Mercurial > repos > iuc > busco
changeset 21:2babe6d5c561 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a
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--- a/busco.xml Mon Mar 18 16:01:49 2024 +0000 +++ b/busco.xml Fri Aug 30 15:19:56 2024 +0000 @@ -14,7 +14,7 @@ <version_command>busco --version</version_command> <command><![CDATA[ -#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'yes': +#if $busco_mode.mode == 'geno' and $busco_mode.use_augustus.use_augustus_selector == 'augustus': 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/ && @@ -40,8 +40,6 @@ #if $lineage_conditional.selector == 'cached': --offline --download_path $lineage_conditional.cached_db.fields.path -#else - --update-data #end if #if $lineage.lineage_mode == "auto_detect": @@ -50,21 +48,20 @@ --lineage_dataset '${lineage.lineage_dataset}' #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.mode == 'geno': + #if $busco_mode.use_augustus.use_augustus_selector == 'miniprot': + --miniprot + #elif $busco_mode.use_augustus.use_augustus_selector == 'augustus': + ${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 str( $busco_mode.mode ) == "geno": - #if $busco_mode.miniprot: - --miniprot + #if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'builtin': + --augustus_species '${busco_mode.use_augustus.aug_prediction.augustus_species}' + #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == 'history': + --augustus_species local + #end if + #else: + --metaeuk #end if #end if @@ -111,14 +108,16 @@ <option value="prot">annotated gene sets (protein)</option> </param> <when value="geno"> - <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk"> - <option value="yes">Yes, use Augustus</option> - <option value="no" selected="true">Use Metaeuk</option> + <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor"> + <option value="augustus">Augustus</option> + <option value="metaeuk">Metaeuk</option> + <option value="miniprot" selected="true">Miniprot</option> + </param> - <when value="no" /> - <when value="yes"> + <when value="metaeuk"/> + <when value="miniprot"/> + <when value="augustus"> <conditional name="aug_prediction"> <param name="augustus_mode" type="select" label="Augustus species model"> <option value="no" selected="true">Use the default species for selected lineage</option> @@ -189,10 +188,7 @@ </data> <data name='busco_gff' format='gff3' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff"> <filter>outputs and 'gff' in outputs</filter> - </data> - <data name='busco_miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff"> - <filter>busco_mode['mode'] == 'geno' and busco_mode['miniprot']</filter> - </data> + </data> </outputs> <tests> @@ -205,23 +201,24 @@ <conditional name="busco_mode"> <param name="mode" value="geno" /> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="yes" /> + <param name="use_augustus_selector" value="augustus" /> </conditional> </conditional> <param name="outputs" value="short_summary,missing,gff" /> - <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> - <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> + <output name="busco_sum"> + <assert_contents> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + <has_text text="Gene predictor used: augustus"/> + </assert_contents> + </output> + <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> <output name="busco_gff"> <assert_contents> <has_n_lines n="1"/> <has_text text="##gff-version 3" /> </assert_contents> </output> - <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> + <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10"/> </test> <test expect_num_outputs="5"> <param name="input" value="proteome.fa" /> @@ -233,9 +230,14 @@ <param name="mode" value="prot" /> </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> - <output name="busco_sum" file="proteome_results/short_summary" compare="re_match_multiline" /> - <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="busco_sum"> + <assert_contents> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + <has_text text="BUSCO was run in mode: proteins" /> + </assert_contents> + </output> + <output name="busco_table" file="proteome_results/full_table" compare="diff" lines_diff="10" /> + <output name="busco_missing" file="proteome_results/missing_buscos_list" compare="diff" lines_diff="10" /> <output name="summary_image" file="proteome_results/summary.png" compare="sim_size" /> <output name="busco_gff"> <assert_contents> @@ -254,13 +256,17 @@ <param name="mode" value="tran" /> </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> - <output name="busco_sum" file="transcriptome_results/short_summary" compare="re_match_multiline" /> + <output name="busco_sum"> + <assert_contents> + <has_text text="BUSCO was run in mode: euk_tran" /> + </assert_contents> + </output> <output name="busco_table" file="transcriptome_results/full_table" compare="diff" lines_diff="6" /> <output name="busco_missing" file="transcriptome_results/missing_buscos_list" compare="diff" lines_diff="6" /> <output name="summary_image" file="transcriptome_results/summary.png" compare="sim_size" /> <output name="busco_gff" file="transcriptome_results/out.gff" compare="diff" /> </test> - <test expect_num_outputs="4"> + <test expect_num_outputs="3"> <param name="input" value="genome.fa" /> <conditional name="lineage"> <param name="lineage_mode" value="select_lineage" /> @@ -268,9 +274,8 @@ </conditional> <conditional name="busco_mode"> <param name="mode" value="geno" /> - <param name="miniprot" value="true"/> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="yes" /> + <param name="use_augustus_selector" value="augustus" /> <conditional name="aug_prediction"> <param name="augustus_mode" value="builtin" /> <param name="augustus_species" value="human" /> @@ -278,16 +283,18 @@ </conditional> </conditional> <param name="outputs" value="short_summary,gff" /> - <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline"/> - <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="4" /> + <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10"> + <assert_contents> + <has_text text="# Gene predictor used: augustus"/> + </assert_contents> + </output> + <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> <output name="busco_gff"> <assert_contents> <has_n_lines n="1"/> <has_text text="##gff-version 3" /> </assert_contents> </output> - <!