# HG changeset patch
# User iuc
# Date 1615843637 0
# Node ID cf13a1e03e5b0a459b362074f25c43a25c8835b7
# Parent  602fb8e63aa7607abe4feaef8aadc56cf89efc64
"planemo upload commit e9c6496b181bbd2665e953a1f9ede35921707e2a"

diff -r 602fb8e63aa7 -r cf13a1e03e5b busco.xml
--- a/busco.xml	Wed Dec 30 14:07:37 2020 +0000
+++ b/busco.xml	Mon Mar 15 21:27:17 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="busco" name="Busco" profile="18.01" version="@TOOL_VERSION@">
+<tool id="busco" name="Busco" profile="20.01" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>assess genome assembly and annotation completeness</description>
     <macros>
         <import>macros.xml</import>
@@ -6,129 +6,262 @@
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">busco</requirement>
         <requirement type="package" version="1.32">tar</requirement>
+        <requirement type="package" version="1">fonts-conda-ecosystem</requirement>
     </requirements>
+    <version_command>busco --version</version_command>
     <command><![CDATA[
 if [ -z "\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\$(dirname \$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\$(realpath \${BUSCO_PATH}/../config) ; fi &&
 cp -r "\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&
 export AUGUSTUS_CONFIG_PATH=`pwd`/augustus_dir/ &&
 
-#if $adv.aug_prediction.augustus_mode == 'history':
+#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes' and $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
     ## Using an augustus model from history, we need to unzip it and let augustus find it
     mkdir -p 'augustus_dir/species/' &&
-    tar -C 'augustus_dir/species/' -xzf '${adv.aug_prediction.augustus_model}' &&
+    tar -C 'augustus_dir/species/' -xzf '${busco_mode.use_augustus.aug_prediction.augustus_model}' &&
 #end if
 
 busco
 --in '${input}'
 --lineage_dataset '${lineage_dataset}'
 --update-data
---mode '${mode}'
--o busco_galaxy
+--mode '${busco_mode.mode}'
+--out busco_galaxy
 --cpu \${GALAXY_SLOTS:-4}
 --evalue ${adv.evalue}
-${adv.long}
 --limit ${adv.limit}
-#if $adv.aug_prediction.augustus_mode == 'builtin':
-    --augustus_species '${adv.aug_prediction.augustus_species}'
-#else if $adv.aug_prediction.augustus_mode == 'history':
-    --augustus_species local
+
+#if $adv.auto_lineage:
+    $adv.auto_lineage
+#end if
+#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes':
+
+    ${busco_mode.use_augustus.long}
+    --augustus
+
+    #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin':
+        --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}'
+    #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history':
+        --augustus_species local
+    #end if
+#end if
+
+#if $adv.outputs and 'image' in $adv.outputs:
+    &&
+    mkdir BUSCO_summaries
+    &&
+    ls -l busco_galaxy/run_*/ &&
+    cp busco_galaxy/short_summary.*.txt BUSCO_summaries/
+    &&
+    generate_plot.py -wd BUSCO_summaries -rt specific
 #end if
-    ]]></command>
 
+]]>    </command>
     <inputs>
-        <param type="data" name="input" format="fasta" label="Sequences to analyse" help="genome, transcriptome or proteome" />
-        <param argument="--mode" type="select" label="Mode">
-            <option value="geno">Genome</option>
-            <option value="tran">Transcriptome</option>
-            <option value="prot">Proteome</option>
-        </param>
+        <param type="data" name="input" format="fasta" label="Sequences to analyse" help="Can be an assembled genome or transcriptome (DNA), or protein sequences from an annotated gene set." />
+        <conditional name="busco_mode">
+            <param argument="--mode" type="select" label="Mode">
+                <option value="geno">Genome assemblies (DNA)</option>
+                <option value="tran">Transcriptome assemblies (DNA)</option>
+                <option value="prot">annotated gene sets (protein)</option>
+            </param>
+            <when value="geno">
+                <conditional name="use_augustus">
+                    <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">
+                        <option value="yes">Yes, use Augustus</option>
+                        <option value="no" selected="true">Use Metaeuk</option>
+                    </param>
+                    <when value="no" />
+                    <when value="yes">
+                        <conditional name="aug_prediction">
+                            <param name="augustus_mode" type="select" label="Augustus species model">
+                                <option value="no" selected="true">Use the default species for selected lineage</option>
+                                <option value="builtin">Use another predefined species model</option>
+                                <option value="history">Use a custom species model</option>
+                            </param>
+                            <when value="no" />
+                            <when value="history">
+                                <param name="augustus_model" type="data" format="augustus" label="Augustus model" />
+                            </when>
+                            <when value="builtin">
+                                <param name="augustus_species" type="select" label="Augustus species model">
+                                    <expand macro="augustus_species" />
+                                </param>
+                            </when>
+                        </conditional>
+                        <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms" />
+                    </when>
+                </conditional>
+            </when>
+            <when value="tran" />
+            <when value="prot" />
+        </conditional>
 
         <param argument="--lineage_dataset" type="select" label="Lineage">
-            <expand macro="lineages"/>
+            <expand macro="lineages" />
         </param>
 
         <section name="adv" title="Advanced Options" expanded="False">
-            <param argument="--evalue" type="float" value="0.01" label="E-value cutoff for BLAST searches."/>
-            <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider"/>
-
-            <conditional name="aug_prediction">
-                <param name="augustus_mode" type="select" label="Augustus species model">
-                    <option value="no" selected="true">Use the default species for selected lineage</option>
-                    <option value="builtin">Use another predefined species model</option>
-                    <option value="history">Use a custom species model</option>
-                </param>
-                <when value="no"/>
-                <when value="history">
-                    <param name="augustus_model" type="data" format="augustus" label="Augustus model"/>
-                </when>
-                <when value="builtin">
-                    <param name="augustus_species" type="select" label="Augustus species model">
-                        <expand macro="augustus_species"/>
-                    </param>
-                </when>
-            </conditional>
-            <param argument="--long" type="boolean" checked="false" truevalue="--long" falsevalue="" label="Optimization mode Augustus self-training" help="Adds considerably to run time, but can improve results for some non-model organisms"/>
+            <param argument="--evalue" type="float" value="0.001" min="0" max="1" label="E-value cutoff for BLAST searches." />
+            <param argument="--limit" type="integer" value="3" label="How many candidate regions to consider" />
+            <param name="auto_lineage" type="select" optional="true" label="Run auto-lineage to find optimal lineage path">
+                <option value="--auto-lineage">Run auto-lineage to find optimum lineage path</option>
+                <option value="--auto-lineage-prok">Run auto-lineage just on non-eukaryote trees to find optimum lineage path</option>
+                <option value="--auto-lineage-euk">Run auto-placement just on eukaryote tree to find optimum lineage path</option>
+            </param>
+            <param name="outputs" type="select" optional="true" multiple="true" label="Which outputs should be generated">
+                <option value="short_summary">short summary text</option>
+                <option value="missing">list with missing IDs</option>
+                <option value="image">summary image</option>
+            </param>
         </section>
     </inputs>
     <outputs>
-        <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt"/>
