| Previous changeset 15:72472698a2df (2023-03-02) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd |
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modified:
macros.xml test-data/test1_report.html test-data/test2.log test-data/test2_report.html test-data/test2_report.pdf test-data/test3.log test-data/test3_report.html test-data/test3_report.pdf |
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| diff -r 72472698a2df -r a3b35edea53a macros.xml --- a/macros.xml Thu Mar 02 10:38:54 2023 +0000 +++ b/macros.xml Tue Nov 12 12:46:19 2024 +0000 |
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| @@ -1,12 +1,13 @@ <macros> - <token name="@TOOL_VERSION@">5.2.0</token> - <token name="@VERSION_SUFFIX@">1</token> - <token name="@PROFILE@">21.01</token> + <token name="@TOOL_VERSION@">5.3.0</token> + <token name="@VERSION_SUFFIX@">0</token> + <token name="@PROFILE@">23.02</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">quast</requirement> - <requirement type="package" version="0.7.17">bwa</requirement> - <requirement type="package" version="2.30.0">bedtools</requirement> + <requirement type="package" version="0.7.18">bwa</requirement> + <requirement type="package" version="2.31.1">bedtools</requirement> + <requirement type="package" version="2.76">perl-gd</requirement> </requirements> </xml> <xml name="bio_tools"> |
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| diff -r 72472698a2df -r a3b35edea53a test-data/test1_report.html --- a/test-data/test1_report.html Thu Mar 02 10:38:54 2023 +0000 +++ b/test-data/test1_report.html Tue Nov 12 12:46:19 2024 +0000 |
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| b'@@ -4181,7 +4181,7 @@\n $(\'#reference_name\').show().find(\'.val\').html(referenceName);\n }\n \n- if (report[0][0] == \'Genome statistics\') { // if first section is empty (no reference), swap it and w/o reference statistics\n+ if (report[0][0] == \'Alignment-based statistics\') { // if first section is empty (no reference), swap it and w/o reference statistics\n var genomeMetrics = report[0][1];\n var isSectionEmpty = true;\n for (var index = 0; index < genomeMetrics.length; index++) {\n@@ -4502,8 +4502,7 @@\n QUAST\n </h1>\n <p class="page_subtitle">\n- <b>Quality Assessment Tool for Genome Assemblies</b>\n- by <a href="http://cab.spbu.ru" class=\'dark_bg_link\'>CAB</a>\n+ <b><a href="http://quast.sf.net" class=\'dark_bg_link\'>Quality Assessment Tool for Genome Assemblies</a></b>\n </p>\n </div>\n </td>\n@@ -4639,7 +4638,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"07 July 2022, Thursday, 16:52:16","assembliesNames":["contig1","contig2"],"referenceName":"dataset_be05aefa-bbf2-47ec-ac87-32bf4b214023","order":[0,1],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["71.579","100.000"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.000","1.000"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["7 + 7 part","13 + 1 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[2030,6650],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[4760,6650],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"NG90","quality":"More is better","values":[1120,6650],"isMain":false},{"metricName":"auNG","quality":"More is better","values":["2960.4","6650.0"],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA90","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"auNA","quality":"More is better","values":["1187.4","6650.0"],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[1610,6650],"isMain":true},{"metricName":"NGA90","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"auNGA","quality":"More is better","values":["1198.1","6650.0"],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"LG90","quality":"Less is better","values":[3,1],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA90","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[2,1],"isMain":true},{"metricName":"LGA90","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"Complete BUSCO (%)","quality":"More is better","values":["0.00","0.00"],"isMain":true},{"metricName":"Partial BUSCO (%)","quality":"Less is better","values":["0.68","0.00"],"isMain":true}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0],"isMain":false},{"metricName'..b' unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Per base quality",[{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120,6650],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0","6650.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[{"metricName":"K-mer-based compl. (%)","quality":"More is better","values":["68.09","100.00"],"isMain":true},{"metricName":"K-mer-based cor. length (%)","quality":"More is better","values":["100.00","100.00"],"isMain":false},{"metricName":"K-mer-based mis. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"K-mer-based undef. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"# k-mer-based misjoins","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # k-mer-based translocations","quality":"Equal","values":[0,0],"isMain":false},{"metricName":" # k-mer-based 100kbp relocations","quality":"Equal","values":[0,0],"isMain":false}]],["BUSCO completeness",[]],["Predicted genes",[{"metricName":"# predicted rRNA genes","quality":"More is better","values":["0 + 0 part","0 + 0 part"],"isMain":true}]],["Similarity statistics",[{"metricName":"# similar correct contigs","quality":"Equal","values":[0,0],"isMain":false},{"metricName":"# similar misassembled blocks","quality":"Equal","values":[0,0],"isMain":false}]],["Reference statistics",[{"metricName":"Reference length","quality":"Equal","values":[6650,6650],"isMain":false},{"metricName":"Reference fragments","quality":"Equal","values":[1,1],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["52.00","52.00"],"isMain":false},{"metricName":"Reference genomic features","quality":"Equal","values":[14,14],"isMain":false},{"metricName":"Reference operons","quality":"Equal","values":[0,0],"isMain":false}]]],"subreferences":[],"subreports":[],"minContig":500}\n </div>\n <div id=\'qualities-json\'>\n {{ qualities }}\n' |
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| diff -r 72472698a2df -r a3b35edea53a test-data/test2.log --- a/test-data/test2.log Thu Mar 02 10:38:54 2023 +0000 +++ b/test-data/test2.log Tue Nov 12 12:46:19 2024 +0000 |
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| b"@@ -1,34 +1,34 @@\n-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat --features /tmp/tmphjbhe4x0/files/3/1/a/dataset_31a7a886-1c84-4423-8fc9-cdfda1537f40.dat --operons /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat --circos --k-mer-stats --k-mer-size 101 --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat --threads 1\n+/usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat --features /tmp/tmplvd_uy2v/files/a/3/1/dataset_a314adcb-6b74-48ce-9b09-e2eba7a43bd1.dat --operons /tmp/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat --circos --k-mer-stats --k-mer-size 101 --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat --threads 1\n \n-Version: 5.2.0\n+Version: 5.3.0\n \n System information:\n- OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64)\n- Python version: 3.9.13\n- CPUs number: 8\n+ OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64)\n+ Python version: 3.12.3\n+ CPUs number: 12\n \n-Started: 2022-07-07 16:53:46\n+Started: 2024-11-12 11:21:53\n \n-Logging to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log\n+Logging to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log\n WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified\n \n-CWD: /tmp/tmphjbhe4x0/job_working_directory/000/12/working\n+CWD: /tmp/tmplvd_uy2v/job_working_directory/000/12/working\n Main parameters: \n MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \\\n ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000\n \n Reference:\n- /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat ==> dataset_adad470c-d758-46ef-afd5-390f178fb362\n+ /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39\n \n Contigs:\n Pre-processing...\n- 1 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat ==> contig1\n- 2 /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat ==> contig2\n+ 1 /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat ==> contig1\n+ 2 /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat ==> contig2\n \n-2022-07-07 16:53:55\n+2024-11-12 11:21:54\n Running Basic statistics processor...\n Reference genome:\n- dataset_adad470c-d758-46ef-afd5-390f178fb362.dat, length = 6650, num fragments = 1, GC % = 52.00\n+ dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat, length = 6650, num fragments = 1, GC % = 52.00\n Contig files: \n 1 contig1\n 2 contig2\n@@ -36,164 +36,164 @@\n 1 contig1, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00\n 2 contig2, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00\n Drawing Nx plot...\n- saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/b"..b'tdir/genome_stats/features_cumulative_plot.pdf\n+ saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf\n Drawing genomic features FRCurve plot...\n- saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf\n+ saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf\n Drawing # complete genomic features histogram...\n- saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf\n+ saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf\n Drawing Genome fraction, % histogram...\n- saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf\n+ saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf\n Done.\n \n NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.\n \n-2022-07-07 16:54:04\n+2024-11-12 11:21:56\n Creating large visual summaries...\n This may take a while: press Ctrl-C to skip this step..\n 1 of 3: Creating PDF with all tables and plots...\n 2 of 3: Creating Icarus viewers...\n 3 of 3: Creating Circos plot...