-- The miniprot.gff file is too large. A file containing only the first 1000 lines is used for this test. --> - <output name="busco_miniprot" file="genome_results/miniprot_1000.gff" compare="contains" lines_diff="304463"/> </test> <test expect_num_outputs="3"> <param name="input" value="genome.fa" /> @@ -298,7 +305,7 @@ <conditional name="busco_mode"> <param name="mode" value="geno" /> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="yes" /> + <param name="use_augustus_selector" value="augustus" /> <conditional name="aug_prediction"> <param name="augustus_mode" value="history" /> <param name="augustus_model" value="local.tar.gz" ftype="augustus" /> @@ -306,9 +313,14 @@ </conditional> </conditional> <param name="outputs" value="short_summary,missing" /> - <output name="busco_sum" file="genome_results/short_summary" compare="re_match_multiline" /> - <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" /> + <output name="busco_sum" file="genome_results/short_summary" compare="diff" lines_diff="10"> + <assert_contents> + <has_text text="# Gene predictor used: augustus"/> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + </assert_contents> + </output> + <output name="busco_table" file="genome_results/full_table" compare="diff" lines_diff="10" /> + <output name="busco_missing" file="genome_results/missing_buscos_list" compare="diff" lines_diff="10" /> </test> <test expect_num_outputs="5"> <param name="input" value="genome.fa" /> @@ -319,19 +331,29 @@ <conditional name="busco_mode"> <param name="mode" value="geno" /> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="no" /> + <param name="use_augustus_selector" value="metaeuk" /> </conditional> </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> - <output name="busco_sum" file="genome_results_metaeuk/short_summary" compare="re_match_multiline" /> - <output name="busco_table" file="genome_results_metaeuk/full_table" compare="diff" lines_diff="6" /> - <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list" compare="diff" lines_diff="6" /> - <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size" /> - <output name="busco_gff" ftype="gff3"> + <output name="busco_sum"> <assert_contents> - <has_n_lines n="13"/> + <has_text text="# Gene predictor used: metaeuk"/> </assert_contents> </output> + <output name="busco_table" file="genome_results_metaeuk/full_table"> + <assert_contents> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + <has_text text="9647at6656"/> + </assert_contents> + </output> + <output name="busco_missing" file="genome_results_metaeuk/missing_buscos_list"> + <assert_contents> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + <has_text text="9647at6656"/> + </assert_contents> + </output> + <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/> + <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" /> </test> <test expect_num_outputs="5"> <param name="input" value="genome.fa" /> @@ -342,32 +364,49 @@ <conditional name="busco_mode"> <param name="mode" value="geno" /> <conditional name="use_augustus"> - <param name="use_augustus_selector" value="no" /> + <param name="use_augustus_selector" value="metaeuk" /> </conditional> </conditional> <param name="outputs" value="short_summary,missing,image,gff" /> - <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" /> - <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="6" /> - <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" /> + <output name="busco_sum"> + <assert_contents> + <has_text text="Gene predictor used: metaeuk"/> + </assert_contents> + </output> + <output name="busco_table"> + <assert_contents> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + <has_text text="The lineage dataset is: eukaryota_odb10"/> + </assert_contents> + </output> + <output name="busco_missing"> + <assert_contents> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + <has_text text="The lineage dataset is: eukaryota_odb10"/> + </assert_contents> + </output> <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" /> <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" /> </test> - <test expect_num_outputs="2"> + <test expect_num_outputs="3"> <param name="input" value="genome.fa" /> - <conditional name="lineage_conditional"> - <param name="selector" value="cached"/> - <param name="cached_db" value="busco-demo-db-20230328"/> - </conditional> <conditional name="lineage"> <param name="lineage_mode" value="select_lineage" /> - <param name="lineage_dataset" value="archaea_odb10" /> + <param name="lineage_dataset" value="arthropoda_odb10" /> </conditional> - <param name="outputs" value="short_summary" /> - <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" /> - <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" /> - <assert_stdout> - <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/> - </assert_stdout> + <param name="outputs" value="short_summary,gff" /> + <output name="busco_sum"> + <assert_contents> + <has_text text="# Gene predictor used: miniprot"/> + </assert_contents> + </output> + <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" /> + <output name="busco_table" file="genome_results_miniprot/full_table"> + <assert_contents> + <has_text text="# BUSCO version is: @TOOL_VERSION@"/> + <has_text text="9647at6656"/> + </assert_contents> + </output> </test> </tests> <help><![CDATA[
