| Previous changeset 20:ea8146ee148f (2024-03-18) Next changeset 22:e5c372c91e46 (2024-10-29) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/busco/ commit 21578f94c8a18c7fd3c2e3aa36897768a4674d2a |
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modified:
busco.xml macros.xml test-data/busco_database.loc test-data/genome_results/full_table test-data/genome_results/full_table_cached test-data/genome_results/missing_buscos_list test-data/genome_results/short_summary test-data/genome_results/short_summary_cached test-data/genome_results_metaeuk/full_table test-data/genome_results_metaeuk/missing_buscos_list test-data/genome_results_metaeuk/short_summary test-data/genome_results_metaeuk/summary.png test-data/genome_results_metaeuk_auto/full_table test-data/genome_results_metaeuk_auto/missing_buscos_list test-data/genome_results_metaeuk_auto/out.gff test-data/genome_results_metaeuk_auto/short_summary test-data/genome_results_metaeuk_auto/summary.png test-data/proteome_results/full_table test-data/proteome_results/missing_buscos_list test-data/proteome_results/short_summary test-data/proteome_results/summary.png test-data/transcriptome_results/full_table test-data/transcriptome_results/missing_buscos_list test-data/transcriptome_results/out.gff test-data/transcriptome_results/short_summary test-data/transcriptome_results/summary.png |
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added:
test-data/busco_downloads/file_versions.tsv test-data/genome_results_metaeuk/out.gff3 test-data/genome_results_miniprot/full_table test-data/genome_results_miniprot/out.gff test-data/genome_results_miniprot/short_summary test-data/test-db/busco_downloads/lineages/archaea_odb10/refseq_db.faa |
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| diff -r ea8146ee148f -r 2babe6d5c561 busco.xml --- a/busco.xml Mon Mar 18 16:01:49 2024 +0000 +++ b/busco.xml Fri Aug 30 15:19:56 2024 +0000 |
| [ |
| b'@@ -14,7 +14,7 @@\n <version_command>busco --version</version_command>\n <command><![CDATA[\n \n-#if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'yes\':\n+#if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'augustus\':\n \n if [ -z "\\$AUGUSTUS_CONFIG_PATH" ] ; then BUSCO_PATH=\\$(dirname \\$(which busco)) ; export AUGUSTUS_CONFIG_PATH=\\$(realpath \\${BUSCO_PATH}/../config) ; fi &&\n cp -r "\\$AUGUSTUS_CONFIG_PATH/" augustus_dir/ &&\n@@ -40,8 +40,6 @@\n #if $lineage_conditional.selector == \'cached\':\n --offline\n --download_path $lineage_conditional.cached_db.fields.path\n-#else\n- --update-data\n #end if\n \n #if $lineage.lineage_mode == "auto_detect":\n@@ -50,21 +48,20 @@\n --lineage_dataset \'${lineage.lineage_dataset}\'\n #end if\n \n-#if $busco_mode.mode == \'geno\' and $busco_mode.use_augustus.use_augustus_selector == \'yes\':\n-\n- ${busco_mode.use_augustus.long}\n- --augustus\n+#if $busco_mode.mode == \'geno\':\n+ #if $busco_mode.use_augustus.use_augustus_selector == \'miniprot\':\n+ --miniprot\n+ #elif $busco_mode.use_augustus.use_augustus_selector == \'augustus\':\n+ ${busco_mode.use_augustus.long}\n+ --augustus\n \n- #if $busco_mode.use_augustus.aug_prediction.augustus_mode == \'builtin\':\n- --augustus_species \'${busco_mode.use_augustus.aug_prediction.augustus_species}\'\n- #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == \'history\':\n- --augustus_species local\n- #end if\n-#end if\n-\n-#if str( $busco_mode.mode ) == "geno":\n- #if $busco_mode.miniprot:\n- --miniprot\n+ #if $busco_mode.use_augustus.aug_prediction.augustus_mode == \'builtin\':\n+ --augustus_species \'${busco_mode.use_augustus.aug_prediction.augustus_species}\'\n+ #else if $busco_mode.use_augustus.aug_prediction.augustus_mode == \'history\':\n+ --augustus_species local\n+ #end if\n+ #else:\n+ --metaeuk\n #end if\n #end if\n \n@@ -111,14 +108,16 @@\n <option value="prot">annotated gene sets (protein)</option>\n </param>\n <when value="geno">\n- <param name="miniprot" type="boolean" checked="false" label="Generate miniprot output"/>\n <conditional name="use_augustus">\n- <param name="use_augustus_selector" type="select" label="Use Augustus instead of Metaeuk">\n- <option value="yes">Yes, use Augustus</option>\n- <option value="no" selected="true">Use Metaeuk</option>\n+ <param name="use_augustus_selector" type="select" label="Select a gene predictor" help="In the case of a prokaryotic genome, Prodigal is the default gene predictor">\n+ <option value="augustus">Augustus</option>\n+ <option value="metaeuk">Metaeuk</option>\n+ <option value="miniprot" selected="true">Miniprot</option>\n+\n </param>\n- <when value="no" />\n- <when value="yes">\n+ <when value="metaeuk"/>\n+ <when value="miniprot"/>\n+ <when value="augustus">\n <conditional name="aug_prediction">\n <param name="augustus_mode" type="select" label="Augustus species model">\n <option value="no" selected="true">Use the default species for selected lineage</option>\n@@ -189,10 +188,7 @@\n </data>\n <data name=\'busco_gff\' format=\'gff3\' label="${tool.name} on ${on_string}: GFF" from_work_dir="busco_output.gff">\n <filter>outputs and \'gff\' in outputs</filter>\n- </data>\n- <data name=\'busco_miniprot\' format=\'gff3\' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="busco_galaxy/run_*/miniprot_output/*.gff">\n- <filter>busco_mode[\'mode\'] == \'geno\' and busco_mode[\'miniprot\']</filter>\n- </data'..b'ntents>\n+ </output>\n+ <output name="summary_image" file="genome_results_metaeuk/summary.png" compare="sim_size"/>\n+ <output name="busco_gff" file="genome_results_metaeuk/out.gff3" compare="diff" lines_diff="6" />\n </test>\n <test expect_num_outputs="5">\n <param name="input" value="genome.fa" />\n@@ -342,32 +364,49 @@\n <conditional name="busco_mode">\n <param name="mode" value="geno" />\n <conditional name="use_augustus">\n- <param name="use_augustus_selector" value="no" />\n+ <param name="use_augustus_selector" value="metaeuk" />\n </conditional>\n </conditional>\n <param name="outputs" value="short_summary,missing,image,gff" />\n- <output name="busco_sum" file="genome_results_metaeuk_auto/short_summary" compare="diff" lines_diff="6" />\n- <output name="busco_table" file="genome_results_metaeuk_auto/full_table" compare="diff" lines_diff="6" />\n- <output name="busco_missing" file="genome_results_metaeuk_auto/missing_buscos_list" compare="diff" lines_diff="2" />\n+ <output name="busco_sum">\n+ <assert_contents>\n+ <has_text text="Gene predictor used: metaeuk"/>\n+ </assert_contents>\n+ </output>\n+ <output name="busco_table">\n+ <assert_contents>\n+ <has_text text="# BUSCO version is: @TOOL_VERSION@"/>\n+ <has_text text="The lineage dataset is: eukaryota_odb10"/>\n+ </assert_contents>\n+ </output>\n+ <output name="busco_missing">\n+ <assert_contents>\n+ <has_text text="# BUSCO version is: @TOOL_VERSION@"/>\n+ <has_text text="The lineage dataset is: eukaryota_odb10"/>\n+ </assert_contents>\n+ </output>\n <output name="summary_image" file="genome_results_metaeuk_auto/summary.png" compare="sim_size" />\n <output name="busco_gff" file="genome_results_metaeuk_auto/out.gff" compare="diff" />\n </test>\n- <test expect_num_outputs="2">\n+ <test expect_num_outputs="3">\n <param name="input" value="genome.fa" />\n- <conditional name="lineage_conditional">\n- <param name="selector" value="cached"/>\n- <param name="cached_db" value="busco-demo-db-20230328"/>\n- </conditional>\n <conditional name="lineage">\n <param name="lineage_mode" value="select_lineage" />\n- <param name="lineage_dataset" value="archaea_odb10" />\n+ <param name="lineage_dataset" value="arthropoda_odb10" />\n </conditional>\n- <param name="outputs" value="short_summary" />\n- <output name="busco_sum" file="genome_results/short_summary_cached" compare="diff" lines_diff="6" />\n- <output