-        <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv"/>
-        <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv"/>
+        <data name='busco_sum' format='txt' label="${tool.name} on ${on_string}: short summary" from_work_dir="busco_galaxy/run_*/short_summary.txt">
+            <filter>adv['outputs'] and 'short_summary' in adv['outputs']</filter>
+        </data>
+        <data name='busco_table' format='tabular' label="${tool.name} on ${on_string}: full table" from_work_dir="busco_galaxy/run_*/full_table.tsv" />
+        <data name='busco_missing' format='tabular' label="${tool.name} on ${on_string}: missing buscos" from_work_dir="busco_galaxy/run_*/missing_busco_list.tsv">
+            <filter>adv['outputs'] and 'missing' in adv['outputs']</filter>
+        </data>
+        <data name='summary_image' format='png' label="${tool.name} on ${on_string}: summary image" from_work_dir="BUSCO_summaries/busco_figure.png">
+            <filter>adv['outputs'] and 'image' in adv['outputs']</filter>
+        </data>
     </outputs>
     <tests>
-        <test>
-            <param name="input" value="genome.fa"/>
-            <param name="lineage_dataset" value="arthropoda_odb10"/>
-            <param name="mode" value="geno"/>
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
+        <test expect_num_outputs="3">
+            <param name="input" value="genome.fa" />
+            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="busco_mode">
+                <param name="mode" value="geno" />
+                <conditional name="use_augustus">
+                    <param name="use_augustus_selector" value="yes" />
+                </conditional>
+            </conditional>
+            <section name="adv">
+                <param name="outputs" value="short_summary,missing" />
+            </section>
+            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
             <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4">
                 <assert_contents>
                     <has_text text="# BUSCO version is: @TOOL_VERSION@" />
                 </assert_contents>
             </output>
         </test>
-        <test>
-            <param name="input" value="proteome.fa"/>
-            <param name="lineage_dataset" value="arthropoda_odb10"/>
-            <param name="mode" value="prot"/>
-            <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4"/>
-            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4"/>
-            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
+        <test expect_num_outputs="4">
+            <param name="input" value="proteome.fa" />
+            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="busco_mode">
+                <param name="mode" value="prot" />
+            </conditional>
+            <section name="adv">
+                <param name="outputs" value="short_summary,missing,image" />
+            </section>
+            <output name="busco_sum" file="proteome_results/short_summary" compare="diff" lines_diff="4" />
+            <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" />
         </test>
-        <test>
-            <param name="input" value="transcriptome.fa"/>
-            <param name="lineage_dataset" value="arthropoda_odb10"/>
-            <param name="mode" value="tran"/>
-            <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4"/>
-            <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4"/>
-            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
+        <test expect_num_outputs="4">
+            <param name="input" value="transcriptome.fa" />
+            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="busco_mode">
+                <param name="mode" value="tran" />
+            </conditional>
+            <section name="adv">
+                <param name="auto_lineage" value="--auto-lineage" />
+                <param name="outputs" value="short_summary,missing,image" />
+            </section>
+            <output name="busco_sum" file="transcriptome_results/short_summary" compare="diff" lines_diff="4" />
+            <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" />
         </test>
-        <test>
-            <param name="input" value="genome.fa"/>
-            <param name="lineage_dataset" value="arthropoda_odb10"/>
-            <param name="mode" value="geno"/>
-            <param name="adv|aug_prediction|augustus_mode" value="builtin"/>
-            <param name="adv|aug_prediction|augustus_species" value="human"/>
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
-            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
+        <test expect_num_outputs="2">
+            <param name="input" value="genome.fa" />
+            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="busco_mode">
+                <param name="mode" value="geno" />
+                <conditional name="use_augustus">
+                    <param name="use_augustus_selector" value="yes" />
+                    <conditional name="aug_prediction">
+                        <param name="augustus_mode" value="builtin" />
+                        <param name="augustus_species" value="human" />
+                    </conditional>
+                </conditional>
+            </conditional>
+            <section name="adv">
+                <param name="outputs" value="short_summary" />
+            </section>
+            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
         </test>
-        <test>
-            <param name="input" value="genome.fa"/>
-            <param name="lineage_dataset" value="arthropoda_odb10"/>
-            <param name="mode" value="geno"/>
-            <param name="adv|aug_prediction|augustus_mode" value="history"/>
-            <param name="adv|aug_prediction|augustus_model" value="local.tar.gz" ftype="augustus"/>
-            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4"/>
-            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4"/>
-            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4"/>
+        <test expect_num_outputs="3">
+            <param name="input" value="genome.fa" />
+            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="busco_mode">
+                <param name="mode" value="geno" />
+                <conditional name="use_augustus">
+                    <param name="use_augustus_selector" value="yes" />
+                    <conditional name="aug_prediction">
+                        <param name="augustus_mode" value="history" />
+                        <param name="augustus_model" value="local.tar.gz" ftype="augustus" />
+                    </conditional>
+                </conditional>
+            </conditional>
+            <section name="adv">
+                <param name="outputs" value="short_summary,missing" />
+            </section>
+            <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="4" />
+            <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="4" />
+        </test>
+        <test expect_num_outputs="4">
+            <param name="input" value="genome.fa" />
+            <param name="lineage_dataset" value="arthropoda_odb10" />
+            <conditional name="busco_mode">
+                <param name="mode" value="geno" />
+                <conditional name="use_augustus">
+                    <param name="use_augustus_selector" value="no" />
+                </conditional>
+            </conditional>
+            <section name="adv">
+                <param name="outputs" value="short_summary,missing,image" />
+            </section>
+            <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="diff" lines_diff="4" />
+            <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="4" />
+            <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="4" />
+            <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" />
         </test>
     </tests>
-    <help>
+    <help><![CDATA[
+
+
 BUSCO: assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs
+--------------------------------------------------------------------------------------------------------------
+
+Interpreting the results
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+BUSCO_ attempts to provide a quantitative assessment of the completeness in terms of the expected gene content of a
+genome assembly, transcriptome, or annotated gene set. The results are simplified into categories of Complete
+and single-copy, Complete and duplicated, Fragmented, or Missing BUSCOs.