\n-/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/circos \\\n--conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err\n+/usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \\\n+2> outputdir/circos/circos.err\n Done\n \n-2022-07-07 16:54:16\n+2024-11-12 11:22:00\n RESULTS:\n- Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex\n- Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex\n- HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.html\n- PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.pdf\n- Circos plot is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)\n- Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/icarus.html\n- Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log\n+ Text versions of total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex\n+ Text versions of transposed total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex\n+ HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.html\n+ PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.pdf\n+ Circos plot is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)\n+ Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/icarus.html\n+ Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log\n \n-Finished: 2022-07-07 16:54:16\n-Elapsed time: 0:00:30.044753\n-NOTICEs: 2; WARNINGs: 4; non-fatal ERRORs: 0\n+Finished: 2024-11-12 11:22:00\n+Elapsed time: 0:00:07.048981\n+NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0\n \n Thank you for using QUAST!\n' |
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| diff -r 72472698a2df -r a3b35edea53a test-data/test2_report.html --- a/test-data/test2_report.html Thu Mar 02 10:38:54 2023 +0000 +++ b/test-data/test2_report.html Tue Nov 12 12:46:19 2024 +0000 |
| [ |
| b'@@ -4181,7 +4181,7 @@\n $(\'#reference_name\').show().find(\'.val\').html(referenceName);\n }\n \n- if (report[0][0] == \'Genome statistics\') { // if first section is empty (no reference), swap it and w/o reference statistics\n+ if (report[0][0] == \'Alignment-based statistics\') { // if first section is empty (no reference), swap it and w/o reference statistics\n var genomeMetrics = report[0][1];\n var isSectionEmpty = true;\n for (var index = 0; index < genomeMetrics.length; index++) {\n@@ -4502,8 +4502,7 @@\n QUAST\n </h1>\n <p class="page_subtitle">\n- <b>Quality Assessment Tool for Genome Assemblies</b>\n- by <a href="http://cab.spbu.ru" class=\'dark_bg_link\'>CAB</a>\n+ <b><a href="http://quast.sf.net" class=\'dark_bg_link\'>Quality Assessment Tool for Genome Assemblies</a></b>\n </p>\n </div>\n </td>\n@@ -4639,7 +4638,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"07 July 2022, Thursday, 16:54:16","assembliesNames":["contig1","contig2"],"referenceName":"dataset_adad470c-d758-46ef-afd5-390f178fb362","order":[0,1],"report":[["Genome statistics",[{"metricName":"Genome fraction (%)","quality":"More is better","values":["71.579","100.000"],"isMain":true},{"metricName":"Duplication ratio","quality":"Less is better","values":["1.000","1.000"],"isMain":true},{"metricName":"# genomic features","quality":"More is better","values":["7 + 7 part","13 + 1 part"],"isMain":true},{"metricName":"Largest alignment","quality":"More is better","values":[2030,6650],"isMain":true},{"metricName":"Total aligned length","quality":"More is better","values":[4760,6650],"isMain":true},{"metricName":"NG50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"NG90","quality":"More is better","values":[1120,6650],"isMain":false},{"metricName":"auNG","quality":"More is better","values":["2960.4","6650.0"],"isMain":false},{"metricName":"NA50","quality":"More is better","values":[1610,6650],"isMain":false},{"metricName":"NA90","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"auNA","quality":"More is better","values":["1187.4","6650.0"],"isMain":false},{"metricName":"NGA50","quality":"More is better","values":[1610,6650],"isMain":true},{"metricName":"NGA90","quality":"More is better","values":[null,6650],"isMain":false},{"metricName":"auNGA","quality":"More is better","values":["1198.1","6650.0"],"isMain":false},{"metricName":"LG50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"LG90","quality":"Less is better","values":[3,1],"isMain":false},{"metricName":"LA50","quality":"Less is better","values":[2,1],"isMain":false},{"metricName":"LA90","quality":"Less is better","values":[null,1],"isMain":false},{"metricName":"LGA50","quality":"Less is better","values":[2,1],"isMain":true},{"metricName":"LGA90","quality":"Less is better","values":[null,1],"isMain":false}]],["Reads mapping",[]],["Misassemblies",[{"metricName":"# misassemblies","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # relocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # translocations","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # inversions","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# misassembled contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Misassembled contigs length","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":"# local misassemblies","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap ext. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# scaffold gap loc. mis.","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# '..b'icName":"Fully unaligned length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# partially unaligned contigs","quality":"Less is better","values":[1,0],"isMain":false},{"metricName":"Partially unaligned length","quality":"Less is better","values":[1950,0],"isMain":false}]],["Per base quality",[{"metricName":"# mismatches per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# mismatches","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# indels per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# indels","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (<= 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":" # indels (> 5 bp)","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"Indels length","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120,6650],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0","6650.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[{"metricName":"K-mer-based compl. (%)","quality":"More is better","values":["68.09","100.00"],"isMain":true},{"metricName":"K-mer-based cor. length (%)","quality":"More is better","values":["100.00","100.00"],"isMain":false},{"metricName":"K-mer-based mis. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"K-mer-based undef. length (%)","quality":"Less is better","values":["0.00","0.00"],"isMain":false},{"metricName":"# k-mer-based misjoins","quality":"Less is better","values":[0,0],"isMain":true},{"metricName":" # k-mer-based translocations","quality":"Equal","values":[0,0],"isMain":false},{"metricName":" # k-mer-based 100kbp relocations","quality":"Equal","values":[0,0],"isMain":false}]],["BUSCO completeness",[]],["Predicted genes",[]],["Similarity statistics",[{"metricName":"# similar correct contigs","quality":"Equal","values":[0,0],"isMain":false},{"metricName":"# similar misassembled blocks","quality":"Equal","values":[0,0],"isMain":false}]],["Reference statistics",[{"metricName":"Reference length","quality":"Equal","values":[6650,6650],"isMain":false},{"metricName":"Reference fragments","quality":"Equal","values":[1,1],"isMain":false},{"metricName":"Reference GC (%)","quality":"Equal","values":["52.00","52.00"],"isMain":false},{"metricName":"Reference genomic features","quality":"Equal","values":[14,14],"isMain":false},{"metricName":"Reference operons","quality":"Equal","values":[0,0],"isMain":false}]]],"subreferences":[],"subreports":[],"minContig":500}\n </div>\n <div id=\'qualities-json\'>\n {{ qualities }}\n' |
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| diff -r 72472698a2df -r a3b35edea53a test-data/test2_report.pdf |
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| Binary file test-data/test2_report.pdf has changed |
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| diff -r 72472698a2df -r a3b35edea53a test-data/test3.log --- a/test-data/test3.log Thu Mar 02 10:38:54 2023 +0000 +++ b/test-data/test3.log Tue Nov 12 12:46:19 2024 +0000 |
| b |
| @@ -1,67 +1,62 @@ -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs --x-for-Nx 90 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat --threads 1 +/usr/local/bin/quast --labels contigs1_fna -o outputdir --eukaryote --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs --x-for-Nx 90 /tmp/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat --threads 1 -Version: 5.2.0 +Version: 5.3.0 System information: - OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) - Python version: 3.9.13 - CPUs number: 8 + OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64) + Python version: 3.12.3 + CPUs number: 12 -Started: 2022-07-07 16:55:02 +Started: 2024-11-12 11:22:10 -Logging to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log +Logging to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified -CWD: /tmp/tmphjbhe4x0/job_working_directory/000/15/working +CWD: /tmp/tmplvd_uy2v/job_working_directory/000/14/working Main parameters: MODE: default, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \ min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 Contigs: Pre-processing... - 1 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat ==> contigs1_fna - 2 /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat ==> contigs2_fna + /tmp/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat ==> contigs1_fna -2022-07-07 16:55:11 +2024-11-12 11:22:11 Running Basic statistics processor... Contig files: - 1 contigs1_fna - 2 contigs2_fna + contigs1_fna Calculating N50 and L50... - 1 contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 - 2 contigs2_fna, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 + contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 Drawing Nx plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/Nx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contigs1_fna GC content plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf - Drawing contigs2_fna GC content plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. -2022-07-07 16:55:13 +2024-11-12 11:22:11 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating PDF with all tables and plots... 