name="busco_table" file="genome_results/full_table_cached" compare="diff" lines_diff="4" />\n- <assert_stdout>\n- <has_text text="Running BUSCO using lineage dataset archaea_odb10 (prokaryota, 2021-02-23)"/>\n- </assert_stdout>\n+ <param name="outputs" value="short_summary,gff" />\n+ <output name="busco_sum">\n+ <assert_contents>\n+ <has_text text="# Gene predictor used: miniprot"/>\n+ </assert_contents>\n+ </output>\n+ <output name="busco_gff" file="genome_results_miniprot/out.gff" compare="diff" />\n+ <output name="busco_table" file="genome_results_miniprot/full_table">\n+ <assert_contents>\n+ <has_text text="# BUSCO version is: @TOOL_VERSION@"/>\n+ <has_text text="9647at6656"/>\n+ </assert_contents>\n+ </output>\n </test>\n </tests>\n <help><![CDATA[\n' |
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| diff -r ea8146ee148f -r 2babe6d5c561 macros.xml --- a/macros.xml Mon Mar 18 16:01:49 2024 +0000 +++ b/macros.xml Fri Aug 30 15:19:56 2024 +0000 |
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| @@ -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"> |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/busco_database.loc --- 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 |
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| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/busco_downloads/file_versions.tsv --- /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 |
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| b'@@ -0,0 +1,213 @@\n+acidobacteria_odb10\t2024-01-08\t13046d110cf6d038af269ee6e0681bdc\tProkaryota\tlineages\n+aconoidasida_odb10\t2024-01-08\t47b6ece13859b681466c79f4e6c6d1ad\tEukaryota\tlineages\n+actinobacteria_class_odb10\t2024-01-08\t0a326071854e20d1977a13a5e3a5f84f\tProkaryota\tlineages\n+actinobacteria_phylum_odb10\t2024-01-08\teaa25a3d973f580d4cf59b7251309e5a\tProkaryota\tlineages\n+actinopterygii_odb10\t2024-01-08\t6b042870822559fcacf129fdedea8927\tEukaryota\tlineages\n+agaricales_odb10\t2024-01-08\t1bf1c632dab6ae5b4ff0be6fad8ff8cf\tEukaryota\tlineages\n+agaricomycetes_odb10\t2024-01-08\t717f3e2543617972c9a45bbd4ac975b6\tEukaryota\tlineages\n+alphaproteobacteria_odb10\t2024-01-08\t22db70ba9f321e8b8f4eed0b2be41b6f\tProkaryota\tlineages\n+alteromonadales_odb10\t2024-01-08\t0a959f97971c349fdd69bc37e7796514\tProkaryota\tlineages\n+alveolata_odb10\t2024-01-08\tcbd2ddb6b18efb2b4ca218a74688aacf\tEukaryota\tlineages\n+apicomplexa_odb10\t2024-01-08\te27eb839243c4a4280e4187108b48596\tEukaryota\tlineages\n+aquificae_odb10\t2024-01-08\t0285bccb18097979aef7badd2b554378\tProkaryota\tlineages\n+arachnida_odb10\t2024-01-08\t625818d0544cd760356af0b8e9a5a412\tEukaryota\tlineages\n+archaea_odb10\t2024-01-08\t3eb26c670c520c0f3b32bff46fce03d7\tProkaryota\tlineages\n+arthropoda_odb10\t2024-01-08\t915ae2790da249b81eceeb1cea2ad922\tEukaryota\tlineages\n+ascomycota_odb10\t2024-01-08\t694c2ad193a01cd6e95487a3ddcbcce8\tEukaryota\tlineages\n+aves_odb10\t2024-01-08\teea0b7e8122b1f528c97c142e9ddfd82\tEukaryota\tlineages\n+bacillales_odb10\t2024-01-08\te2fb5d46b90c76f849d9ec9c49ae79ca\tProkaryota\tlineages\n+bacilli_odb10\t2024-01-08\te8dc4ad8c6e26e2dfc47e155736896bd\tProkaryota\tlineages\n+bacteria_odb10\t2024-01-08\tbff9523df89980699c01e8f31e490496\tProkaryota\tlineages\n+bacteroidales_odb10\t2024-01-08\t60e4d09d2526ad90561bc0ad4c67f783\tProkaryota\tlineages\n+bacteroidetes-chlorobi_group_odb10\t2024-01-08\t4d2ae5165b8aec5f42f42d79e98bc05d\tProkaryota\tlineages\n+bacteroidetes_odb10\t2024-01-08\t81eddd495a27b2c15b661eb2f018b01b\tProkaryota\tlineages\n+bacteroidia_odb10\t2024-01-08\t1756db675bfee79e3a3a6e9946003038\tProkaryota\tlineages\n+basidiomycota_odb10\t2024-01-08\t55ee0a0b2ca18812393fd43faf4f1897\tEukaryota\tlineages\n+betaproteobacteria_odb10\t2024-01-08\t040cf23dfcfc0fa632bd48fde213b61f\tProkaryota\tlineages\n+boletales_odb10\t2024-01-08\t7a