_types/MM	40
+pair_types/NM	21
+pair_types/DD	9
+cis_1kb+	185
+cis_2kb+	171
+cis_4kb+	151
+cis_10kb+	114
+cis_20kb+	80
+cis_40kb+	46
+summary/frac_cis	0.7634271099744245
+summary/frac_cis_1kb+	0.23657289002557544
+summary/frac_cis_2kb+	0.2186700767263427
+summary/frac_cis_4kb+	0.19309462915601022
+summary/frac_cis_10kb+	0.14578005115089515
+summary/frac_cis_20kb+	0.10230179028132992
+summary/frac_cis_40kb+	0.058823529411764705
+summary/frac_dups	0.011378002528445006
+summary/complexity_naive	34495.88583157276
+summary/dist_freq_convergence/convergence_dist	1333521
+summary/dist_freq_convergence/strands_w_max_convergence_dist	++
+summary/dist_freq_convergence/convergence_rel_diff_threshold	0.05
+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/++	49
+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/--	58
+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/-+	65
+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist/+-	425
+summary/dist_freq_convergence/n_cis_pairs_below_convergence_dist_all_strands	597
+summary/dist_freq_convergence/n_cis_pairs_above_convergence_dist_all_strands	0
+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/++	0.08207705192629816
+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/--	0.09715242881072027
+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/-+	0.10887772194304858
+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist/+-	0.711892797319933
+summary/dist_freq_convergence/frac_cis_in_cis_below_convergence_dist_all_strands	1.0
+summary/dist_freq_convergence/frac_cis_in_cis_above_convergence_dist_all_strands	0.0
+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/++	0.061946902654867256
+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/--	0.07332490518331226
+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/-+	0.08217446270543616
+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist/+-	0.5372945638432364
+summary/dist_freq_convergence/frac_total_mapped_in_cis_below_convergence_dist_all_strands	0.754740834386852
+summary/dist_freq_convergence/frac_total_mapped_in_cis_above_convergence_dist_all_strands	0.0
+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/++	0.06265984654731457
+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/--	0.0741687979539642
+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/-+	0.08312020460358056
+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist/+-	0.5434782608695652
+summary/dist_freq_convergence/frac_total_nodups_in_cis_below_convergence_dist_all_strands	0.7634271099744245
+summary/dist_freq_convergence/frac_total_nodups_in_cis_above_convergence_dist_all_strands	0.0
+chrom_freq/chrIV/chrIV	83
+chrom_freq/chrVII/chrVII	55
+chrom_freq/chrXV/chrXV	53
+chrom_freq/chrXIII/chrXIII	46
+chrom_freq/chrII/chrII	41
+chrom_freq/chrXVI/chrXVI	40
+chrom_freq/chrXIV/chrXIV	37
+chrom_freq/chrX/chrX	37
+chrom_freq/chrXII/chrXII	36
+chrom_freq/chrXI/chrXI	36
+chrom_freq/chrM/chrM	33
+chrom_freq/chrVIII/chrVIII	30
+chrom_freq/chrIX/chrIX	22
+chrom_freq/chrV/chrV	21
+chrom_freq/chrIII/chrIII	12
+chrom_freq/chrVI/chrVI	8
+chrom_freq/chrI/chrI	7
+chrom_freq/chrVII/chrXV	6
+chrom_freq/chrIV/chrXII	6
+chrom_freq/chrIV/chrXIII	6
+chrom_freq/chrVII/chrXII	6
+chrom_freq/chrII/chrVII	5
+chrom_freq/chrXII/chrXIII	5
+chrom_freq/chrIV/chrX	5
+chrom_freq/chrX/chrXIV	4
+chrom_freq/chrII/chrIV	4
+chrom_freq/chrII/chrXVI	4
+chrom_freq/chrXIV/chrXVI	4
+chrom_freq/chrII/chrXIV	4
+chrom_freq/chrVII/chrXIV	4
+chrom_freq/chrXI/chrXV	4
+chrom_freq/chrXI/chrXII	4
+chrom_freq/chrIV/chrVII	4
+chrom_freq/chrXIII/chrXV	3
+chrom_freq/chrXI/chrXVI	3
+chrom_freq/chrII/chrXIII	3
+chrom_freq/chrXI/chrXIII	3
+chrom_freq/chrVII/chrIX	3
+chrom_freq/chrVIII/chrXIII	3