+
+BUSCO completeness results make sense only in the context of the biology of your organism.
+You have to understand whether missing or duplicated genes are of biological or technical origin.
+For instance, a high level of duplication may be explained by a recent whole duplication event
+(biological) or a chimeric assembly of haplotypes (technical).
+Transcriptomes and protein sets that are not filtered for isoforms will lead to a high proportion of duplicates.
+Therefore you should filter them before a BUSCO analysis.
+Finally, focusing on specific tissues or specific life stages and conditions in a transcriptomic experiment
+is unlikely to produce a BUSCO-complete transcriptome. In this case, consistency across your samples
+is what you will be aiming for.
+
+For more information please refer to the Busco_ `user guide <https: / /busco.ezlab.org /busco_userguide.html#interpreting-the-results>`_
+.
 
 .. _BUSCO: http://busco.ezlab.org/
-    </help>
-    <expand macro="citations"/>
+
+    ]]>    </help>
+    <expand macro="citations" />
 </tool>
diff -r 602fb8e63aa7 -r cf13a1e03e5b macros.xml
--- a/macros.xml	Wed Dec 30 14:07:37 2020 +0000
+++ b/macros.xml	Mon Mar 15 21:27:17 2021 +0000
@@ -1,6 +1,7 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">4.1.4</token>
+    <token name="@TOOL_VERSION@">5.0.0</token>
+    <token name="@VERSION_SUFFIX@">0</token>
 
     <xml name="citations">
         <citations>
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results/full_table
--- a/test-data/genome_results/full_table	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/genome_results/full_table	Mon Mar 15 21:27:17 2021 +0000
@@ -1,6 +1,6 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
-# Busco id	Status	Sequence	Gene Start	Gene End	Score	Length	OrthoDB url	Description
+# Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
 774at6656	Missing
 980at6656	Missing
 997at6656	Missing
@@ -509,7 +509,7 @@
 93535at6656	Missing
 93797at6656	Missing
 94054at6656	Missing
-94238at6656	Complete	sample	34764	38486	60.7	116	https://www.orthodb.org/v10?query=94238at6656	checkpoint protein HUS1
+94238at6656	Complete	sample	34764	38486	-	60.7	116	https://www.orthodb.org/v10?query=94238at6656	checkpoint protein HUS1
 94263at6656	Missing
 94304at6656	Missing
 94473at6656	Missing
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results/missing_buscos_list
--- a/test-data/genome_results/missing_buscos_list	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/genome_results/missing_buscos_list	Mon Mar 15 21:27:17 2021 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results/short_summary
--- a/test-data/genome_results/short_summary	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/genome_results/short_summary	Mon Mar 15 21:27:17 2021 +0000
@@ -1,7 +1,8 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmp0yshlkbl/files/d/c/0/dataset_dc06dd53-8ed0-477c-b8bd-dd9fe68fd7e0.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmp7tgu744e/files/3/3/6/dataset_336adf79-955a-4ca8-aeda-96fc1fce9a4c.dat
 # BUSCO was run in mode: genome
+# Gene predictor used: augustus
 
 	***** Results: *****
 
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/full_table
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_metaeuk/full_table	Mon Mar 15 21:27:17 2021 +0000
@@ -0,0 +1,1016 @@
+# BUSCO version is: 5.0.0 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
+# Busco id	Status	Sequence	Gene Start	Gene End	Strand	Score	Length	OrthoDB url	Description
+774at6656	Missing
+980at6656	Missing
+997at6656	Missing
+1166at6656	Missing
+1885at6656	Missing
+1990at6656	Missing
+2148at6656	Missing
+2456at6656	Missing
+2473at6656	Missing
+3310at6656	Missing
+3585at6656	Missing
+3644at6656	Missing
+4136at6656	Missing
+4227at6656	Missing
+4864at6656	Missing
+5277at6656	Missing
+5616at6656	Missing
+6453at6656	Missing
+6563at6656	Missing
+6715at6656	Missing
+6820at6656	Missing
+7210at6656	Missing
+8145at6656	Missing
+8495at6656	Missing
+8847at6656	Missing
+8913at6656	Missing
+9647at6656	Missing
+9648at6656	Missing
+10240at6656	Missing
+10573at6656	Missing
+11384at6656	Missing
+12029at6656	Missing
+12174at6656	Missing
+12383at6656	Missing
+12771at6656	Missing
+12846at6656	Missing
+13019at6656	Missing
+13051at6656	Missing
+13736at6656	Missing
+13833at6656	Missing
+13858at6656	Missing
+13890at6656	Missing
+13934at6656	Missing
+14090at6656	Missing
+14257at6656	Missing
+14447at6656	Missing
+14995at6656	Missing
+15200at6656	Missing
+15697at6656	Missing
+15905at6656	Missing
+16061at6656	Missing
+16084at6656	Missing
+16220at6656	Missing
+16630at6656	Missing
+16648at6656	Missing
+17096at6656	Missing
+17122at6656	Missing
+17128at6656	Missing
+17748at6656	Missing
+18036at6656	Missing
+18055at6656	Missing
+18073at6656	Missing
+18630at6656	Missing
+18929at6656	Missing
+19044at6656	Missing
+19058at6656	Missing
+19104at6656	Missing
+19129at6656	Missing
+19208at6656	Missing
+19289at6656	Missing
+19590at6656	Missing
+19760at6656	Missing