7b1635d171d069a5525ee24faf8c83\tEukaryota\tlineages\n+brassicales_odb10\t2024-01-08\t7f96488b36e2f391dd594a099b31ea24\tEukaryota\tlineages\n+burkholderiales_odb10\t2024-01-08\tb41288c7ab665a79a592214850af3dcf\tProkaryota\tlineages\n+campylobacterales_odb10\t2024-01-08\t950fa5f90829dfbfe879e71f22d8a6f1\tProkaryota\tlineages\n+capnodiales_odb10\t2024-01-08\ta1601671360646aa38c968520f81a9bc\tEukaryota\tlineages\n+carnivora_odb10\t2024-01-08\ta81b85b7d90b046315b8cb1bea8605c1\tEukaryota\tlineages\n+cellvibrionales_odb10\t2024-01-08\t4284a714433698dfcf38b7297bc6ef4b\tProkaryota\tlineages\n+cetartiodactyla_odb10\t2024-01-08\t7d348bed34a92a77c86adb4194a4d0cc\tEukaryota\tlineages\n+chaetothyriales_odb10\t2024-01-08\t721a498d4da22ab75c48a705cb7ffafe\tEukaryota\tlineages\n+chlamydiae_odb10\t2024-01-08\tf9a0d5d18b525f5b25ffd28cbc79511a\tProkaryota\tlineages\n+chlorobi_odb10\t2024-01-08\t1accab3fc927c6e614d96d3b76eb7d41\tProkaryota\tlineages\n+chloroflexi_odb10\t2024-01-08\t9633d49879fba7efe9d59e9ec1f6fb70\tProkaryota\tlineages\n+chlorophyta_odb10\t2024-01-08\t7dbcc25dd421be9fbb0f0ae0d7095284\tEukaryota\tlineages\n+chromatiales_odb10\t2024-01-08\t113389b263ee38c451831b513a56ae85\tProkaryota\tlineages\n+chroococcales_odb10\t2024-01-08\t319aa6d9e5ce2606aecfc0bce4419eb8\tProkaryota\tlineages\n+clostridiales_odb10\t2024-01-08\t9b90a303dc2395f6197c1d64f03fbfc0\tProkaryota\tlineages\n+clostridia_odb10\t2024-01-08\t7eeb8a01b7c4643aa9fbbd1fd03c887f\tProkaryota\tlineages\n+coccidia_odb10\t2024-01-08\tec804a941baabf38053a0f8b8c7021dd\tEukaryota\tlineages\n+coriobacteriales_odb10\t2024-01-08\t18776c9d1cf45a170a71a57e6b0bf32c\tProkaryota\tlineages\n+coriobacteriia_odb10\t2024-01-08\t6837d15f63527b8b9ad624f9e4a26daf\tProkaryota\tlineages\n+corynebacteriales_odb10\t2024-01-08\taf866d8ea389f71092f9344fb9603f5c\tProkaryota\tlineages\n+cyanobacteria_odb10\t2024-01'..b'6c7a944c1f36dc22353a62e663065b\tProkaryota\tlineages\n+thermoplasmata_odb10\t2024-01-08\tf3ec5b6d8fa79c4c6caa37e6b0c09776\tProkaryota\tlineages\n+thermoproteales_odb10\t2024-01-08\tc92700b9bc1018ba50741c453632a758\tProkaryota\tlineages\n+thermoprotei_odb10\t2024-01-08\te9c08ac322b0c8e4d1c052e6738ad85d\tProkaryota\tlineages\n+thermotogae_odb10\t2024-01-08\t546306dabbd386be2d9940a2c0d0deb1\tProkaryota\tlineages\n+thiotrichales_odb10\t2024-01-08\t7871f11be31cf3dfb0f57e8a1f5b31f1\tProkaryota\tlineages\n+tissierellales_odb10\t2024-01-08\td5651b1b2e07433fc212881bd1482b72\tProkaryota\tlineages\n+tissierellia_odb10\t2024-01-08\tf56b85fda5d5cb55322a8cbd452dd365\tProkaryota\tlineages\n+tree.archaea_odb10.nwk\t2019-12-16\t23a9602460ca3ba12a4382964c40add4\tProkaryota\tplacement_files\n+tree.bacteria_odb10.nwk\t2019-12-16\t3cbe2d6292e02ee78b92b42ec7c13bf5\tProkaryota\tplacement_files\n+tree.eukaryota_odb10.nwk\t2019-12-16\tcb0d434ee9d87f5d6babd1832a3fa419\tEukaryota\tplacement_files\n+tree_metadata.archaea_odb10.txt\t2019-12-16\t1cc8a1284c883d9a5a8e33e70a81a743\tProkaryota\tplacement_files\n+tree_metadata.bacteria_odb10.txt\t2019-12-16\t04a34d1dbcc0814bd0f5acee1d2a9c3f\tProkaryota\tplacement_files\n+tree_metadata.eukaryota_odb10.txt\t2019-12-16\t589ac2a41cb79863d4b0b061e472afea\tEukaryota\tplacement_files\n+tremellomycetes_odb10\t2024-01-08\ta0bfe1ffe4313753173cd341ddcc4c07\tEukaryota\tlineages\n+verrucomicrobia_odb10\t2024-01-08\t1c380e10eaac2482a9485fe14b7bad47\tProkaryota\tlineages\n+vertebrata_odb10\t2024-01-08\td292737afaec0ac95bde4f4a8d2ea814\tEukaryota\tlineages\n+vibrionales_odb10\t2024-01-08\te9ec5827bed867a01d07d7d03aaddc4c\tProkaryota\tlineages\n+viridiplantae_odb10\t2024-01-08\t90d6ce27fde83f1e4aba1d6a8f523673\tEukaryota\tlineages\n+xanthomonadales_odb10\t2024-01-08\t47dd98a24916b28b52500e9a036eb8a8\tProkaryota\tlineages\n+alphaherpesvirinae_odb10\t2024-01-08\t44433a26b31aa50e4314a013eb2d1ff4\tVirus\tlineages\n+baculoviridae_odb10\t2024-01-08\t78a612f186cb5b88