--- a/macros.xml Mon Mar 18 16:01:49 2024 +0000 +++ b/macros.xml Fri Aug 30 15:19:56 2024 +0000 @@ -1,6 +1,6 @@ <?xml version="1.0"?> <macros> - <token name="@TOOL_VERSION@">5.5.0</token> + <token name="@TOOL_VERSION@">5.7.1</token> <token name="@VERSION_SUFFIX@">0</token> <xml name="citations">
--- a/test-data/busco_database.loc Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/busco_database.loc Fri Aug 30 15:19:56 2024 +0000 @@ -3,4 +3,4 @@ # - name # - version # - /path/to/data -busco-demo-db-20230328 BUSCO-DEMO-DB-20230328 5.4.6 ${__HERE__}/test-db/busco_downloads +busco-demo-db-20230328 BUSCO-DEMO-DB-20230328 5.4.6 ${__HERE__}/test-db/busco_downloads \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/busco_downloads/file_versions.tsv Fri Aug 30 15:19:56 2024 +0000 @@ -0,0 +1,213 @@ +acidobacteria_odb10 2024-01-08 13046d110cf6d038af269ee6e0681bdc Prokaryota lineages +aconoidasida_odb10 2024-01-08 47b6ece13859b681466c79f4e6c6d1ad Eukaryota lineages +actinobacteria_class_odb10 2024-01-08 0a326071854e20d1977a13a5e3a5f84f Prokaryota lineages +actinobacteria_phylum_odb10 2024-01-08 eaa25a3d973f580d4cf59b7251309e5a Prokaryota lineages +actinopterygii_odb10 2024-01-08 6b042870822559fcacf129fdedea8927 Eukaryota lineages +agaricales_odb10 2024-01-08 1bf1c632dab6ae5b4ff0be6fad8ff8cf Eukaryota lineages +agaricomycetes_odb10 2024-01-08 717f3e2543617972c9a45bbd4ac975b6 Eukaryota lineages +alphaproteobacteria_odb10 2024-01-08 22db70ba9f321e8b8f4eed0b2be41b6f Prokaryota lineages +alteromonadales_odb10 2024-01-08 0a959f97971c349fdd69bc37e7796514 Prokaryota lineages +alveolata_odb10 2024-01-08 cbd2ddb6b18efb2b4ca218a74688aacf Eukaryota 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Eukaryota lineages +chaetothyriales_odb10 2024-01-08 721a498d4da22ab75c48a705cb7ffafe Eukaryota lineages +chlamydiae_odb10 2024-01-08 f9a0d5d18b525f5b25ffd28cbc79511a Prokaryota lineages +chlorobi_odb10 2024-01-08 1accab3fc927c6e614d96d3b76eb7d41 Prokaryota lineages +chloroflexi_odb10 2024-01-08 9633d49879fba7efe9d59e9ec1f6fb70 Prokaryota lineages +chlorophyta_odb10 2024-01-08 7dbcc25dd421be9fbb0f0ae0d7095284 Eukaryota lineages +chromatiales_odb10 2024-01-08 113389b263ee38c451831b513a56ae85 Prokaryota lineages +chroococcales_odb10 2024-01-08 319aa6d9e5ce2606aecfc0bce4419eb8 Prokaryota lineages +clostridiales_odb10 2024-01-08 9b90a303dc2395f6197c1d64f03fbfc0 Prokaryota lineages +clostridia_odb10 2024-01-08 7eeb8a01b7c4643aa9fbbd1fd03c887f Prokaryota lineages +coccidia_odb10 2024-01-08 ec804a941baabf38053a0f8b8c7021dd Eukaryota lineages +coriobacteriales_odb10 2024-01-08 18776c9d1cf45a170a71a57e6b0bf32c Prokaryota lineages +coriobacteriia_odb10 2024-01-08 6837d15f63527b8b9ad624f9e4a26daf Prokaryota lineages +corynebacteriales_odb10 2024-01-08 af866d8ea389f71092f9344fb9603f5c Prokaryota lineages +cyanobacteria_odb10 2024-01-08 26b249d637a4146011f38bcf70c6d6f3 Prokaryota lineages +cyprinodontiformes_odb10 2024-01-08 4f85a35eafec1392512eba8b6011dfce Eukaryota lineages +cytophagales_odb10 2024-01-08 6ec59af7cc8d6f6d5de4c6f22f5eb5f0 Prokaryota lineages +cytophagia_odb10 2024-01-08 ccecc5c2a542cf3d75330c1eacbd3100 Prokaryota lineages +delta-epsilon-subdivisions_odb10 2024-01-08 911bdaa6c96bef4feaadd29846681cbd Prokaryota lineages +deltaproteobacteria_odb10 2024-01-08 93caf5a115cffaf8089f47b7e592024a Prokaryota lineages +desulfobacterales_odb10 2024-01-08 6a47df2907b67b809b29291ad9baadeb Prokaryota lineages +desulfovibrionales_odb10 2024-01-08 2e4e5bc1e1e38533273013a92d59e6f8 Prokaryota lineages +desulfurococcales_odb10 2024-01-08 74cc4abc7ed82901712888c2408fb667 Prokaryota lineages +desulfuromonadales_odb10 2024-01-08 b6aad868c8158fc9f92f7c7969e6bd65 Prokaryota lineages +diptera_odb10 2024-01-08 da520a013d41c04d92a4b18b59803628 Eukaryota lineages +dothideomycetes_odb10 2024-01-08 f3b8e2745f0d1cca41d9d4c171b1e70e Eukaryota lineages +embryophyta_odb10 2024-01-08 7d4e9894b0727223f8ef24cf05b7a71d Eukaryota lineages +endopterygota_odb10 2024-01-08 fd7f8c8e521f96c0d273c1b25ef262ea Eukaryota lineages +enterobacterales_odb10 2024-01-08 989af5b1fe5e6b7ff7692511a412c1f6 Prokaryota lineages +entomoplasmatales_odb10 2024-01-08 65893ded2df1ffc7bf4cc8abce3a858a Prokaryota lineages +epsilonproteobacteria_odb10 2024-01-08 b0eaa68282aab72d8a2447da767219da Prokaryota lineages +euarchontoglires_odb10 2024-01-08 4f6b07a49e990f1a821db285f808f7a7 Eukaryota lineages +eudicots_odb10 2024-01-08 38ece5baf0523143fc6594030bca4487 Eukaryota lineages +euglenozoa_odb10 2024-01-08 2422e36739d888b5400211e128442e6f Eukaryota lineages +eukaryota_odb10 2024-01-08 93e2a6ec05708dbf0f23db078b88c5a8 Eukaryota lineages +eurotiales_odb10 2024-01-08 476a061e592590139598c5ed610d1883 Eukaryota lineages +eurotiomycetes_odb10 2024-01-08 077c5b9805d1bd69772851e7a3ef7e2f Eukaryota lineages +euryarchaeota_odb10 2024-01-08 152262b6845431b05feb15919745af78 Prokaryota lineages +eutheria_odb10 2024-01-08 2a3b171b152e781d8b905fb1861b701a Eukaryota lineages +fabales_odb10 2024-01-08 