+20093at6656	Missing
+20162at6656	Missing
+20267at6656	Missing
+20935at6656	Missing
+20936at6656	Missing
+21019at6656	Missing
+21191at6656	Missing
+21361at6656	Missing
+21367at6656	Missing
+21385at6656	Missing
+22098at6656	Missing
+22148at6656	Missing
+22358at6656	Missing
+22364at6656	Missing
+22468at6656	Missing
+22611at6656	Missing
+22887at6656	Missing
+23309at6656	Missing
+23388at6656	Missing
+23429at6656	Missing
+23917at6656	Missing
+24255at6656	Missing
+24427at6656	Missing
+24459at6656	Missing
+24556at6656	Missing
+24573at6656	Missing
+25554at6656	Missing
+25680at6656	Missing
+26078at6656	Missing
+26653at6656	Missing
+26734at6656	Missing
+27198at6656	Missing
+27515at6656	Missing
+27617at6656	Missing
+27655at6656	Missing
+28325at6656	Missing
+28380at6656	Missing
+28519at6656	Missing
+28685at6656	Missing
+28872at6656	Missing
+29213at6656	Missing
+29237at6656	Missing
+29365at6656	Missing
+29730at6656	Missing
+29744at6656	Missing
+30156at6656	Missing
+30184at6656	Missing
+30267at6656	Missing
+30463at6656	Missing
+30512at6656	Missing
+30526at6656	Missing
+30642at6656	Missing
+30822at6656	Missing
+30918at6656	Missing
+30962at6656	Missing
+31014at6656	Missing
+31119at6656	Missing
+31196at6656	Missing
+31333at6656	Missing
+31480at6656	Missing
+31615at6656	Missing
+31634at6656	Missing
+31820at6656	Missing
+31886at6656	Missing
+31919at6656	Missing
+32694at6656	Missing
+32733at6656	Missing
+32851at6656	Missing
+33187at6656	Missing
+33566at6656	Missing
+33794at6656	Missing
+34586at6656	Missing
+34917at6656	Missing
+35035at6656	Missing
+35548at6656	Missing
+35680at6656	Missing
+35708at6656	Missing
+35995at6656	Missing
+36374at6656	Missing
+36387at6656	Missing
+36403at6656	Missing
+36463at6656	Missing
+37030at6656	Missing
+37297at6656	Missing
+37387at6656	Missing
+37678at6656	Missing
+38140at6656	Missing
+38186at6656	Missing
+38303at6656	Missing
+38391at6656	Missing
+38567at6656	Missing
+38819at6656	Missing
+38928at6656	Missing
+39506at6656	Missing
+39548at6656	Missing
+39783at6656	Missing
+39809at6656	Missing
+39821at6656	Missing
+40065at6656	Missing
+40092at6656	Missing
+40213at6656	Missing
+40240at6656	Missing
+40319at6656	Missing
+40323at6656	Missing
+40399at6656	Missing
+40691at6656	Missing
+40929at6656	Missing
+41522at6656	Missing
+41990at6656	Missing
+42577at6656	Missing
+42622at6656	Missing
+42819at6656	Missing
+42842at6656	Missing
+42929at6656	Missing
+42943at6656	Missing
+42992at6656	Missing
+43045at6656	Missing
+43236at6656	Missing
+43245at6656	Missing
+43540at6656	Missing
+43728at6656	Missing
+43774at6656	Missing
+44001at6656	Missing
+44123at6656	Missing
+44359at6656	Missing
+44389at6656	Missing
+44504at6656	Missing
+44630at6656	Missing
+44694at6656	Missing
+44953at6656	Missing
+45131at6656	Missing
+45367at6656	Missing
+45528at6656	Missing
+45556at6656	Missing
+45732at6656	Missing
+45915at6656	Missing
+46430at6656	Missing
+46437at6656	Missing
+46671at6656	Missing
+46679at6656	Missing
+46692at6656	Missing
+46750at6656	Missing
+46960at6656	Missing
+47270at6656	Missing
+47443at6656	Missing
+47495at6656	Missing
+47500at6656	Missing
+47967at6656	Missing
+48195at6656	Missing
+48466at6656	Missing
+48519at6656	Missing
+48657at6656	Missing
+48836at6656	Missing
+49070at6656	Missing
+49526at6656	Missing
+49936at6656	Missing
+50191at6656	Missing
+50493at6656	Missing
+50740at6656	Missing
+50792at6656	Missing
+50947at6656	Missing
+51037at6656	Missing
+51280at6656	Missing
+51364at6656	Missing
+51757at6656	Missing
+52210at6656	Missing
+52224at6656	Missing
+52320at6656	Missing
+52422at6656	Missing
+52643at6656	Missing
+52828at6656	Missing
+53201at6656	Missing
+53243at6656	Missing
+53298at6656	Missing
+53318at6656	Missing
+53993at6656	Missing
+54236at6656	Missing
+54527at6656	Missing
+54679at6656	Missing
+55036at6656	Missing
+55094at6656	Missing
+55108at6656	Missing
+55260at6656	Missing
+55417at6656	Missing
+55450at6656	Missing
+55599at6656	Missing
+55847at6656	Missing
+55932at6656	Missing
+55953at6656	Missing
+56010at6656	Missing
+56322at6656	Missing
+56449at6656	Missing
+56523at6656	Missing
+56687at6656	Missing
+56836at6656	Missing
+57262at6656	Missing
+57597at6656	Missing
+57605at6656	Missing
+57624at6656	Missing
+57932at6656	Missing
+58012at6656	Missing
+58027at6656	Missing
+58110at6656	Missing
+58119at6656	Missing
+58276at6656	Missing
+59084at6656	Missing
+59193at6656	Missing
+59197at6656	Missing
+59200at6656	Missing
+59226at6656	Missing
+59393at6656	Missing
+59430at6656	Missing
+59681at6656	Missing
+59824at6656	Missing
+59833at6656	Missing
+60067at6656	Missing
+60299at6656	Missing
+60333at6656	Missing
+60356at6656	Missing
+60468at6656	Missing
+60682at6656	Missing
+60729at6656	Missing
+60750at6656	Missing
+60762at6656	Missing
+61081at6656	Missing
+61096at6656	Missing
+61153at6656	Missing
+61180at6656	Missing
+61261at6656	Missing
+61577at6656	Missing
+61612at6656	Missing
+62010at6656	Missing
+62275at6656	Missing
+62580at6656	Missing
+62678at6656	Missing
+62914at6656	Missing
+62979at6656	Missing
+63193at6656	Missing
