| Previous changeset 16:a3b35edea53a (2024-11-12) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 5b2225491719b922003c69f0394bfc3eb238b360 |
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modified:
macros.xml quast.xml test-data/test10_tabular_report.tab test-data/test2.log test-data/test2_report.html test-data/test2_report.pdf test-data/test2_report.tab test-data/test3.log test-data/test3_report.html test-data/test3_report.pdf test-data/test5.tab test-data/test6.tab test-data/test7.tab |
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| diff -r a3b35edea53a -r 1b1cf0c96501 macros.xml --- a/macros.xml Tue Nov 12 12:46:19 2024 +0000 +++ b/macros.xml Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">5.3.0</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.02</token> <xml name="requirements"> <requirements> |
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| diff -r a3b35edea53a -r 1b1cf0c96501 quast.xml --- a/quast.xml Tue Nov 12 12:46:19 2024 +0000 +++ b/quast.xml Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -39,7 +39,7 @@ #if $assembly.type == 'metagenome' and $assembly.ref.origin == 'list' #set $temp_ref_list_fp = 'temp_ref_list' - #for $i in $assembly.ref.references_list.split(',') + #for $i in str($assembly.ref.references_list).split(',') echo $i >> $temp_ref_list_fp && #end for #end if @@ -247,6 +247,10 @@ #end if --threads \${GALAXY_SLOTS:-1} +#if 'krona' not in $output_files or $assembly.ref.origin != 'silva' + --no-krona +#end if + #if $assembly.type == 'genome' && mkdir -p '$report_html.files_path' && cp outputdir/*.html '$report_html.files_path' @@ -445,10 +449,10 @@ <param argument="--local-mis-size" type="integer" value="200" optional="true" label="Minimal local misassembly size" help="Lower threshold for the local misassembly size. Shorter inconsistencies are considered as (long) indels. The default value is 200 bp. Note that the threshold should be equal to or lower than minimal extensive misassembly size, which is 1000 bp by default"/> </section> <section name="advanced" title="Advanced options"> - <param argument="--contig-thresholds" type="text" value="0,1000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/> + <param argument="--contig-thresholds" type="text" value="0,1000,5000,10000,25000,50000" label="Comma-separated list of contig length thresholds (in bp)" help="Used in # contigs ≥ x and total length (≥ x) metrics"/> <param argument="--strict-NA" type="boolean" truevalue="--strict-NA" falsevalue="" checked="false" label="Break contigs at every misassembly event (including local ones) to compute NAx and NGAx statistics?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> <param argument="--extensive-mis-size" type="integer" value="1000" min="85" label="Lower threshold for the relocation size (gap or overlap size between left and right flanking sequence)" help="Shorter relocations are considered as local misassemblies. It does not affect other types of extensive misassemblies (inversions and translocations). The default value is 1000 bp. Note that the threshold should be greater than maximum indel length which is 85 bp."/> - <param argument="--scaffold-gap-max-size" type="integer" value="1000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/> + <param argument="--scaffold-gap-max-size" type="integer" value="10000" label="Max allowed scaffold gap length difference for detecting corresponding type of misassemblies" help="Longer inconsistencies are considered as relocations and thus, counted as extensive misassemblies. The default value is 10000 bp. Note that the threshold make sense only if it is greater than extensive misassembly size"/> <param argument="--unaligned-part-size" type="integer" value="500" label="Lower threshold for detecting partially unaligned contigs" help=""/> <param argument="--skip-unaligned-mis-contigs" type="boolean" truevalue="" falsevalue="--skip-unaligned-mis-contigs" checked="true" label="Distinguish contigs with more than 50% unaligned bases as a separate group of contigs?" help="By default, QUAST breaks contigs only at extensive misassemblies (not local ones)."/> <param argument="--fragmented-max-indent" type="integer" min="0" value="" optional="true" label="Fragment max indent" help="Mark translocation as fake if both alignments are located no further than N bases from the ends of the reference fragments. The value should be less than extensive misassembly size.Default value is 50. Note: requires --fragmented option" /> @@ -510,7 +514,7 @@ <filter>assembly['type'] == 'metagenome' and 'summary' in output_files</filter> </collection> <data name="krona" format="html" label="${tool.name} on ${on_string}: Krona chart" from_work_dir="outputdir/krona_charts/*.html"> - <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files</filter> + <filter>assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'silva' and 'krona' in output_files</filter> </data> </outputs> <tests> @@ -1001,7 +1005,7 @@ <has_text text="# contigs (>= 0 bp)"/> <has_text text="contig1"/> <has_text text="# N's per 100 kbp"/> - <has_n_lines n="22"/> + <has_n_lines n="30"/> </assert_contents> </output> </test> @@ -1036,7 +1040,7 @@ <has_text text="# contigs (>= 0 bp)"/> <has_text text="contig1"/> <has_text text="# N's per 100 kbp"/> - <has_n_lines n="15"/> + <has_n_lines n="23"/> </assert_contents> </output> </test> @@ -1080,7 +1084,7 @@ <has_text text="# contigs (>= 0 bp)"/> <has_text text="contigs1"/> <has_text text="# N's per 100 kbp"/> - <has_n_lines n="22"/> + <has_n_lines n="30"/> </assert_contents> </output> </test> |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test10_tabular_report.tab --- a/test-data/test10_tabular_report.tab Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test10_tabular_report.tab Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -1,8 +1,16 @@ Assembly contig1 contig2 # contigs (>= 0 bp) 3 1 # contigs (>= 1000 bp) 3 1 +# contigs (>= 5000 bp) 0 1 +# contigs (>= 10000 bp) 0 0 +# contigs (>= 25000 bp) 0 0 +# contigs (>= 50000 bp) 0 0 Total length (>= 0 bp) 6710 6650 Total length (>= 1000 bp) 6710 6650 +Total length (>= 5000 bp) 0 6650 +Total length (>= 10000 bp) 0 0 +Total length (>= 25000 bp) 0 0 +Total length (>= 50000 bp) 0 0 # contigs 3 1 Largest contig 3980 6650 Total length 6710 6650 |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test2.log --- a/test-data/test2.log Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test2.log Sat Oct 04 15:49:08 2025 +0000 |