b830d5061c0edd67d49a69800ac58598 Eukaryota lineages +firmicutes_odb10 2024-01-08 4610a6bc81861850b4d8fc3b33fa7a5c Prokaryota lineages +flavobacteriales_odb10 2024-01-08 d8514f1c520e2fe1f3c7d36906f895c4 Prokaryota lineages +flavobacteriia_odb10 2024-01-08 d4bead34b6d89f0a3e36b5250941726d Prokaryota lineages +fungi_odb10 2024-01-08 d389cb627ded374b47db05630191494e Eukaryota lineages +fusobacteriales_odb10 2024-01-08 c25c6d2e434d2ad8f91f6d5bccce30a5 Prokaryota lineages +fusobacteria_odb10 2024-01-08 4e249141ccd9f730e52d386f2b9c0185 Prokaryota lineages +gammaproteobacteria_odb10 2024-01-08 5ade21bee041306a5a12a4c2047d978d Prokaryota lineages +glires_odb10 2024-01-08 e556d8cd17fc9ed1ee6ffd1275809268 Eukaryota lineages +glomerellales_odb10 2024-01-08 d1de6bb04a0d4ed8c816dbb62586faff Eukaryota lineages +halobacteriales_odb10 2024-01-08 79b455d2fe7a132673d7e40a3d123370 Prokaryota lineages +halobacteria_odb10 2024-01-08 0b1efa4df56adb7423df34505c1c7814 Prokaryota lineages +haloferacales_odb10 2024-01-08 99e1945897e61256586c478dd8678cdc Prokaryota lineages +helotiales_odb10 2024-01-08 68b7b6ae8f5f933a282000711e163a3a Eukaryota lineages +hemiptera_odb10 2024-01-08 02bc28602cd3ec17f3b3bda43e3a2888 Eukaryota lineages +hymenoptera_odb10 2024-01-08 9d10047e5500f51c48104c9784baf6e5 Eukaryota lineages +hypocreales_odb10 2024-01-08 2f85af3da8d3e9b20daf47c924ad4385 Eukaryota lineages +insecta_odb10 2024-01-08 fe5d4360ef9829c3c663acab4fe1f1da Eukaryota lineages +lactobacillales_odb10 2024-01-08 1377e13f55575410373f78d984e6d49b Prokaryota lineages +laurasiatheria_odb10 2024-01-08 4b69d3754077ee8a121ff4c1a814038b Eukaryota lineages +legionellales_odb10 2024-01-08 0432b6cbcce14bcf292ae8fd01202f81 Prokaryota lineages +leotiomycetes_odb10 2024-01-08 7c6ef2d12e2c7529097ac033b46f43df Eukaryota lineages +lepidoptera_odb10 2024-01-08 4ad4f7c458c170c0b3245712b4e1cf1e Eukaryota lineages +liliopsida_odb10 2024-01-08 154552d116896e02c282a7d91791cb7d Eukaryota lineages +lineages_list.txt 2021-12-14 ebe3d982a830281588e287cf72f3b5e1 NaN information +list_of_reference_markers.archaea_odb10.txt 2019-12-16 0143477e3666a5bcdec26a826eb01ab4 Prokaryota placement_files +list_of_reference_markers.bacteria_odb10.txt 2019-12-16 e82a39f3060123f4322057c632d7691c Prokaryota placement_files +list_of_reference_markers.eukaryota_odb10.txt 2019-12-16 95a02d2bbe1659778bda594d59c90ee1 Eukaryota placement_files +mammalia_odb10 2024-01-08 5e1b55c306640771a7700d36ae67e1e2 Eukaryota lineages +mapping_taxid-lineage.archaea_odb10.txt 2019-12-16 5a05ab8eb491f6d4ae9f7774fd778f7e Prokaryota placement_files +mapping_taxid-lineage.bacteria_odb10.txt 2019-12-16 b25a5a807f4ff70f4343ef7500d26975 Prokaryota placement_files +mapping_taxid-lineage.eukaryota_odb10.txt 2019-12-16 e5b047a09cee36f1116f7de1453276b4 Eukaryota placement_files +mapping_taxids-busco_dataset_name.archaea_odb10.txt 2019-12-16 d8cc75b75e052e475e07d84cb4d8cd06 Prokaryota placement_files +mapping_taxids-busco_dataset_name.bacteria_odb10.txt 2019-12-16 79514724345b6cae32bb05ecacc11386 Prokaryota placement_files +mapping_taxids-busco_dataset_name.eukaryota_odb10.txt 2019-12-16 435492f974732bb2d562d5abe54bd494 Eukaryota placement_files +metazoa_odb10 2024-01-08 3372747bddabccabfdc291fcd4114899 Eukaryota lineages +methanobacteria_odb10 2024-01-08 36df24c0adf12f76fbd7d26ce417b2c1 Prokaryota lineages +methanococcales_odb10 2024-01-08 bfb1b8d0781c6d55bc89fa4fd84f5a1d Prokaryota lineages +methanomicrobiales_odb10 2024-01-08 4b210069ed2c656fd1f60b55d35a70ad Prokaryota lineages +methanomicrobia_odb10 2024-01-08 2e63c7dfddb70829fd1d3ed87d30611f Prokaryota lineages +micrococcales_odb10 2024-01-08 fdb78019a92964e96b4745defaafc1c4 Prokaryota lineages +microsporidia_odb10 2024-01-08 c6c96c9fddc451b403ba83630506101e Eukaryota lineages +mollicutes_odb10 2024-01-08 893e2e596fe937d72b92b81700d5b3e4 Prokaryota lineages +mollusca_odb10 2024-01-08 d35dfcd38630fb8cb15c646c2482835b Eukaryota lineages +mucorales_odb10 2024-01-08 3cc5cf5b74b429aad5d62704a041c355 Eukaryota lineages +mucoromycota_odb10 2024-01-08 4210498ca504de64e5c9818c8f64962a Eukaryota lineages +mycoplasmatales_odb10 2024-01-08 36cd7fda07a206d9db3ce0c97cdc0025 Prokaryota lineages +natrialbales_odb10 2024-01-08 efa92043b2440ada26425919f875349a Prokaryota lineages +neisseriales_odb10 2024-01-08 b829a1f5314ebf1f949af4f0e28de0e2 Prokaryota lineages +nematoda_odb10 2024-01-08 ec87bb045e2a81868518b1071029d759 Eukaryota lineages +nitrosomonadales_odb10 2024-01-08 5877c85915cbb39a3cf66c9b8c296cf8 Prokaryota lineages +nostocales_odb10 2024-01-08 2564ddc82836e0d1164d8ab43a78b68a Prokaryota lineages +oceanospirillales_odb10 2024-01-08 68600b75c362f9fe8ff2811d141e9cc0 Prokaryota lineages +onygenales_odb10 2024-01-08 6e6b4e1334bb077295ae799c20b38c85 Eukaryota lineages +oscillatoriales_odb10 2024-01-08 58987c4c5fff2c82d473a26c40c6b661 Prokaryota lineages +passeriformes_odb10 2024-01-08 41e0a9cbc2c93aa4fd5cd3e8c2876b56 Eukaryota lineages +pasteurellales_odb10 2024-01-08 d9d0d1500ddc1c79f705ea58d233aff8 Prokaryota lineages +planctomycetes_odb10 2024-01-08 4779117e2b4f688e2bdf84faa5806294 Prokaryota lineages +plasmodium_odb10 2024-01-08 dcc21aada8d28ab5caf7db5b13b19db6 Eukaryota lineages +pleosporales_odb10 2024-01-08 724410708694d64cabc152f5d343a48b Eukaryota lineages +poales_odb10 2024-01-08 e816664c71d968404b2e0acc49d18a44 Eukaryota lineages +polyporales_odb10 2024-01-08 27e685efdb0e3abe27c1b7635a07360d Eukaryota lineages +primates_odb10 2024-01-08 321262a9dd0dcb01b92680e90ec6f344 Eukaryota lineages +propionibacteriales_odb10 