+chrom_freq/chrX/chrXII	3
+chrom_freq/chrX/chrXIII	3
+chrom_freq/chrXIII/chrXIV	3
+chrom_freq/chrV/chrXVI	3
+chrom_freq/chrIV/chrV	3
+chrom_freq/chrIV/chrVIII	3
+chrom_freq/chrIV/chrXI	3
+chrom_freq/chrIV/chrXV	3
+chrom_freq/chrIV/chrXVI	3
+chrom_freq/chrXV/chrXVI	3
+chrom_freq/chrIX/chrXII	3
+chrom_freq/chrXIII/chrXVI	2
+chrom_freq/chrX/chrXVI	2
+chrom_freq/chrIV/chrVI	2
+chrom_freq/chrIV/chrXIV	2
+chrom_freq/chrXI/chrXIV	2
+chrom_freq/chrVII/chrXVI	2
+chrom_freq/chrIX/chrX	2
+chrom_freq/chrVII/chrVIII	2
+chrom_freq/chrIII/chrX	2
+chrom_freq/chrIX/chrXV	2
+chrom_freq/chrIII/chrV	2
+chrom_freq/chrXIV/chrXV	2
+chrom_freq/chrXII/chrXV	2
+chrom_freq/chrV/chrX	2
+chrom_freq/chrI/chrX	2
+chrom_freq/chrII/chrXV	2
+chrom_freq/chrII/chrVIII	1
+chrom_freq/chrXII/chrXIV	1
+chrom_freq/chrXII/chrXVI	1
+chrom_freq/chrII/chrX	1
+chrom_freq/chrI/chrXV	1
+chrom_freq/chrIII/chrXIII	1
+chrom_freq/chrII/chrXI	1
+chrom_freq/chrVI/chrX	1
+chrom_freq/chrIII/chrVIII	1
+chrom_freq/chrIX/chrXI	1
+chrom_freq/chrV/chrM	1
+chrom_freq/chrV/chrVI	1
+chrom_freq/chrV/chrXI	1
+chrom_freq/chrV/chrXIII	1
+chrom_freq/chrV/chrXIV	1
+chrom_freq/chrV/chrXV	1
+chrom_freq/chrVI/chrXI	1
+chrom_freq/chrVIII/chrXV	1
+chrom_freq/chrVI/chrXII	1
+chrom_freq/chrVI/chrXIII	1
+chrom_freq/chrVI/chrXIV	1
+chrom_freq/chrVI/chrXVI	1
+chrom_freq/chrVII/chrXIII	1
+chrom_freq/chrVIII/chrIX	1
+chrom_freq/chrVIII/chrXI	1
+chrom_freq/chrVIII/chrXII	1
+chrom_freq/chrVI/chrVII	1
+dist_freq/0-1/+-	0
+dist_freq/0-1/-+	0
+dist_freq/0-1/--	0
+dist_freq/0-1/++	0
+dist_freq/1-2/+-	0
+dist_freq/1-2/-+	0
+dist_freq/1-2/--	0
+dist_freq/1-2/++	0
+dist_freq/2-3/+-	0
+dist_freq/2-3/-+	0
+dist_freq/2-3/--	0
+dist_freq/2-3/++	0
+dist_freq/3-4/+-	0
+dist_freq/3-4/-+	0
+dist_freq/3-4/--	0
+dist_freq/3-4/++	0
+dist_freq/4-6/+-	0
+dist_freq/4-6/-+	1
+dist_freq/4-6/--	0
+dist_freq/4-6/++	1
+dist_freq/6-7/+-	0
+dist_freq/6-7/-+	0
+dist_freq/6-7/--	0
+dist_freq/6-7/++	0
+dist_freq/7-10/+-	0
+dist_freq/7-10/-+	0
+dist_freq/7-10/--	0
+dist_freq/7-10/++	0
+dist_freq/10-13/+-	0
+dist_freq/10-13/-+	0
+dist_freq/10-13/--	0
+dist_freq/10-13/++	0
+dist_freq/13-18/+-	0
+dist_freq/13-18/-+	0
+dist_freq/13-18/--	0
+dist_freq/13-18/++	0
+dist_freq/18-24/+-	0
+dist_freq/18-24/-+	0
+dist_freq/18-24/--	0
+dist_freq/18-24/++	0
+dist_freq/24-32/+-	0
+dist_freq/24-32/-+	0
+dist_freq/24-32/--	0
+dist_freq/24-32/++	0
+dist_freq/32-42/+-	0
+dist_freq/32-42/-+	0
+dist_freq/32-42/--	0
+dist_freq/32-42/++	0
+dist_freq/42-56/+-	0
+dist_freq/42-56/-+	0
+dist_freq/42-56/--	0
+dist_freq/42-56/++	0
+dist_freq/56-75/+-	0
+dist_freq/56-75/-+	0
+dist_freq/56-75/--	0
+dist_freq/56-75/++	0
+dist_freq/75-100/+-	0
+dist_freq/75-100/-+	1
+dist_freq/75-100/--	0
+dist_freq/75-100/++	0
+dist_freq/100-133/+-	1
+dist_freq/100-133/-+	0
+dist_freq/100-133/--	1
+dist_freq/100-133/++	0
+dist_freq/133-178/+-	6
+dist_freq/133-178/-+	2
+dist_freq/133-178/--	1
+dist_freq/133-178/++	0
+dist_freq/178-237/+-	116
+dist_freq/178-237/-+	3
+dist_freq/178-237/--	0
+dist_freq/178-237/++	0
+dist_freq/237-316/+-	218
+dist_freq/237-316/-+	6
+dist_freq/237-316/--	1
+dist_freq/237-316/++	0
+dist_freq/316-422/+-	32
+dist_freq/316-422/-+	3
+dist_freq/316-422/--	0
+dist_freq/316-422/++	0
+dist_freq/422-562/+-	2
+dist_freq/422-562/-+	4
+dist_freq/422-562/--	0
+dist_freq/422-562/++	0
+dist_freq/562-750/+-	1
+dist_freq/562-750/-+	3
+dist_freq/562-750/--	0
+dist_freq/562-750/++	0
+dist_freq/750-1000/+-	0
+dist_freq/750-1000/-+	8
+dist_freq/750-1000/--	0
+dist_freq/750-1000/++	1
+dist_freq/1000-1334/+-	0
+dist_freq/1000-1334/-+	1
+dist_freq/1000-1334/--	2
+dist_freq/1000-1334/++	0
+dist_freq/1334-1778/+-	0
+dist_freq/1334-1778/-+	4
+dist_freq/1334-1778/--	4