+63228at6656	Missing
+63461at6656	Missing
+63923at6656	Missing
+63924at6656	Missing
+64046at6656	Missing
+64896at6656	Missing
+65490at6656	Missing
+65508at6656	Missing
+65532at6656	Missing
+65949at6656	Missing
+66028at6656	Missing
+66229at6656	Missing
+66299at6656	Missing
+66366at6656	Missing
+66597at6656	Missing
+66770at6656	Missing
+67113at6656	Missing
+67166at6656	Missing
+67191at6656	Missing
+67491at6656	Missing
+67583at6656	Missing
+67710at6656	Missing
+68468at6656	Missing
+68491at6656	Missing
+68731at6656	Missing
+68876at6656	Missing
+68939at6656	Missing
+68961at6656	Missing
+68981at6656	Missing
+68987at6656	Complete	sample	40255	42070	+	122.8	266	https://www.orthodb.org/v10?query=68987at6656	mannose-1-phosphate guanyltransferase alpha
+69201at6656	Missing
+69238at6656	Missing
+69284at6656	Missing
+69394at6656	Missing
+69403at6656	Missing
+69742at6656	Missing
+69897at6656	Missing
+70078at6656	Missing
+70201at6656	Missing
+70300at6656	Missing
+70550at6656	Missing
+70663at6656	Missing
+71018at6656	Missing
+71110at6656	Missing
+71129at6656	Missing
+71199at6656	Missing
+71230at6656	Missing
+71251at6656	Missing
+71483at6656	Missing
+71937at6656	Missing
+72450at6656	Missing
+72578at6656	Missing
+72583at6656	Missing
+72586at6656	Missing
+72782at6656	Missing
+72857at6656	Missing
+73084at6656	Missing
+73301at6656	Missing
+73455at6656	Missing
+73456at6656	Missing
+73547at6656	Missing
+74030at6656	Missing
+74384at6656	Missing
+74655at6656	Missing
+74692at6656	Missing
+74836at6656	Missing
+75692at6656	Missing
+75704at6656	Missing
+75764at6656	Missing
+75982at6656	Missing
+76308at6656	Missing
+76342at6656	Missing
+76573at6656	Missing
+76745at6656	Missing
+76812at6656	Missing
+77197at6656	Missing
+77688at6656	Missing
+77770at6656	Missing
+77883at6656	Missing
+77976at6656	Missing
+77987at6656	Missing
+78110at6656	Missing
+78202at6656	Missing
+78254at6656	Missing
+78695at6656	Missing
+78758at6656	Missing
+78777at6656	Missing
+78844at6656	Missing
+78854at6656	Missing
+78919at6656	Missing
+78921at6656	Missing
+78947at6656	Missing
+78968at6656	Missing
+79241at6656	Missing
+79377at6656	Missing
+79915at6656	Missing
+79993at6656	Missing
+80067at6656	Missing
+80294at6656	Missing
+80317at6656	Missing
+80348at6656	Missing
+80689at6656	Missing
+80693at6656	Missing
+80948at6656	Missing
+81292at6656	Missing
+81307at6656	Missing
+81406at6656	Missing
+81413at6656	Missing
+81423at6656	Missing
+81650at6656	Missing
+81703at6656	Missing
+81708at6656	Missing
+81919at6656	Missing
+81950at6656	Missing
+83102at6656	Missing
+83164at6656	Missing
+83303at6656	Missing
+83350at6656	Missing
+83372at6656	Missing
+83376at6656	Missing
+83613at6656	Missing
+83673at6656	Missing
+83755at6656	Missing
+83765at6656	Missing
+84028at6656	Missing
+84097at6656	Missing
+84149at6656	Missing
+84169at6656	Missing
+84422at6656	Missing
+84576at6656	Missing
+84819at6656	Missing
+84925at6656	Missing
+85103at6656	Missing
+85509at6656	Missing
+85574at6656	Missing
+85680at6656	Missing
+85810at6656	Missing
+86262at6656	Missing
+86318at6656	Missing
+86488at6656	Missing
+86654at6656	Missing
+86715at6656	Missing
+86889at6656	Missing
+86930at6656	Missing
+87014at6656	Missing
+87089at6656	Missing
+87103at6656	Missing
+87114at6656	Missing
+87139at6656	Missing
+87142at6656	Missing
+87527at6656	Missing
+87575at6656	Missing
+87695at6656	Missing
+87728at6656	Missing
+87910at6656	Missing
+87928at6656	Missing
+87933at6656	Missing
+88051at6656	Missing
+88711at6656	Missing
+89064at6656	Missing
+89153at6656	Missing
+89677at6656	Missing
+89713at6656	Missing
+89810at6656	Missing
+89840at6656	Missing
+89864at6656	Missing
+90126at6656	Missing
+90322at6656	Missing
+90580at6656	Missing
+90600at6656	Missing
+90822at6656	Missing
+90928at6656	Missing
+90931at6656	Missing
+91002at6656	Missing
+91005at6656	Missing
+91022at6656	Missing
+91313at6656	Missing
+91418at6656	Missing
+91468at6656	Missing
+91933at6656	Missing
+91946at6656	Missing
+92167at6656	Missing
+92184at6656	Missing
+92420at6656	Missing
+92576at6656	Missing
+92777at6656	Missing
+92854at6656	Missing
+93061at6656	Missing
+93085at6656	Missing
+93152at6656	Missing
+93168at6656	Missing
+93408at6656	Missing
+93432at6656	Missing
+93483at6656	Missing
+93507at6656	Missing
+93535at6656	Missing
+93797at6656	Missing
+94054at6656	Missing
+94238at6656	Complete	sample	34845	35678	-	60.7	116	https://www.orthodb.org/v10?query=94238at6656	checkpoint protein HUS1
+94263at6656	Missing
+94304at6656	Missing
+94473at6656	Missing
+94476at6656	Missing
+94842at6656	Missing
+94878at6656	Missing
+95028at6656	Missing
+95089at6656	Missing
+95294at6656	Missing
+95524at6656	Missing
+96251at6656	Missing
+96444at6656	Missing
+96569at6656	Missing
+96592at6656	Missing
+96601at6656	Missing
+96956at6656	Missing
+96971at6656	Missing
+97225at6656	Missing
+97492at6656	Missing
+97749at6656	Missing
+97763at6656	Missing
+97865at6656	Missing
+98066at6656	Missing
+98251at6656	Missing
+98544at6656	Missing
+98620at6656	Missing
+98725at6656	Missing
+98755at6656	Missing