2024-01-08 ec081179e55c395689bb9099dedeceb7 Prokaryota lineages +proteobacteria_odb10 2024-01-08 6bb05a7389ee093cbd2bf9261ea4c608 Prokaryota lineages +pseudomonadales_odb10 2024-01-08 b966b8bb3e542085dd4337ef5e692f83 Prokaryota lineages +rhizobiales_odb10 2024-01-08 17f8d1d055dc8f4ff121cad29a86f200 Prokaryota lineages +rhizobium-agrobacterium_group_odb10 2024-01-08 6bcf42ae66ea48608394b737d54cecfb Prokaryota lineages +rhodobacterales_odb10 2024-01-08 95a00f9c488274d5eb2d00f20485741b Prokaryota lineages +rhodospirillales_odb10 2024-01-08 0890d70c48d570c36a09abea2575cc6a Prokaryota lineages +rickettsiales_odb10 2024-01-08 3a3c78aa761117f38cb9a43cd3fd3f64 Prokaryota lineages +saccharomycetes_odb10 2024-01-08 8b6e1a7e088592717f9677fdf15da697 Eukaryota lineages +sauropsida_odb10 2024-01-08 9cc70aa59593e937612bef7c27d1edaf Eukaryota lineages +selenomonadales_odb10 2024-01-08 56c4bd6baa137ddd0d83f9c924261ec4 Prokaryota lineages +solanales_odb10 2024-01-08 66f358ec9289490e465b49c534d68963 Eukaryota lineages +sordariomycetes_odb10 2024-01-08 d2eaf7b7dcdc98c696193200a64f680b Eukaryota lineages +sphingobacteriia_odb10 2024-01-08 242603fe2ff0935de82a73610d3c7ecf Prokaryota lineages +sphingomonadales_odb10 2024-01-08 0d2a778d7223204d457fed9159c3cd0b Prokaryota lineages +spirochaetales_odb10 2024-01-08 25566c0ec1f4157549b29909987fe2dc Prokaryota lineages +spirochaetes_odb10 2024-01-08 791cb6d5240aee08cbfc31aa46c95fea Prokaryota lineages +spirochaetia_odb10 2024-01-08 2d872abdb7804ed46d064ebf1a4af183 Prokaryota lineages +stramenopiles_odb10 2024-01-08 c47e74b9b44f96393aab60a94da41d9b Eukaryota lineages +streptomycetales_odb10 2024-01-08 0fa3b1d4ad18d32f22cfa3e9df6c5f24 Prokaryota lineages +streptosporangiales_odb10 2024-01-08 efc360354567844fa58da793f464eb81 Prokaryota lineages +sulfolobales_odb10 2024-01-08 8a61f401552651f1a65901602ebeafe8 Prokaryota lineages +supermatrix.aln.archaea_odb10.faa 2019-12-16 e9d2c8065a7779f9447b154b9030bcf8 Prokaryota placement_files +supermatrix.aln.bacteria_odb10.faa 2019-12-16 eba6a090cbe21abe1db69d841e8231bc Prokaryota placement_files +supermatrix.aln.eukaryota_odb10.faa 2019-12-16 3584e9fb12211b8c8c3ad63666444be1 Eukaryota placement_files +synechococcales_odb10 2024-01-08 9a472bbb3c02e033f3672644bbb27779 Prokaryota lineages +synergistetes_odb10 2024-01-08 a5bf4d9973e8ea1fbdf3ea8284bd8957 Prokaryota lineages +tenericutes_odb10 2024-01-08 f2bbba733d5b3a531ba14d7338d2fb8f Prokaryota lineages +tetrapoda_odb10 2024-01-08 536277f71a4369b266c77c46d7e4fc1b Eukaryota lineages +thaumarchaeota_odb10 2024-01-08 216d7dfaa4b307e5bf6f136bf310cece Prokaryota lineages +thermoanaerobacterales_odb10 2024-01-08 d66c7a944c1f36dc22353a62e663065b Prokaryota lineages +thermoplasmata_odb10 2024-01-08 f3ec5b6d8fa79c4c6caa37e6b0c09776 Prokaryota lineages +thermoproteales_odb10 2024-01-08 c92700b9bc1018ba50741c453632a758 Prokaryota lineages +thermoprotei_odb10 2024-01-08 e9c08ac322b0c8e4d1c052e6738ad85d Prokaryota lineages +thermotogae_odb10 2024-01-08 546306dabbd386be2d9940a2c0d0deb1 Prokaryota lineages +thiotrichales_odb10 2024-01-08 7871f11be31cf3dfb0f57e8a1f5b31f1 Prokaryota lineages +tissierellales_odb10 2024-01-08 d5651b1b2e07433fc212881bd1482b72 Prokaryota lineages +tissierellia_odb10 2024-01-08 f56b85fda5d5cb55322a8cbd452dd365 Prokaryota lineages +tree.archaea_odb10.nwk 2019-12-16 23a9602460ca3ba12a4382964c40add4 Prokaryota placement_files +tree.bacteria_odb10.nwk 2019-12-16 3cbe2d6292e02ee78b92b42ec7c13bf5 Prokaryota placement_files +tree.eukaryota_odb10.nwk 2019-12-16 cb0d434ee9d87f5d6babd1832a3fa419 Eukaryota placement_files +tree_metadata.archaea_odb10.txt 2019-12-16 1cc8a1284c883d9a5a8e33e70a81a743 Prokaryota placement_files +tree_metadata.bacteria_odb10.txt 2019-12-16 04a34d1dbcc0814bd0f5acee1d2a9c3f Prokaryota placement_files +tree_metadata.eukaryota_odb10.txt 2019-12-16 589ac2a41cb79863d4b0b061e472afea Eukaryota placement_files +tremellomycetes_odb10 2024-01-08 a0bfe1ffe4313753173cd341ddcc4c07 Eukaryota lineages +verrucomicrobia_odb10 2024-01-08 1c380e10eaac2482a9485fe14b7bad47 Prokaryota lineages +vertebrata_odb10 2024-01-08 d292737afaec0ac95bde4f4a8d2ea814 Eukaryota lineages +vibrionales_odb10 2024-01-08 e9ec5827bed867a01d07d7d03aaddc4c Prokaryota lineages +viridiplantae_odb10 2024-01-08 90d6ce27fde83f1e4aba1d6a8f523673 Eukaryota lineages +xanthomonadales_odb10 2024-01-08 47dd98a24916b28b52500e9a036eb8a8 Prokaryota lineages +alphaherpesvirinae_odb10 2024-01-08 44433a26b31aa50e4314a013eb2d1ff4 Virus lineages +baculoviridae_odb10 2024-01-08 78a612f186cb5b88ec8c030661e46487 Virus lineages +rudiviridae_odb10 2024-01-08 afad43502a74667304b97a39459700b4 Virus lineages +betaherpesvirinae_odb10 2024-01-08 1fd9d15097a377d712c6458451bf65af Virus lineages +herpesviridae_odb10 2024-01-08 79856510300f9379e518cc8180ad14fb Virus lineages +poxviridae_odb10 2024-01-08 4cb2e71a92b2088a0a0b1f4ff20f94ef Virus lineages +tevenvirinae_odb10 2024-01-08 fac34fac2c70199fcbe69c0a7a663d71 Virus lineages +aviadenovirus_odb10 2024-01-08 f9c946051627e87ff717ad466d6c5966 Virus lineages +enquatrovirus_odb10 2024-01-08 f6c05f3de730a09cc7eaf58bcc50636c Virus lineages +teseptimavirus_odb10 2024-01-08 18d63d8e679c6fc6086d906d6b917f05 Virus lineages +bclasvirinae_odb10 2024-01-08 51a9dce485c577e575d411d10c566820 Virus lineages +fromanvirus_odb10 2024-01-08 48f5b7b57afa387315c9e006410f55b9 Virus lineages +skunavirus_odb10 2024-01-08 68fbb8404853ae930651c3af1baa7b49 Virus lineages +betabaculovirus_odb10 2024-01-08 aab73c1e308f8a1cec4f4529b06ee3d4 Virus lineages +pahexavirus_odb10 