2 of 2: Creating Icarus viewers... Done -2022-07-07 16:55:14 +2024-11-12 11:22:11 RESULTS: - Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex - Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex - HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.html - PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.pdf - Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/icarus.html - Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log + Text versions of total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex + HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.pdf + Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/icarus.html + Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log -Finished: 2022-07-07 16:55:14 -Elapsed time: 0:00:11.737584 +Finished: 2024-11-12 11:22:11 +Elapsed time: 0:00:01.104288 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST! |
| b |
| diff -r 72472698a2df -r a3b35edea53a test-data/test3_report.html --- a/test-data/test3_report.html Thu Mar 02 10:38:54 2023 +0000 +++ b/test-data/test3_report.html Tue Nov 12 12:46:19 2024 +0000 |
| [ |
| b'@@ -4060,7 +4060,7 @@\n \n \n <script type="text/javascript">\n- var colors = ["#FF0000","#0000FF"];\n+ var colors = ["#FF0000"];\n var broken_scaffolds_labels = [];\n </script>\n <script type="text/javascript">\n@@ -4181,7 +4181,7 @@\n $(\'#reference_name\').show().find(\'.val\').html(referenceName);\n }\n \n- if (report[0][0] == \'Genome statistics\') { // if first section is empty (no reference), swap it and w/o reference statistics\n+ if (report[0][0] == \'Alignment-based statistics\') { // if first section is empty (no reference), swap it and w/o reference statistics\n var genomeMetrics = report[0][1];\n var isSectionEmpty = true;\n for (var index = 0; index < genomeMetrics.length; index++) {\n@@ -4502,8 +4502,7 @@\n QUAST\n </h1>\n <p class="page_subtitle">\n- <b>Quality Assessment Tool for Genome Assemblies</b>\n- by <a href="http://cab.spbu.ru" class=\'dark_bg_link\'>CAB</a>\n+ <b><a href="http://quast.sf.net" class=\'dark_bg_link\'>Quality Assessment Tool for Genome Assemblies</a></b>\n </p>\n </div>\n </td>\n@@ -4639,7 +4638,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"date":"07 July 2022, Thursday, 16:55:14","assembliesNames":["contigs1_fna","contigs2_fna"],"referenceName":"","order":[0,1],"report":[["Genome statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Mismatches",[{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00","0.00"],"isMain":true},{"metricName":"# N\'s","quality":"Less is better","values":[0,0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3,1],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"# contigs (>= 500 bp)","quality":"Equal","values":[3,1],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980,6650],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710,6650],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710,6650],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980,6650],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120,6650],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0","6650.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1,1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3,1],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28","52.00"],"isMain":false}]],["K-mer-based statistics",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500}\n+ {"date":"12 November 2024, Tuesday, 11:22:11","assembliesNames":["contigs1_fna"],"referenceName":"","order":[0],"report":[["Alignment-based statistics",[]],["Reads mapping",[]],["Misassemblies",[]],["Unaligned",[]],["Per base quality",[{"metricName":"# N\'s per 100 kbp","quality":"Less is better","values":["0.00"],"isMain":true},{"metricName":"# N\'s","quality":"Less is better","values":[0],"isMain":false}]],["Statistics without reference",[{"metricName":"# contigs","quality":"Equal","values":[3],"isMain":true},{"metricName":"# contigs (>= 0 bp)","quality":"Equal","values":[3],"isMain":false},{"metricName":"# contigs (>= 1000 bp)","quality":"Equal","values":[3],"isMain":false},{"metricName":"#'..b'_of_lengths":[[3980,1610,1120],[6650]]}\n+ {"filenames":["contigs1_fna"],"lists_of_lengths":[[3980,1610,1120]]}\n </div>\n <div id=\'assemblies-lengths-json\'>\n {{ assembliesLengths }}\n@@ -4661,7 +4660,7 @@\n {"tickX":1}\n </div>\n <div id=\'coord-nx-json\'>\n- {"coord_x":[[0.0,1e-10,59.31445603576751,59.314456035867515,83.30849478390462,83.30849478400462,100.0,100.0000000001],[0.0,1e-10,100.0,100.0000000001]],"coord_y":[[3980,3980,3980,1610,1610,1120,1120,0.0],[6650,6650,6650,0.0]],"filenames":["contigs1_fna","contigs2_fna"]}\n+ {"coord_x":[[0.0,1e-10,59.31445603576751,59.314456035867515,83.30849478390462,83.30849478400462,100.0,100.0000000001]],"coord_y":[[3980,3980,3980,1610,1610,1120,1120,0.0]],"filenames":["contigs1_fna"]}\n </div>\n <div id=\'coord-ngx-json\'>\n {{ coordNGx }}\n@@ -4701,7 +4700,7 @@\n {{ krona }}\n </div>\n <div id=\'gc-json\'>\n- 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{"links":["icarus_viewers/contig_size_viewer.html"],"links_names":["View in Icarus contig browser"]}\n' |
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