+dist_freq/1334-1778/++	1
+dist_freq/1778-2371/+-	1
+dist_freq/1778-2371/-+	4
+dist_freq/1778-2371/--	1
+dist_freq/1778-2371/++	0
+dist_freq/2371-3162/+-	4
+dist_freq/2371-3162/-+	3
+dist_freq/2371-3162/--	1
+dist_freq/2371-3162/++	0
+dist_freq/3162-4217/+-	1
+dist_freq/3162-4217/-+	2
+dist_freq/3162-4217/--	3
+dist_freq/3162-4217/++	3
+dist_freq/4217-5623/+-	3
+dist_freq/4217-5623/-+	2
+dist_freq/4217-5623/--	3
+dist_freq/4217-5623/++	1
+dist_freq/5623-7499/+-	6
+dist_freq/5623-7499/-+	2
+dist_freq/5623-7499/--	6
+dist_freq/5623-7499/++	2
+dist_freq/7499-10000/+-	3
+dist_freq/7499-10000/-+	2
+dist_freq/7499-10000/--	3
+dist_freq/7499-10000/++	3
+dist_freq/10000-13335/+-	5
+dist_freq/10000-13335/-+	1
+dist_freq/10000-13335/--	3
+dist_freq/10000-13335/++	6
+dist_freq/13335-17783/+-	2
+dist_freq/13335-17783/-+	3
+dist_freq/13335-17783/--	5
+dist_freq/13335-17783/++	4
+dist_freq/17783-23714/+-	5
+dist_freq/17783-23714/-+	0
+dist_freq/17783-23714/--	4
+dist_freq/17783-23714/++	4
+dist_freq/23714-31623/+-	4
+dist_freq/23714-31623/-+	4
+dist_freq/23714-31623/--	4
+dist_freq/23714-31623/++	1
+dist_freq/31623-42170/+-	4
+dist_freq/31623-42170/-+	2
+dist_freq/31623-42170/--	3
+dist_freq/31623-42170/++	6
+dist_freq/42170-56234/+-	2
+dist_freq/42170-56234/-+	2
+dist_freq/42170-56234/--	4
+dist_freq/42170-56234/++	4
+dist_freq/56234-74989/+-	2
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+dist_freq/56234-74989/--	4
+dist_freq/56234-74989/++	2
+dist_freq/74989-100000/+-	0
+dist_freq/74989-100000/-+	1
+dist_freq/74989-100000/--	1
+dist_freq/74989-100000/++	3
+dist_freq/100000-133352/+-	1
+dist_freq/100000-133352/-+	0
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+dist_freq/133352-177828/+-	2
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+dist_freq/421697-562341/++	1
+dist_freq/562341-749894/+-	1
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+dist_freq/562341-749894/++	1
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+dist_freq/749894-1000000/-+	0
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+dist_freq/1000000-1333521/+-	0
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+dist_freq/749894209-1000000000/++	0
+dist_freq/1000000000+/+-	0
+dist_freq/1000000000+/-+	0
+dist_freq/1000000000+/--	0
+dist_freq/1000000000+/++	0
diff -r 1206c725e45a -r b7e8663db1ec test-data/porechop.log
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/porechop.log	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,153 @@
+
+Loading reads
+/tmp/tmp4zxnky4h/files/5/c/1/dataset_5c125cad-e633-41bc-8f37-36d6af3f5f0f.dat
+9 reads loaded
+
+
+Looking for known adapter sets
+
0 / 9 (0.0%)
9 / 9 (100.0%)
9 / 9 (100.0%)
+                                        Best               
+                                        read       Best    
+                                        start      read end
+  Set                                   %ID        %ID     
+  SQK-NSK007                                96.4       95.5
+  Rapid                                     62.5        0.0
+  RBK004_upstream                           72.7        0.0
+  SQK-MAP006                                62.2       63.6
+  SQK-MAP006 short                          60.7       60.0
+  PCR adapters 1                            66.7       73.9
+  PCR adapters 2                            66.7       63.6
+  PCR adapters 3                            68.0       72.0
+  1D^2 part 1                               62.1       58.8
+  1D^2 part 2                               79.4       68.8
+  cDNA SSP                                  57.1       61.4
+  Barcode 1 (reverse)                       59.4       66.7
+  Barcode 2 (reverse)                       66.7       63.0