2024-01-08 3b1410a4b594471e05c0b4d466e3173b Virus lineages +alphabaculovirus_odb10 2024-01-08 ec04ed01eab6001f35c1a6ebfc70180f Virus lineages +tunavirinae_odb10 2024-01-08 fe8a69addddcbc43732a4504aff538e2 Virus lineages +simplexvirus_odb10 2024-01-08 fffd2907f63fe04c78fabd61d2f56919 Virus lineages +gammaherpesvirinae_odb10 2024-01-08 da764ed072f3fb78cae2ff7e90868a9f Virus lineages +varicellovirus_odb10 2024-01-08 43c79da0fb65e9d5941d71458cf844ad Virus lineages +cheoctovirus_odb10 2024-01-08 74dacf2a763c2a462356ded5e79921db Virus lineages +guernseyvirinae_odb10 2024-01-08 484f59b9efc120c118fae2e6c178ffaa Virus lineages +tequatrovirus_odb10 2024-01-08 67a3c9d25ded118212840dfd87c37d96 Virus lineages +chordopoxvirinae_odb10 2024-01-08 c5ff51b8e86771a94400c0df8f8eb383 Virus lineages +peduovirus_odb10 2024-01-08 660b6c8dae78bf76bddd9ba1be2c8bd9 Virus lineages +iridoviridae_odb10 2024-01-08 3b3e67bb85d616fd874b26479d6abaea Virus lineages +spounavirinae_odb10 2024-01-08 286365f43fe02aad53b89555d36cd6b0 Virus lineages +virus_datasets.txt 2020-11-26 a7d1e4d4bb6327d01efde3bcc8658cb3 NaN information
--- a/test-data/genome_results/full_table Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results/full_table Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id Status Sequence Gene Start Gene End Strand Score Length OrthoDB url Description 774at6656 Missing 980at6656 Missing @@ -509,7 +509,7 @@ 93535at6656 Missing 93797at6656 Missing 94054at6656 Missing -94238at6656 Complete sample:34764-38486 34764 38486 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1 +94238at6656 Complete sample 38486 34764 - 60.7 116 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1 94263at6656 Missing 94304at6656 Missing 94473at6656 Missing
--- a/test-data/genome_results/full_table_cached Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results/full_table_cached Fri Aug 30 15:19:56 2024 +0000 @@ -1,4 +1,4 @@ -# BUSCO version is: 5.5.0 +# BUSCO version is: 5.7.1 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194) # Busco id Status Sequence Gene Start Gene End Strand Score Length 860at2157 Missing
--- a/test-data/genome_results/missing_buscos_list Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 100136at6656
--- a/test-data/genome_results/short_summary Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results/short_summary Fri Aug 30 15:19:56 2024 +0000 @@ -1,35 +1,36 @@ -# BUSCO version is: 5\.5\.0 -# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) -# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/7/a/3/dataset_7a33f452-1064-4b4a-943f-b0efef6a4a4a.dat # BUSCO was run in mode: euk_genome_aug # Gene predictor used: augustus - \*\*\*\*\* Results: \*\*\*\*\* + ***** Results: ***** - C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013 - 1 Complete BUSCOs \(C\) - 1 Complete and single-copy BUSCOs \(S\) - 0 Complete and duplicated BUSCOs \(D\) - 0 Fragmented BUSCOs \(F\) - 1012 Missing BUSCOs \(M\) + C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1012 Missing BUSCOs (M) 1013 Total BUSCO groups searched Assembly Statistics: 1 Number of scaffolds 1 Number of contigs 62370 Total length - 0\.000% Percent gaps + 0.000% Percent gaps 62 KB Scaffold N50 62 KB Contigs N50 Dependencies and versions: - hmmsearch: [0-9\.\+]+ - bbtools: [0-9\.\+]+ - makeblastdb: [0-9\.\+]+ - tblastn: [0-9\.\+]+ - augustus: [0-9\.\+]+ - gff2gbSmallDNA\.pl: None - new_species\.pl: None + hmmsearch: 3.1 + bbtools: 39.06 + makeblastdb: 2.15.0+ + tblastn: 2.15.0+ + augustus: 3.5.0 + gff2gbSmallDNA.pl: None + new_species.pl: None etraining: None - busco: [0-9\.\+]+ + python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0) + busco: 5.7.1
--- a/test-data/genome_results/short_summary_cached Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results/short_summary_cached Fri Aug 30 15:19:56 2024 +0000 @@ -1,7 +1,7 @@ -# BUSCO version is: 5.5.0 +# BUSCO version is: 5.7.1 # The lineage dataset is: archaea_odb10 (Creation date: 2021-02-23, number of genomes: 404, number of BUSCOs: 194) -# Summarized benchmarking in BUSCO notation for file /tmp/tmpbmq1q2c6/files/3/3/0/dataset_330f49ed-7a6b-4380-870f-22494bb4b257.dat -# BUSCO was run in mode: prok_genome +# Summarized benchmarking in BUSCO notation for file /tmp/tmprlx1s52v/files/e/8/d/dataset_e8d136af-46c1-4ffa-abaf-e8899526d2b0.dat +# BUSCO was run in mode: prok_genome_prod # Gene predictor used: prodigal ***** Results: ***** @@ -27,4 +27,5 @@ hmmsearch: 3.1 bbtools: 39.01 prodigal: 2.6.3 - busco: 5.5.0 + python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0) + busco: 5.7.1
--- a/test-data/genome_results_metaeuk/full_table Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results_metaeuk/full_table Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id Status Sequence Gene Start Gene End Strand Score Length OrthoDB url Description 774at6656 Missing 980at6656 Missing @@ -340,7 +340,7 @@ 68939at6656 Missing 68961at6656 Missing 68981at6656 Missing -68987at6656 Complete sample:40255-42070 40255 42070 + 122.8 266 https://www.orthodb.org/v10?query=68987at6656 mannose-1-phosphate guanyltransferase alpha +68987at6656 Complete sample 40255 42070 + 122.8 266 https://v10-1.orthodb.org/?query=68987at6656 Nucleotidyl transferase domain 69201at6656 Missing 69238at6656 Missing 69284at6656 Missing @@ -509,7 +509,7 @@ 93535at6656 Missing 93797at6656 Missing 94054at6656 Missing -94238at6656 Complete sample:35678-34845 34845 35678 - 60.7 116 https://www.orthodb.org/v10?query=94238at6656 checkpoint protein HUS1 +94238at6656 Complete sample 35693 34845 - 60.6 116 https://v10-1.orthodb.org/?query=94238at6656 Checkpoint protein HUS1 94263at6656 Missing 94304at6656 Missing 94473at6656 Missing