ec8c030661e46487\tVirus\tlineages\n+rudiviridae_odb10\t2024-01-08\tafad43502a74667304b97a39459700b4\tVirus\tlineages\n+betaherpesvirinae_odb10\t2024-01-08\t1fd9d15097a377d712c6458451bf65af\tVirus\tlineages\n+herpesviridae_odb10\t2024-01-08\t79856510300f9379e518cc8180ad14fb\tVirus\tlineages\n+poxviridae_odb10\t2024-01-08\t4cb2e71a92b2088a0a0b1f4ff20f94ef\tVirus\tlineages\n+tevenvirinae_odb10\t2024-01-08\tfac34fac2c70199fcbe69c0a7a663d71\tVirus\tlineages\n+aviadenovirus_odb10\t2024-01-08\tf9c946051627e87ff717ad466d6c5966\tVirus\tlineages\n+enquatrovirus_odb10\t2024-01-08\tf6c05f3de730a09cc7eaf58bcc50636c\tVirus\tlineages\n+teseptimavirus_odb10\t2024-01-08\t18d63d8e679c6fc6086d906d6b917f05\tVirus\tlineages\n+bclasvirinae_odb10\t2024-01-08\t51a9dce485c577e575d411d10c566820\tVirus\tlineages\n+fromanvirus_odb10\t2024-01-08\t48f5b7b57afa387315c9e006410f55b9\tVirus\tlineages\n+skunavirus_odb10\t2024-01-08\t68fbb8404853ae930651c3af1baa7b49\tVirus\tlineages\n+betabaculovirus_odb10\t2024-01-08\taab73c1e308f8a1cec4f4529b06ee3d4\tVirus\tlineages\n+pahexavirus_odb10\t2024-01-08\t3b1410a4b594471e05c0b4d466e3173b\tVirus\tlineages\n+alphabaculovirus_odb10\t2024-01-08\tec04ed01eab6001f35c1a6ebfc70180f\tVirus\tlineages\n+tunavirinae_odb10\t2024-01-08\tfe8a69addddcbc43732a4504aff538e2\tVirus\tlineages\n+simplexvirus_odb10\t2024-01-08\tfffd2907f63fe04c78fabd61d2f56919\tVirus\tlineages\n+gammaherpesvirinae_odb10\t2024-01-08\tda764ed072f3fb78cae2ff7e90868a9f\tVirus\tlineages\n+varicellovirus_odb10\t2024-01-08\t43c79da0fb65e9d5941d71458cf844ad\tVirus\tlineages\n+cheoctovirus_odb10\t2024-01-08\t74dacf2a763c2a462356ded5e79921db\tVirus\tlineages\n+guernseyvirinae_odb10\t2024-01-08\t484f59b9efc120c118fae2e6c178ffaa\tVirus\tlineages\n+tequatrovirus_odb10\t2024-01-08\t67a3c9d25ded118212840dfd87c37d96\tVirus\tlineages\n+chordopoxvirinae_odb10\t2024-01-08\tc5ff51b8e86771a94400c0df8f8eb383\tVirus\tlineages\n+peduovirus_odb10\t2024-01-08\t660b6c8dae78bf76bddd9ba1be2c8bd9\tVirus\tlineages\n+iridoviridae_odb10\t2024-01-08\t3b3e67bb85d616fd874b26479d6abaea\tVirus\tlineages\n+spounavirinae_odb10\t2024-01-08\t286365f43fe02aad53b89555d36cd6b0\tVirus\tlineages\n+virus_datasets.txt\t2020-11-26\ta7d1e4d4bb6327d01efde3bcc8658cb3\tNaN\tinformation\n' |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/full_table --- 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 |
| b |
| @@ -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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/full_table_cached --- 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 |
| b |
| @@ -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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/missing_buscos_list --- 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 |
| b |
| @@ -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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/short_summary --- 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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results/short_summary_cached --- 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 |
| b |
| @@ -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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/full_table --- 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 |
| b |
| @@ -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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/missing_buscos_list --- 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 |
| b |
| @@ -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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/out.gff3 --- /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 |
| b |
| @@ -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 |
| b |
| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/short_summary --- 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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk/summary.png |