+  Barcode 3 (reverse)                       69.2       72.0
+  Barcode 4 (reverse)                       66.7       63.3
+  Barcode 5 (reverse)                       62.5       66.7
+  Barcode 6 (reverse)                       73.1       62.5
+  Barcode 7 (reverse)                       65.4       65.5
+  Barcode 8 (reverse)                       69.2       58.3
+  Barcode 9 (reverse)                       75.0       66.7
+  Barcode 10 (reverse)                      62.5       60.0
+  Barcode 11 (reverse)                      69.2       60.5
+  Barcode 12 (reverse)                      65.6       64.0
+  Barcode 1 (forward)                       65.4       61.5
+  Barcode 2 (forward)                       69.2       70.4
+  Barcode 3 (forward)                       73.1       68.0
+  Barcode 4 (forward)                       73.1       64.3
+  Barcode 5 (forward)                       62.5       66.7
+  Barcode 6 (forward)                       65.5       65.6
+  Barcode 7 (forward)                       73.1       66.7
+  Barcode 8 (forward)                       62.1       60.7
+  Barcode 9 (forward)                       68.0       70.8
+  Barcode 10 (forward)                      69.2       66.7
+  Barcode 11 (forward)                      65.4       60.7
+  Barcode 12 (forward)                      64.3       66.7
+  Barcode 13 (forward)                      64.3       69.2
+  Barcode 14 (forward)                      63.3       66.7
+  Barcode 15 (forward)                      66.7       66.7
+  Barcode 16 (forward)                      70.8       65.5
+  Barcode 17 (forward)                      69.2       66.7
+  Barcode 18 (forward)                      70.4       70.4
+  Barcode 19 (forward)                      65.5       64.0
+  Barcode 20 (forward)                      65.5       64.0
+  Barcode 21 (forward)                      64.3       66.7
+  Barcode 22 (forward)                      69.2       68.0
+  Barcode 23 (forward)                      61.5       66.7
+  Barcode 24 (forward)                      66.7       65.4
+  Barcode 25 (forward)                      64.0       65.5
+  Barcode 26 (forward)                      72.0       72.0
+  Barcode 27 (forward)                      77.8       60.7
+  Barcode 28 (forward)                      65.5       66.7
+  Barcode 29 (forward)                      62.5       66.7
+  Barcode 30 (forward)                      68.0       65.4
+  Barcode 31 (forward)                      62.5       69.2
+  Barcode 32 (forward)                      68.0       70.8
+  Barcode 33 (forward)                      62.5       70.4
+  Barcode 34 (forward)                      64.0       62.5
+  Barcode 35 (forward)                      65.5       65.4
+  Barcode 36 (forward)                      63.0       63.0
+  Barcode 37 (forward)                      67.9       64.3
+  Barcode 38 (forward)                      64.0       62.1
+  Barcode 39 (forward)                      64.0       69.2
+  Barcode 40 (forward)                      62.5       64.0
+  Barcode 41 (forward)                      68.0       65.5
+  Barcode 42 (forward)                      70.4       69.2
+  Barcode 43 (forward)                      63.3       63.3
+  Barcode 44 (forward)                      60.0       66.7
+  Barcode 45 (forward)                      73.1       65.4
+  Barcode 46 (forward)                      65.4       60.7
+  Barcode 47 (forward)                      65.5       64.0
+  Barcode 48 (forward)                      71.4       62.1
+  Barcode 49 (forward)                      69.2       62.1
+  Barcode 50 (forward)                      66.7       63.0