+98821at6656	Missing
+98845at6656	Missing
+98927at6656	Missing
+98948at6656	Missing
+99204at6656	Missing
+99270at6656	Missing
+99307at6656	Missing
+99377at6656	Missing
+99519at6656	Missing
+99625at6656	Missing
+99998at6656	Missing
+100070at6656	Missing
+100136at6656	Missing
+100216at6656	Missing
+100227at6656	Missing
+100296at6656	Missing
+100612at6656	Missing
+100664at6656	Missing
+100673at6656	Missing
+100760at6656	Missing
+101349at6656	Missing
+101359at6656	Missing
+101491at6656	Missing
+101531at6656	Missing
+101621at6656	Missing
+101727at6656	Missing
+101761at6656	Missing
+101767at6656	Missing
+101829at6656	Missing
+101886at6656	Missing
+102321at6656	Missing
+102714at6656	Missing
+102770at6656	Missing
+103125at6656	Missing
+103207at6656	Missing
+103479at6656	Missing
+103590at6656	Missing
+103747at6656	Missing
+103749at6656	Missing
+103752at6656	Missing
+103908at6656	Missing
+103914at6656	Missing
+104063at6656	Missing
+104122at6656	Missing
+104198at6656	Missing
+104410at6656	Missing
+104588at6656	Missing
+104595at6656	Missing
+104604at6656	Missing
+104769at6656	Missing
+104898at6656	Missing
+105000at6656	Missing
+105099at6656	Missing
+105170at6656	Missing
+105364at6656	Missing
+105457at6656	Missing
+105771at6656	Missing
+105887at6656	Missing
+106116at6656	Missing
+106126at6656	Missing
+106466at6656	Missing
+106470at6656	Missing
+106634at6656	Missing
+106639at6656	Missing
+106788at6656	Missing
+106988at6656	Missing
+107030at6656	Missing
+107139at6656	Missing
+107226at6656	Missing
+107353at6656	Missing
+107427at6656	Missing
+107453at6656	Missing
+107615at6656	Missing
+107802at6656	Missing
+107806at6656	Missing
+107844at6656	Missing
+108162at6656	Missing
+108207at6656	Missing
+108240at6656	Missing
+108693at6656	Missing
+108702at6656	Missing
+108705at6656	Missing
+108808at6656	Missing
+109131at6656	Missing
+109174at6656	Missing
+109325at6656	Missing
+109444at6656	Missing
+109484at6656	Missing
+109562at6656	Missing
+109664at6656	Missing
+109724at6656	Missing
+109793at6656	Missing
+109919at6656	Missing
+109923at6656	Missing
+110129at6656	Missing
+110504at6656	Missing
+110787at6656	Missing
+110982at6656	Missing
+111082at6656	Missing
+111153at6656	Missing
+111236at6656	Missing
+111239at6656	Missing
+111545at6656	Missing
+111851at6656	Missing
+112281at6656	Missing
+112328at6656	Missing
+112360at6656	Missing
+112556at6656	Missing
+112634at6656	Missing
+112645at6656	Missing
+112759at6656	Missing
+113015at6656	Missing
+113300at6656	Missing
+113432at6656	Missing
+113604at6656	Missing
+113622at6656	Missing
+113641at6656	Missing
+113668at6656	Missing
+113713at6656	Missing
+113817at6656	Missing
+113818at6656	Missing
+113865at6656	Missing
+113960at6656	Missing
+114019at6656	Missing
+114360at6656	Missing
+114463at6656	Missing
+114609at6656	Missing
+114738at6656	Missing
+114765at6656	Missing
+115001at6656	Missing
+115208at6656	Missing
+115229at6656	Missing
+115252at6656	Missing
+115256at6656	Missing
+115462at6656	Missing
+115537at6656	Missing
+115841at6656	Missing
+115917at6656	Missing
+115959at6656	Missing
+115986at6656	Missing
+116117at6656	Missing
+116401at6656	Missing
+116608at6656	Missing
+116688at6656	Missing
+116804at6656	Missing
+116982at6656	Missing
+117173at6656	Missing
+117335at6656	Missing
+117399at6656	Missing
+117413at6656	Missing
+117586at6656	Missing
+117742at6656	Missing
+117811at6656	Missing
+117843at6656	Missing
+117947at6656	Missing
+118014at6656	Missing
+118037at6656	Missing
+118496at6656	Missing
+118527at6656	Missing
+118761at6656	Missing
+118780at6656	Missing
+118807at6656	Missing
+118831at6656	Missing
+118904at6656	Missing
+119012at6656	Missing
+119144at6656	Missing
+119188at6656	Missing
+119194at6656	Missing
+119438at6656	Missing
+119541at6656	Missing
+119951at6656	Missing
+120047at6656	Missing
+120383at6656	Missing
+120445at6656	Missing
+120875at6656	Missing
+120907at6656	Missing
+120958at6656	Missing
+121002at6656	Missing
+121220at6656	Missing
+121530at6656	Missing
+121558at6656	Missing
+121847at6656	Missing
+121894at6656	Missing
+122526at6656	Missing
+122665at6656	Missing
+122816at6656	Missing
+123035at6656	Missing
+123320at6656	Missing
+123409at6656	Missing
+123631at6656	Missing
+123672at6656	Missing
+123790at6656	Missing
+123793at6656	Missing
+123853at6656	Missing
+124174at6656	Missing
+124282at6656	Missing
+124400at6656	Missing
+124452at6656	Missing
+124628at6656	Missing
+124707at6656	Missing
+124720at6656	Missing
+124730at6656	Missing
+124981at6656	Missing
+125100at6656	Missing
+125127at6656	Missing
+125210at6656	Missing
+125234at6656	Missing
+125238at6656	Missing
+125414at6656	Missing
+125446at6656	Missing
+125452at6656	Missing
+125716at6656	Missing
+126074at6656	Missing
+126225at6656	Missing
+126442at6656	Missing
+126483at6656	Missing
+126733at6656	Missing
+127349at6656	Missing
+127511at6656	Missing
+127602at6656	Missing
+127649at6656	Missing
+127661at6656	Missing
+127775at6656	Missing
+127998at6656	Missing
+128030at6656	Missing
+128188at6656	Missing
+128216at6656	Missing
+128331at6656	Missing