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| Binary file test-data/genome_results_metaeuk/summary.png has changed |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/full_table --- 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 |
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| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/missing_buscos_list --- 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 |
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| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/out.gff --- 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 |
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| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/short_summary --- 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 |
| b |
| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_metaeuk_auto/summary.png |
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| Binary file test-data/genome_results_metaeuk_auto/summary.png has changed |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/genome_results_miniprot/full_table --- /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 |
| b |
| b'@@ -0,0 +1,1016 @@\n+# BUSCO version is: 5.7.1 \n+# The lineage dataset is: arthropoda_odb10 (Creation date: 2024-01-08, number of genomes: 90, number of BUSCOs: 1013)\n+# Busco id\tStatus\tSequence\tGene Start\tGene End\tStrand\tScore\tLength\tOrthoDB url\tDescription\n+774at6656\tMissing\n+980at6656\tMissing\n+997at6656\tMissing\n+1166at6656\tMissing\n+1885at6656\tMissing\n+1990at6656\tMissing\n+2148at6656\tMissing\n+2456at6656\tMissing\n+2473at6656\tMissing\n+3310at6656\tMissing\n+3585at6656\tMissing\n+3644at6656\tMissing\n+4136at6656\tMissing\n+4227at6656\tMissing\n+4864at6656\tMissing\n+5277at6656\tMissing\n+5616at6656\tMissing\n+6453at6656\tMissing\n+6563at6656\tMissing\n+6715at6656\tMissing\n+6820at6656\tMissing\n+7210at6656\tMissing\n+8145at6656\tMissing\n+8495at6656\tMissing\n+8847at6656\tMissing\n+8913at6656\tMissing\n+9647at6656\tMissing\n+9648at6656\tMissing\n+10240at6656\tMissing\n+10573at6656\tMissing\n+11384at6656\tMissing\n+12029at6656\tMissing\n+12174at6656\tMissing\n+12383at6656\tMissing\n+12771at6656\tMissing\n+12846at6656\tMissing\n+13019at6656\tMissing\n+13051at6656\tMissing\n+13736at6656\tMissing\n+13833at6656\tMissing\n+13858at6656\tMissing\n+13890at6656\tMissing\n+13934at6656\tMissing\n+14090at6656\tMissing\n+14257at6656\tMissing\n+14447at6656\tMissing\n+14995at6656\tMissing\n+15200at6656\tMissing\n+15697at6656\tMissing\n+15905at6656\tMissing\n+16061at6656\tMissing\n+16084at6656\tMissing\n+16220at6656\tMissing\n+16630at6656\tMissing\n+16648at6656\tMissing\n+17096at6656\tMissing\n+17122at6656\tMissing\n+17128at6656\tMissing\n+17748at6656\tMissing\n+18036at6656\tMissing\n+18055at6656\tMissing\n+18073at6656\tMissing\n+18630at6656\tMissing\n+18929at6656\tMissing\n+19044at6656\tMissing\n+19058at6656\tMissing\n+19104at6656\tMissing\n+19129at6656\tMissing\n+19208at6656\tMissing\n+19289at6656\tMissing\n+19590at6656\tMissing\n+19760at6656\tMissing\n+20093at6656\tMissing\n+20162at6656\tMissing\n+20267at6656\tMissing\n+20935at6656\tMissing\n+20936at6656\tMissing\n+21019at6656\tMissing\n+21191at6656\tMissing\n+21361at6656\tMissing\n+21367at6656\tMissing\n+21385at6656\tMissing\n+22098at6656\tMissing\n+22148at6656\tMissing\n+22358at6656\tMissing\n+22364at6656\tMissing\n+22468at6656\tMissing\n+22611at6656\tMissing\n+22887at6656\tMissing\n+23309at6656\tMissing\n+23388at6656\tMissing\n+23429at6656\tMissing\n+23917at6656\tMissing\n+24255at6656\tMissing\n+24427at6656\tMissing\n+24459at6656\tMissing\n+24556at6656\tMissing\n+24573at6656\tMissing\n+25554at6656\tMissing\n+25680at6656\tMissing\n+26078at6656\tMissing\n+26653at6656\tMissing\n+26734at6656\tMissing\