--- a/test-data/genome_results_metaeuk/missing_buscos_list Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results_metaeuk/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 100136at6656
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_metaeuk/out.gff3 Fri Aug 30 15:19:56 2024 +0000 @@ -0,0 +1,3 @@ +##gff-version 3 +sample MetaEuk gene 40256 42071 198 + . Target_ID=68987at6656_29053_0:00071c;TCS_ID=68987at6656_29053_0:00071c|sample|+|40255 +sample MetaEuk gene 34846 35694 527 - . Target_ID=94238at6656_7245_0:00200b;TCS_ID=94238at6656_7245_0:00200b|sample|-|34845
--- a/test-data/genome_results_metaeuk/short_summary Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results_metaeuk/short_summary Fri Aug 30 15:19:56 2024 +0000 @@ -1,30 +1,32 @@ -# BUSCO version is: 5\.5\.0 -# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) -# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ -# BUSCO was run in mode: euk_genome_met -# Gene predictor used: metaeuk +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/f/3/1/dataset_f31d44e3-c824-4cdf-92ba-99a2c26071d2.dat +# BUSCO was run in mode: euk_genome_min +# Gene predictor used: miniprot - \*\*\*\*\* Results: \*\*\*\*\* + ***** 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 \(M\) + C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1012 Missing BUSCOs (M) 1013 Total BUSCO groups searched Assembly Statistics: 1 Number of scaffolds 1 Number of contigs 62370 Total length - 0\.000% Percent gaps + 0.000% Percent gaps 62 KB Scaffold N50 62 KB Contigs N50 Dependencies and versions: - hmmsearch: [0-9\.\+]+ - bbtools: [0-9\.\+]+ - metaeuk: [0-9a-z\.\+]+ - busco: [0-9\.\+]+ + hmmsearch: 3.1 + bbtools: 39.06 + miniprot_index: 0.13-r248 + miniprot_align: 0.13-r248 + python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0) + busco: 5.7.1
--- a/test-data/genome_results_metaeuk_auto/full_table Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results_metaeuk_auto/full_table Fri Aug 30 15:19:56 2024 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255) -# Busco id Status Sequence Gene Start Gene End Strand Score Length +# BUSCO version is: 5.7.1 +# The lineage dataset is: eukaryota_odb10 (Creation date: 2024-01-08, number of genomes: 70, number of BUSCOs: 255) +# Busco id Status Sequence Gene Start Gene End Strand Score Length OrthoDB url Description 39650at2759 Missing 83779at2759 Missing 87842at2759 Missing @@ -131,7 +131,7 @@ 1041560at2759 Missing 1049599at2759 Missing 1051021at2759 Missing -1053181at2759 Complete sample:35678-34845 34845 35678 - 45.0 149 +1053181at2759 Complete sample 35693 34845 - 44.7 149 https://v10-1.orthodb.org/?query=1053181at2759 Checkpoint protein Hus1/Mec3 1057950at2759 Missing 1065019at2759 Missing 1076134at2759 Missing
--- a/test-data/genome_results_metaeuk_auto/missing_buscos_list Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results_metaeuk_auto/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255) +# BUSCO version is: 5.7.1 +# The lineage dataset is: eukaryota_odb10 (Creation date: 2024-01-08, number of genomes: 70, number of BUSCOs: 255) # Busco id 1001705at2759 1003258at2759
--- a/test-data/genome_results_metaeuk_auto/out.gff Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results_metaeuk_auto/out.gff Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,2 @@ ##gff-version 3 sample MetaEuk gene 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845 -sample MetaEuk mRNA 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_mRNA;Parent=1053181at2759_7245_0:00200b|sample|-|34845 -sample MetaEuk exon 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_exon_0;Parent=1053181at2759_7245_0:00200b|sample|-|34845_mRNA -sample MetaEuk CDS 34846 35694 527 - . Target_ID=1053181at2759_7245_0:00200b;TCS_ID=1053181at2759_7245_0:00200b|sample|-|34845_CDS_0;Parent=1053181at2759_7245_0:00200b|sample|-|34845_exon_0
--- a/test-data/genome_results_metaeuk_auto/short_summary Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/genome_results_metaeuk_auto/short_summary Fri Aug 30 15:19:56 2024 +0000 @@ -1,6 +1,6 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: eukaryota_odb10 (Creation date: 2020-09-10, number of genomes: 70, number of BUSCOs: 255) -# Summarized benchmarking in BUSCO notation for file /tmp/tmp5_syjrgy/files/a/5/a/dataset_a5adf25d-f667-41d6-9472-f8661403e128.dat +# BUSCO version is: 5.7.1 +# The lineage dataset is: eukaryota_odb10 (Creation date: 2024-01-08, number of genomes: 70, number of BUSCOs: 255) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpg41og118/files/f/5/e/dataset_f5e13834-6f57-4cb4-af82-b730a3e03fdb.dat # BUSCO was run in mode: euk_genome_met # Gene predictor used: metaeuk @@ -25,7 +25,8 @@ Dependencies and versions: hmmsearch: 3.1 - bbtools: 39.01 + bbtools: 39.06 prodigal: 2.6.3 - busco: 5.5.0 - metaeuk: 6.a5d39d9 + python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0) + busco: 5.7.1 + metaeuk: 7.bba0d80