+128464at6656	Missing
+128916at6656	Missing
+129077at6656	Missing
+129131at6656	Missing
+129200at6656	Missing
+129593at6656	Missing
+129618at6656	Missing
+129675at6656	Missing
+129886at6656	Missing
+129902at6656	Missing
+129989at6656	Missing
+130105at6656	Missing
+130126at6656	Missing
+130176at6656	Missing
+130363at6656	Missing
+130514at6656	Missing
+130563at6656	Missing
+130663at6656	Missing
+130825at6656	Missing
+130923at6656	Missing
+131276at6656	Missing
+131307at6656	Missing
+131495at6656	Missing
+131516at6656	Missing
+131588at6656	Missing
+131642at6656	Missing
+131668at6656	Missing
+131720at6656	Missing
+131751at6656	Missing
+131921at6656	Missing
+132329at6656	Missing
+132340at6656	Missing
+132441at6656	Missing
+132495at6656	Missing
+132760at6656	Missing
+132854at6656	Missing
+132857at6656	Missing
+133015at6656	Missing
+133329at6656	Missing
+133362at6656	Missing
+133422at6656	Missing
+133603at6656	Missing
+133735at6656	Missing
+133949at6656	Missing
+134073at6656	Missing
+134209at6656	Missing
+134216at6656	Missing
+134673at6656	Missing
+134708at6656	Missing
+134776at6656	Missing
+134835at6656	Missing
+134853at6656	Missing
+134865at6656	Missing
+134885at6656	Missing
+135065at6656	Missing
+135075at6656	Missing
+135107at6656	Missing
+135123at6656	Missing
+135203at6656	Missing
+135204at6656	Missing
+135215at6656	Missing
+135357at6656	Missing
+135373at6656	Missing
+135391at6656	Missing
+135526at6656	Missing
+135676at6656	Missing
+135690at6656	Missing
+135702at6656	Missing
+135764at6656	Missing
+135828at6656	Missing
+135834at6656	Missing
+135859at6656	Missing
+135975at6656	Missing
+135994at6656	Missing
+136055at6656	Missing
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+136119at6656	Missing
+136224at6656	Missing
+136365at6656	Missing
+136559at6656	Missing
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+137050at6656	Missing
+137197at6656	Missing
+137202at6656	Missing
+137334at6656	Missing
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+137422at6656	Missing
+137609at6656	Missing
+137688at6656	Missing
+137709at6656	Missing
+137711at6656	Missing
+138243at6656	Missing
+138271at6656	Missing
+138379at6656	Missing
+138401at6656	Missing
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+138684at6656	Missing
+138937at6656	Missing
+139217at6656	Missing
+139553at6656	Missing
+139638at6656	Missing
+139744at6656	Missing
+139834at6656	Missing
+140076at6656	Missing
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+141298at6656	Missing
+141804at6656	Missing
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+141916at6656	Missing
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+142415at6656	Missing
+142522at6656	Missing
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+142833at6656	Missing
+143154at6656	Missing
+143279at6656	Missing
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+143709at6656	Missing
+143812at6656	Missing
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+144337at6656	Missing
+144652at6656	Missing
+144836at6656	Missing
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+145033at6656	Missing
+145102at6656	Missing
+145443at6656	Missing
+145610at6656	Missing
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+146007at6656	Missing
+146036at6656	Missing
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+146102at6656	Missing
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+146600at6656	Missing
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+147002at6656	Missing
+147025at6656	Missing
+147322at6656	Missing
+147657at6656	Missing
+147723at6656	Missing
+147852at6656	Missing
+147891at6656	Missing
+147980at6656	Missing
+148134at6656	Missing
+148619at6656	Missing
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+148851at6656	Missing
+148890at6656	Missing
+149101at6656	Missing
+149126at6656	Missing
+149251at6656	Missing
+149405at6656	Missing
+149680at6656	Missing
+149753at6656	Missing
+149796at6656	Missing
+149819at6656	Missing
+149973at6656	Missing
+149977at6656	Missing
+150005at6656	Missing
+150049at6656	Missing
+150137at6656	Missing
+150182at6656	Missing
+150251at6656	Missing
+150327at6656	Missing
+150479at6656	Missing
+150583at6656	Missing
+150585at6656	Missing
+150667at6656	Missing
+150765at6656	Missing
+151102at6656	Missing
+151111at6656	Missing
+151114at6656	Missing
+151393at6656	Missing
+151436at6656	Missing
+151642at6656	Missing
+151658at6656	Missing
+152032at6656	Missing
+152109at6656	Missing
+152402at6656	Missing
+152534at6656	Missing
+152871at6656	Missing
+153155at6656	Missing
+153232at6656	Missing
+153312at6656	Missing
+153534at6656	Missing
+153693at6656	Missing
+153873at6656	Missing
+154133at6656	Missing
+154415at6656	Missing
+154507at6656	Missing
+155285at6656	Missing
+156057at6656	Missing
+156081at6656	Missing
+156111at6656	Missing
+156305at6656	Missing
+156395at6656	Missing
+156728at6656	Missing
+156824at6656	Missing
+156882at6656	Missing
+156975at6656	Missing
+157486at6656	Missing
+157579at6656	Missing
+157851at6656	Missing
