- {"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":"# 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":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"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}]],["Mismatches",[{"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}]],["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} + {"date":"12 November 2024, Tuesday, 11:21:38","assembliesNames":["contig1","contig2"],"referenceName":"dataset_caf89206-8bd6-4a9e-a08e-3a7a79abf47e","order":[0,1],"report":[["Alignment-based 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":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"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",[{"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}

{{ qualities }} 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 @@ -1,34 +1,34 @@ -/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 +/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 -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 16:53:46 +Started: 2024-11-12 11:21:53 -Logging to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log +Logging to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified -CWD: /tmp/tmphjbhe4x0/job_working_directory/000/12/working +CWD: /tmp/tmplvd_uy2v/job_working_directory/000/12/working Main parameters: MODE: default, threads: 1, 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 Reference: - /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat ==> dataset_adad470c-d758-46ef-afd5-390f178fb362 + /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39 Contigs: Pre-processing... - 1 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat ==> contig1 - 2 /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat ==> contig2 + 1 /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat ==> contig1 + 2 /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat ==> contig2 -2022-07-07 16:53:55 +2024-11-12 11:21:54 Running Basic statistics processor... Reference genome: - dataset_adad470c-d758-46ef-afd5-390f178fb362.dat, length = 6650, num fragments = 1, GC % = 52.00 + dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat, length = 6650, num fragments = 1, GC % = 52.00 Contig files: 1 contig1 2 contig2 @@ -36,164 +36,164 @@ 1 contig1, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 2 contig2, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 Drawing Nx plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf Drawing NGx plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contig1 GC content plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf Drawing contig2 GC content plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf Done. -2022-07-07 16:53:58 +2024-11-12 11:21:54 Running analysis based on unique 101-mers... +NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/kmc. KMC will be downloaded to home directory /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast +Downloading KMC (file: kmc)... +KMC successfully downloaded! +Downloading KMC (file: kmc_tools)... +KMC successfully downloaded! Running KMC on reference... -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ --t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \ -outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc outputdir/k_mer_stats/tmp \ +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \ +outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp \ >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ --t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ -outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc.histo.txt \ +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc.histo.txt \ >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err Analyzing assemblies completeness... 1 contig1 -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ --t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ --t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ -outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \ +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ +outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \ +intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc >> \ +outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc.histo.txt \ >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ --t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \ -outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc.histo.txt >> \ -outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 2 contig2 -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ --t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \ +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \ outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ --t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ -outputdir/k_mer_stats/tmp/contig2.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \ +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ +outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \ +intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc >> \ +outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc.histo.txt \ >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ --t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \ -outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc.histo.txt >> \ -outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err Analyzing assemblies correctness... Downsampling k-mers... -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ --t1 -hp filter outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ -outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.fasta -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.filtered.fasta \ ->> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \ +outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.fasta \ +-ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.filtered.fasta >> outputdir/k_mer_stats/kmc.log \ +2>> outputdir/k_mer_stats/kmc.err 1 contig1 - /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ - -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ - > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err + /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 \ + outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \ + 2>> outputdir/k_mer_stats/kmc.err 2 contig2 - /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ - -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ - > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err + /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 \ + outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \ + 2>> outputdir/k_mer_stats/kmc.err Creating total report... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex Done. -2022-07-07 16:54:01 +2024-11-12 11:21:55 Running Contig analyzer... 1 contig1 - 1 Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... + 1 Logging to files /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... 1 Aligning contigs to the reference - 1 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ - -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \ - 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \ + 1 /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \ + 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \ outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \ 2>> outputdir/contigs_reports/contigs_report_contig1.stderr 1 Analysis is finished. 2 contig2 - 2 Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... + 2 Logging to files /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... 2 Aligning contigs to the reference - 2 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ - -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \ - 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \ + 2 /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \ + 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \ outputdir/quast_corrected_input/contig2 > outputdir/contigs_reports/minimap_output/contig2.coords_tmp \ 2>> outputdir/contigs_reports/contigs_report_contig2.stderr 2 Analysis is finished. Creating total report... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Drawing misassemblies by types plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf Done. -2022-07-07 16:54:01 +2024-11-12 11:21:55 Running NA-NGA calculation... 1 contig1, Largest alignment = 2030, NA50 = 1610, NGA50 = 1610, LA50 = 2, LGA50 = 2 2 contig2, Largest alignment = 6650, NA50 = 6650, NGA50 = 6650, LA50 = 1, LGA50 = 1 Drawing cumulative plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf Drawing NAx plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf Drawing NGAx plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf Done. -2022-07-07 16:54:02 +2024-11-12 11:21:56 Running Genome analyzer... Loaded 14 genomic features of type "ANY" NOTICE: Reference name in file with genomic features of type "ANY" (NC_000913.3) does not match the name in the reference file (NC_000913.3_1-6650). QUAST will ignore this issue and count as if they match. WARNING: Incorrect format of operon's file! GFF, NCBI and the plain TXT format accepted. See manual. -WARNING: /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat was skipped +WARNING: /tmp/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat was skipped WARNING: No genomic features of type "operon" were loaded. 1 contig1 1 Analysis is finished. 2 contig2 2 Analysis is finished. Drawing genomic features cumulative plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf Drawing genomic features FRCurve plot... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf Drawing # complete genomic features histogram... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf Drawing Genome fraction, % histogram... - saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf + saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. -2022-07-07 16:54:04 +2024-11-12 11:21:56 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 3: Creating PDF with all tables and plots... 2 of 3: Creating Icarus viewers... 3 of 3: Creating Circos plot... -/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/circos \ --conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err +/usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \ +2> outputdir/circos/circos.err Done -2022-07-07 16:54:16 +2024-11-12 11:22:00 RESULTS: - Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex - 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 - HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.html - PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.pdf - 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) - Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/icarus.html - Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log + 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 + 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 + HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.pdf + 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) + Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/icarus.html + Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log -Finished: 2022-07-07 16:54:16 -Elapsed time: 0:00:30.044753 -NOTICEs: 2; WARNINGs: 4; non-fatal ERRORs: 0 +Finished: 2024-11-12 11:22:00 +Elapsed time: 0:00:07.048981 +NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0 Thank you for using QUAST! 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 @@ -4181,7 +4181,7 @@ $('#reference_name').show().find('.val').html(referenceName); } - if (report[0][0] == 'Genome statistics') { // if first section is empty (no reference), swap it and w/o reference statistics + if (report[0][0] == 'Alignment-based statistics') { // if first section is empty (no reference), swap it and w/o reference statistics var genomeMetrics = report[0][1]; var isSectionEmpty = true; for (var index = 0; index < genomeMetrics.length; index++) { @@ -4502,8 +4502,7 @@ QUAST

- Quality Assessment Tool for Genome Assemblies - by CAB + Quality Assessment Tool for Genome Assemblies

@@ -4639,7 +4638,7 @@

- {"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":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"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}]],["Mismatches",[{"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}]],["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} + {"date":"12 November 2024, Tuesday, 11:22:00","assembliesNames":["contig1","contig2"],"referenceName":"dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39","order":[0,1],"report":[["Alignment-based 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":"# unaligned mis. contigs","quality":"Less is better","values":[0,0],"isMain":false}]],["Unaligned",[{"metricName":"# fully unaligned contigs","quality":"Less is better","values":[0,0],"isMain":false},{"metricName":"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}

{{ qualities }} diff -r 72472698a2df -r a3b35edea53a test-data/test2_report.pdf Binary file test-data/test2_report.pdf has changed 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 @@ -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! 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 @@ -4060,7 +4060,7 @@