+  Barcode 51 (forward)                      69.2       64.3
+  Barcode 52 (forward)                      66.7       64.0
+  Barcode 53 (forward)                      67.9       69.0
+  Barcode 54 (forward)                      69.2       64.0
+  Barcode 55 (forward)                      66.7       73.1
+  Barcode 56 (forward)                      66.7       72.0
+  Barcode 57 (forward)                      69.0       60.0
+  Barcode 58 (forward)                      70.4       72.0
+  Barcode 59 (forward)                      56.7       66.7
+  Barcode 60 (forward)                      66.7       66.7
+  Barcode 61 (forward)                      70.8       65.5
+  Barcode 62 (forward)                      66.7       68.0
+  Barcode 63 (forward)                      66.7       60.7
+  Barcode 64 (forward)                      69.2       66.7
+  Barcode 65 (forward)                      61.5       69.0
+  Barcode 66 (forward)                      64.3       63.0
+  Barcode 67 (forward)                      66.7       67.9
+  Barcode 68 (forward)                      67.9       69.2
+  Barcode 69 (forward)                      69.2       75.0
+  Barcode 70 (forward)                      64.3       73.1
+  Barcode 71 (forward)                      64.0       71.4
+  Barcode 72 (forward)                      66.7       62.1
+  Barcode 73 (forward)                      67.7       64.0
+  Barcode 74 (forward)                      64.5       68.0
+  Barcode 75 (forward)                      65.4       65.5
+  Barcode 76 (forward)                      70.4       70.8
+  Barcode 77 (forward)                      65.4       64.3
+  Barcode 78 (forward)                      67.7       63.0
+  Barcode 79 (forward)                      70.8       69.2
+  Barcode 80 (forward)                      71.4       72.0
+  Barcode 81 (forward)                      68.0       66.7
+  Barcode 82 (forward)                      64.7       66.7
+  Barcode 83 (forward)                      69.2       68.0
+  Barcode 84 (forward)                      70.8       67.9
+  Barcode 85 (forward)                      61.5       60.0
+  Barcode 86 (forward)                      64.3       65.4
+  Barcode 87 (forward)                      66.7       65.4
+  Barcode 88 (forward)                      63.3       60.7
+  Barcode 89 (forward)                      69.2       66.7
+  Barcode 90 (forward)                      66.7       64.0
+  Barcode 91 (forward)                      68.0       64.3
+  Barcode 92 (forward)                      65.5       68.0
+  Barcode 93 (forward)                      69.2       73.1
+  Barcode 94 (forward)                      63.0       68.0
+  Barcode 95 (forward)                      64.0       63.3
+  Barcode 96 (forward)                      69.0       68.0
+
+
+Trimming adapters from read ends
+     SQK-NSK007_Y_Top: AATGTACTTCGTTCAGTTACGTATTGCT
+  SQK-NSK007_Y_Bottom: GCAATACGTAACTGAACGAAGT
+
+
0 / 9 (0.0%)
9 / 9 (100.0%)
9 / 9 (100.0%)
+
+4 / 9 reads had adapters trimmed from their start (74 bp removed)
+3 / 9 reads had adapters trimmed from their end (49 bp removed)
+
+
+Splitting reads containing middle adapters
+
0 / 9 (0.0%)
9 / 9 (100.0%)
10 / 9 (111.1%)
9 / 9 (100.0%)
+
+4 / 9 reads were split based on middle adapters
+
+
+Saving trimmed reads to file
+
+Saved result to /tmp/tmp4zxnky4h/job_working_directory/000/2/working/out.fasta
+
diff -r 1206c725e45a -r b7e8663db1ec test-data/snippy.txt
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/snippy.txt	Tue Feb 18 23:17:45 2025 +0000
@@ -0,0 +1,5 @@
+ID	LENGTH	ALIGNED	UNALIGNED	VARIANT	HET	MASKED	LOWCOV
+a	700	51	649	0	0	0	0
+b	700	51	649	1	0	0	0
+c	700	51	649	1	0	0	0
+Reference	700	700	0	0	0	0	0