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome_results_miniprot/full_table Fri Aug 30 15:19:56 2024 +0000 @@ -0,0 +1,1016 @@ +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 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 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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 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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 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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 Missing +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 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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 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Missing +93797at6656 Missing +94054at6656 Missing +94238at6656 Complete sample 35679 34845 - 60.7 116 https://v10-1.orthodb.org/?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 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+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
--- a/test-data/proteome_results/full_table Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/proteome_results/full_table Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id Status Sequence Score Length OrthoDB url Description 774at6656 Missing 980at6656 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 1355.6 788 https://v10-1.orthodb.org/?query=22364at6656 Importin repeat 4 22468at6656 Missing 22611at6656 Missing 22887at6656 Missing
--- a/test-data/proteome_results/missing_buscos_list Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/proteome_results/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 100136at6656
--- a/test-data/proteome_results/short_summary Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/proteome_results/short_summary Fri Aug 30 15:19:56 2024 +0000 @@ -1,18 +1,19 @@ -# BUSCO version is: 5\.5\.0 -# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) -# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/e/0/f/dataset_e0f4947a-b95c-45dc-bee8-301d13fe1fe5.dat # BUSCO was run in mode: proteins - \*\*\*\*\* Results: \*\*\*\*\* + ***** Results: ***** - C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013 - 1 Complete BUSCOs \(C\) - 1 Complete and single-copy BUSCOs \(S\) - 0 Complete and duplicated BUSCOs \(D\) - 0 Fragmented BUSCOs \(F\) - 1012 Missing BUSCOs \(M\) + C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1012 Missing BUSCOs (M) 1013 Total BUSCO groups searched Dependencies and versions: - hmmsearch: [0-9\.\+]+ - busco: [0-9\.\+]+ + hmmsearch: 3.1 + python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0) + busco: 5.7.1
--- a/test-data/transcriptome_results/full_table Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/transcriptome_results/full_table Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id Status Sequence Score Length OrthoDB url Description 774at6656 Missing 980at6656 Missing @@ -86,7 +86,7 @@ 22098at6656 Missing 22148at6656 Missing 22358at6656 Missing -22364at6656 Complete BUSCOaEOG7B0HST:0-2699 1355.6 788 https://www.orthodb.org/v10?query=22364at6656 importin-5 +22364at6656 Complete BUSCOaEOG7B0HST:0-2699 1355.6 788 https://v10-1.orthodb.org/?query=22364at6656 Importin repeat 4 22468at6656 Missing 22611at6656 Missing 22887at6656 Missing
--- a/test-data/transcriptome_results/missing_buscos_list Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/transcriptome_results/missing_buscos_list Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,5 @@ -# BUSCO version is: 5.5.0 -# The lineage dataset is: arthropoda_odb10 (Creation date: 2020-09-10, number of genomes: 90, number of BUSCOs: 1013) +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) # Busco id 100070at6656 100136at6656
--- a/test-data/transcriptome_results/out.gff Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/transcriptome_results/out.gff Fri Aug 30 15:19:56 2024 +0000 @@ -1,5 +1,2 @@ ##gff-version 3 BUSCOaEOG7B0HST MetaEuk gene 1 2700 1493 + . Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0 -BUSCOaEOG7B0HST MetaEuk mRNA 1 2700 1493 + . Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_mRNA;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0 -BUSCOaEOG7B0HST MetaEuk exon 1 2700 1493 + . Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_exon_0;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_mRNA -BUSCOaEOG7B0HST MetaEuk CDS 1 2700 1493 + . Target_ID=22364at6656_211228_0:002349;TCS_ID=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_CDS_0;Parent=22364at6656_211228_0:002349|BUSCOaEOG7B0HST|+|0_exon_0
--- a/test-data/transcriptome_results/short_summary Mon Mar 18 16:01:49 2024 +0000 +++ b/test-data/transcriptome_results/short_summary Fri Aug 30 15:19:56 2024 +0000 @@ -1,19 +1,20 @@ -# BUSCO version is: 5\.5\.0 -# The lineage dataset is: arthropoda_odb10 \(Creation date: [0-9]{4}-[0-9]{2}-[0-9]{2}, number of genomes: 90, number of BUSCOs: 1013\) -# Summarized benchmarking in BUSCO notation for file [a-z0-9_\-/\.]+ +# BUSCO version is: 5.7.1 +# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013) +# Summarized benchmarking in BUSCO notation for file /tmp/tmpl5l1blpe/files/8/1/5/dataset_8150f803-80e8-4d16-9c33-eec04107fced.dat # BUSCO was run in mode: euk_tran - \*\*\*\*\* Results: \*\*\*\*\* + ***** Results: ***** - C:0\.1%\[S:0\.1%,D:0\.0%\],F:0\.0%,M:99\.9%,n:1013 - 1 Complete BUSCOs \(C\) - 1 Complete and single-copy BUSCOs \(S\) - 0 Complete and duplicated BUSCOs \(D\) - 0 Fragmented BUSCOs \(F\) - 1012 Missing BUSCOs \(M\) + C:0.1%[S:0.1%,D:0.0%],F:0.0%,M:99.9%,n:1013 + 1 Complete BUSCOs (C) + 1 Complete and single-copy BUSCOs (S) + 0 Complete and duplicated BUSCOs (D) + 0 Fragmented BUSCOs (F) + 1012 Missing BUSCOs (M) 1013 Total BUSCO groups searched Dependencies and versions: - hmmsearch: [0-9\.\+]+ - metaeuk: [0-9a-z\.\+]+ - busco: [0-9\.\+]+ + hmmsearch: 3.1 + metaeuk: 7.bba0d80 + python: sys.version_info(major=3, minor=9, micro=19, releaselevel='final', serial=0) + busco: 5.7.1