n+27198at6656\tMissing\n+27515at6656\tMissing\n+27617at6656\tMissing\n+27655at6656\tMissing\n+28325at6656\tMissing\n+28380at6656\tMissing\n+28519at6656\tMissing\n+28685at6656\tMissing\n+28872at6656\tMissing\n+29213at6656\tMissing\n+29237at6656\tMissing\n+29365at6656\tMissing\n+29730at6656\tMissing\n+29744at6656\tMissing\n+30156at6656\tMissing\n+30184at6656\tMissing\n+30267at6656\tMissing\n+30463at6656\tMissing\n+30512at6656\tMissing\n+30526at6656\tMissing\n+30642at6656\tMissing\n+30822at6656\tMissing\n+30918at6656\tMissing\n+30962at6656\tMissing\n+31014at6656\tMissing\n+31119at6656\tMissing\n+31196at6656\tMissing\n+31333at6656\tMissing\n+31480at6656\tMissing\n+31615at6656\tMissing\n+31634at6656\tMissing\n+31820at6656\tMissing\n+31886at6656\tMissing\n+31919at6656\tMissing\n+32694at6656\tMissing\n+32733at6656\tMissing\n+32851at6656\tMissing\n+33187at6656\tMissing\n+33566at6656\tMissing\n+33794at6656\tMissing\n+34586at6656\tMissing\n+34917at6656\tMissing\n+35035at6656\tMissing\n+35548at6656\tMissing\n+35680at6656\tMissing\n+35708at6656\tMissing\n+35995at6656\tMissing\n+36374at6656\tMissing\n+36387at6656\tMissing\n+36403at6656\tMissing\n+36463at6656\tMissing\n+37030at6656\tMissing\n+37297at6656\tMissing\n+37387at6656\tMissing\n+37678at6656\tMissing\n+38140at6656\tMissing\n+38186at6656\tMissing\n+38303at6656\tMissing\n+38391at6656\tMissing\n+38567at6656\tMissing\n+38819at6656\tMissing\n+38928at6656\tMissing\n+39506at6656\tMissing\n+39548at6656\tMissing\n+39783at6656\tMissing\n+39809at6656\tMissing\n+39821at6656\tMissing\n+40065at6656\tMissing\n+40092at6656\tMissing\n+40213at6656\tMissing\n+40240at6656\tMissing\n+40319at6656\tMissing\n+40323at6656\tMissing\n+40399at6656\tMissing\n+40691at6656\tMissing\n+40929at6656\tMissing\n+41522at6656\t'..b'90at6656\tMissing\n+135702at6656\tMissing\n+135764at6656\tMissing\n+135828at6656\tMissing\n+135834at6656\tMissing\n+135859at6656\tMissing\n+135975at6656\tMissing\n+135994at6656\tMissing\n+136055at6656\tMissing\n+136095at6656\tMissing\n+136119at6656\tMissing\n+136224at6656\tMissing\n+136365at6656\tMissing\n+136559at6656\tMissing\n+136888at6656\tMissing\n+137050at6656\tMissing\n+137197at6656\tMissing\n+137202at6656\tMissing\n+137334at6656\tMissing\n+137338at6656\tMissing\n+137422at6656\tMissing\n+137609at6656\tMissing\n+137688at6656\tMissing\n+137709at6656\tMissing\n+137711at6656\tMissing\n+138243at6656\tMissing\n+138271at6656\tMissing\n+138379at6656\tMissing\n+138401at6656\tMissing\n+138502at6656\tMissing\n+138553at6656\tMissing\n+138659at6656\tMissing\n+138684at6656\tMissing\n+138937at6656\tMissing\n+139217at6656\tMissing\n+139553at6656\tMissing\n+139638at6656\tMissing\n+139744at6656\tMissing\n+139834at6656\tMissing\n+140076at6656\tMissing\n+140197at6656\tMissing\n+140198at6656\tMissing\n+140403at6656\tMissing\n+140461at6656\tMissing\n+140693at6656\tMissing\n+140874at6656\tMissing\n+140903at6656\tMissing\n+141031at6656\tMissing\n+141163at6656\tMissing\n+141166at6656\tMissing\n+141175at6656\tMissing\n+141298at6656\tMissing\n+141804at6656\tMissing\n+141859at6656\tMissing\n+141916at6656\tMissing\n+142388at6656\tMissing\n+142415at6656\tMissing\n+142522at6656\tMissing\n+142613at6656\tMissing\n+142661at6656\tMissing\n+142833at6656\tMissing\n+143154at6656\tMissing\n+143279at6656\tMissing\n+143459at6656\tMissing\n+143489at6656\tMissing\n+143562at6656\tMissing\n+143626at6656\tMissing\n+143709at6656\tMissing\n+143812at6656\tMissing\n+143930at6656\tMissing\n+144337at6656\tMissing\n+144652at6656\tMissing\n+144836at6656\tMissing\n+144851at6656\tMissing\n+144853at6656\tMissing\n+145033at6656\tMissing\n+145102at6656\tMissing\n+145443at6656\tMissing\n+145610at6656\tMissing\n+145811at6656\tMissing\n+145996at6656\tMissing\n+146007at6656\tMissing\n+146036at6656\tMissing\n+146087at6656\tMissing\n+146102at6656\tMissing\n+146103at6656\tMissing\n+146383at6656\tMissing\n+146600at6656