+157879at6656	Missing
+158194at6656	Missing
+158760at6656	Missing
+159231at6656	Missing
+159420at6656	Missing
+159542at6656	Missing
+160675at6656	Missing
+160705at6656	Missing
+161435at6656	Missing
+162059at6656	Missing
+162147at6656	Missing
+162594at6656	Missing
+162628at6656	Missing
+162841at6656	Missing
+163670at6656	Missing
+163896at6656	Missing
+164354at6656	Missing
+164512at6656	Missing
+165142at6656	Missing
+165207at6656	Missing
+165493at6656	Missing
+166476at6656	Missing
+166479at6656	Missing
+166485at6656	Missing
+169220at6656	Missing
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/missing_buscos_list
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_metaeuk/missing_buscos_list	Mon Mar 15 21:27:17 2021 +0000
@@ -0,0 +1,1014 @@
+# BUSCO version is: 5.0.0 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
+# Busco id
+100070at6656
+100136at6656
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diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/short_summary
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/genome_results_metaeuk/short_summary	Mon Mar 15 21:27:17 2021 +0000
@@ -0,0 +1,15 @@
+# BUSCO version is: 5.0.0 
+# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
+# Summarized benchmarking in BUSCO notation for file /tmp/tmp7tgu744e/files/3/e/e/dataset_3ee78f14-2ccd-4666-af87-075e725e09bd.dat
+# BUSCO was run in mode: genome
+# Gene predictor used: metaeuk
+
+	***** Results: *****
+
+	C:0.2%[S:0.2%,D:0.0%],F:0.0%,M:99.8%,n:1013	   
+	2	Complete BUSCOs (C)			   
+	2	Complete and single-copy BUSCOs (S)	   
+	0	Complete and duplicated BUSCOs (D)	   
+	0	Fragmented BUSCOs (F)			   
+	1011	Missing BUSCOs (M)			   
+	1013	Total BUSCO groups searched		   
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/genome_results_metaeuk/summary.png
Binary file test-data/genome_results_metaeuk/summary.png has changed
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/full_table
--- a/test-data/proteome_results/full_table	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/proteome_results/full_table	Mon Mar 15 21:27:17 2021 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/missing_buscos_list
--- a/test-data/proteome_results/missing_buscos_list	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/proteome_results/missing_buscos_list	Mon Mar 15 21:27:17 2021 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/short_summary
--- a/test-data/proteome_results/short_summary	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/proteome_results/short_summary	Mon Mar 15 21:27:17 2021 +0000
@@ -1,6 +1,6 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmp0yshlkbl/files/0/9/0/dataset_090e32f3-7f4a-47b2-b1c3-c80bb88da90f.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmp7tgu744e/files/8/e/0/dataset_8e0c0f40-2615-49a6-a2aa-9e5ad5f5a163.dat
 # BUSCO was run in mode: proteins
 
 	***** Results: *****
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/proteome_results/summary.png
Binary file test-data/proteome_results/summary.png has changed
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/full_table
--- a/test-data/transcriptome_results/full_table	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/transcriptome_results/full_table	Mon Mar 15 21:27:17 2021 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
 # Busco id	Status	Sequence	Score	Length	OrthoDB url	Description
 774at6656	Missing
@@ -86,7 +86,7 @@
 22098at6656	Missing
 22148at6656	Missing
 22358at6656	Missing
-22364at6656	Complete	BUSCOaEOG7B0HST	1355.6	788	https://www.orthodb.org/v10?query=22364at6656	importin-5
+22364at6656	Complete	BUSCOaEOG7B0HST:0-2699	1355.6	788	https://www.orthodb.org/v10?query=22364at6656	importin-5
 22468at6656	Missing
 22611at6656	Missing
 22887at6656	Missing
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/missing_buscos_list
--- a/test-data/transcriptome_results/missing_buscos_list	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/transcriptome_results/missing_buscos_list	Mon Mar 15 21:27:17 2021 +0000
@@ -1,4 +1,4 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
 # Busco id
 100070at6656
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/short_summary
--- a/test-data/transcriptome_results/short_summary	Wed Dec 30 14:07:37 2020 +0000
+++ b/test-data/transcriptome_results/short_summary	Mon Mar 15 21:27:17 2021 +0000
@@ -1,6 +1,6 @@
-# BUSCO version is: 4.1.4 
+# BUSCO version is: 5.0.0 
 # The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of species: 90, number of BUSCOs: 1013)
-# Summarized benchmarking in BUSCO notation for file /tmp/tmp0yshlkbl/files/c/d/5/dataset_cd590461-e7d2-4927-8b96-f3282e2da236.dat
+# Summarized benchmarking in BUSCO notation for file /tmp/tmpn3gmbt1s/files/4/1/3/dataset_413f631e-7113-4502-9085-5f25549301e4.dat
 # BUSCO was run in mode: transcriptome
 
 	***** Results: *****
diff -r 602fb8e63aa7 -r cf13a1e03e5b test-data/transcriptome_results/summary.png
Binary file test-data/transcriptome_results/summary.png has changed