\tMissing\n+146920at6656\tMissing\n+147002at6656\tMissing\n+147025at6656\tMissing\n+147322at6656\tMissing\n+147657at6656\tMissing\n+147723at6656\tMissing\n+147852at6656\tMissing\n+147891at6656\tMissing\n+147980at6656\tMissing\n+148134at6656\tMissing\n+148619at6656\tMissing\n+148713at6656\tMissing\n+148851at6656\tMissing\n+148890at6656\tMissing\n+149101at6656\tMissing\n+149126at6656\tMissing\n+149251at6656\tMissing\n+149405at6656\tMissing\n+149680at6656\tMissing\n+149753at6656\tMissing\n+149796at6656\tMissing\n+149819at6656\tMissing\n+149973at6656\tMissing\n+149977at6656\tMissing\n+150005at6656\tMissing\n+150049at6656\tMissing\n+150137at6656\tMissing\n+150182at6656\tMissing\n+150251at6656\tMissing\n+150327at6656\tMissing\n+150479at6656\tMissing\n+150583at6656\tMissing\n+150585at6656\tMissing\n+150667at6656\tMissing\n+150765at6656\tMissing\n+151102at6656\tMissing\n+151111at6656\tMissing\n+151114at6656\tMissing\n+151393at6656\tMissing\n+151436at6656\tMissing\n+151642at6656\tMissing\n+151658at6656\tMissing\n+152032at6656\tMissing\n+152109at6656\tMissing\n+152402at6656\tMissing\n+152534at6656\tMissing\n+152871at6656\tMissing\n+153155at6656\tMissing\n+153232at6656\tMissing\n+153312at6656\tMissing\n+153534at6656\tMissing\n+153693at6656\tMissing\n+153873at6656\tMissing\n+154133at6656\tMissing\n+154415at6656\tMissing\n+154507at6656\tMissing\n+155285at6656\tMissing\n+156057at6656\tMissing\n+156081at6656\tMissing\n+156111at6656\tMissing\n+156305at6656\tMissing\n+156395at6656\tMissing\n+156728at6656\tMissing\n+156824at6656\tMissing\n+156882at6656\tMissing\n+156975at6656\tMissing\n+157486at6656\tMissing\n+157579at6656\tMissing\n+157851at6656\tMissing\n+157879at6656\tMissing\n+158194at6656\tMissing\n+158760at6656\tMissing\n+159231at6656\tMissing\n+159420at6656\tMissing\n+159542at6656\tMissing\n+160675at6656\tMissing\n+160705at6656\tMissing\n+161435at6656\tMissing\n+162059at6656\tMissing\n+162147at6656\tMissing\n+162594at6656\tMissing\n+162628at6656\tMissing\n+162841at6656\tMissing\n+163670at6656\tMissing\n+163896at6656\tMissing\n+164354at6656\tMissing\n+164512at6656\tMissing\n+165142at6656\tMissing\n+165207at6656\tMissing\n+165493at6656\tMissing\n+166476at6656\tMissing\n+166479at6656\tMissing\n+166485at6656\tMissing\n+169220at6656\tMissing\n' |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/full_table --- 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 |
| b |
| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/missing_buscos_list --- 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 |
| b |
| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/short_summary --- 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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/proteome_results/summary.png |
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| Binary file test-data/proteome_results/summary.png has changed |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/full_table --- 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 |
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| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/missing_buscos_list --- 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 |
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| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/out.gff --- 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 |
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| @@ -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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/short_summary --- 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 |
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| diff -r ea8146ee148f -r 2babe6d5c561 test-data/transcriptome_results/summary.png |
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| Binary file test-data/transcriptome_results/summary.png has changed |