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| b"@@ -1,34 +1,34 @@\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+/usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpq9nvn3a2/files/a/e/5/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat --features /tmp/tmpq9nvn3a2/files/e/3/b/dataset_e3be549f-4e49-4036-99da-1e346867a949.dat --operons /tmp/tmpq9nvn3a2/files/9/d/7/dataset_9d73dece-daed-4cb5-aa43-3d6af6987252.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 0,1000,5000,10000,25000,50000 --extensive-mis-size 1000 --scaffold-gap-max-size 10000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmpq9nvn3a2/files/2/3/6/dataset_236c1256-0b90-4170-989f-3e12c0513907.dat /tmp/tmpq9nvn3a2/files/0/9/f/dataset_09f43799-9fb9-40e4-930c-f5c1bf60b4f3.dat --threads 1 --no-krona\n \n Version: 5.3.0\n \n System information:\n- OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64)\n+ OS: Linux-6.8.0-83-generic-x86_64-with-glibc2.36 (linux_64)\n Python version: 3.12.3\n- CPUs number: 12\n+ CPUs number: 8\n \n-Started: 2024-11-12 11:21:53\n+Started: 2025-09-26 14:26:15\n \n-Logging to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log\n+Logging to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/quast.log\n WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified\n \n-CWD: /tmp/tmplvd_uy2v/job_working_directory/000/12/working\n+CWD: /tmp/tmpq9nvn3a2/job_working_directory/000/6/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/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39\n+ /tmp/tmpq9nvn3a2/files/a/e/5/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat ==> dataset_ae5c9f35-24a9-480d-913f-29f428c81140\n \n Contigs:\n Pre-processing...\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+ 1 /tmp/tmpq9nvn3a2/files/2/3/6/dataset_236c1256-0b90-4170-989f-3e12c0513907.dat ==> contig1\n+ 2 /tmp/tmpq9nvn3a2/files/0/9/f/dataset_09f43799-9fb9-40e4-930c-f5c1bf60b4f3.dat ==> contig2\n \n-2024-11-12 11:21:54\n+2025-09-26 14:26:16\n Running Basic statistics processor...\n Reference genome:\n- dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat, length = 6650, num fragments = 1, GC % = 52.00\n+ dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat, length = 6650, num fragments = 1, GC % = 52.00\n Contig files: \n 1 contig1\n 2 contig2\n@@ -36,61 +36,61 @@\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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf\n+ saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic"..b'9a-44dc-4abf-88ec-691e4984bd83.dat was skipped\n+WARNING: /tmp/tmpq9nvn3a2/files/9/d/7/dataset_9d73dece-daed-4cb5-aa43-3d6af6987252.dat was skipped\n WARNING: No genomic features of type "operon" were loaded.\n 1 contig1\n 1 Analysis is finished.\n 2 contig2\n 2 Analysis is finished.\n Drawing genomic features cumulative plot...\n- saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf\n+ saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/features_cumulative_plot.pdf\n Drawing genomic features FRCurve plot...\n- saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf\n+ saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/features_frcurve_plot.pdf\n Drawing # complete genomic features histogram...\n- saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf\n+ saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/complete_features_histogram.pdf\n Drawing Genome fraction, % histogram...\n- saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf\n+ saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/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-2024-11-12 11:21:56\n+2025-09-26 14:26:21\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@@ -182,18 +182,18 @@\n 2> outputdir/circos/circos.err\n Done\n \n-2024-11-12 11:22:00\n+2025-09-26 14:26:29\n RESULTS:\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+ Text versions of total report are saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/report.txt, report.tsv, and report.tex\n+ Text versions of transposed total report are saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex\n+ HTML version (interactive tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/report.html\n+ PDF version (tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/report.pdf\n+ Circos plot is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)\n+ Icarus (contig browser) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/icarus.html\n+ Log is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/quast.log\n \n-Finished: 2024-11-12 11:22:00\n-Elapsed time: 0:00:07.048981\n+Finished: 2025-09-26 14:26:29\n+Elapsed time: 0:00:13.957566\n NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0\n \n Thank you for using QUAST!\n' |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test2_report.html --- a/test-data/test2_report.html Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test2_report.html Sat Oct 04 15:49:08 2025 +0000 |
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| b'@@ -4638,7 +4638,7 @@\n \n <div class=\'json-code\'>\n <div id=\'total-report-json\'>\n- {"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 b'..b'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":"# contigs (>= 5000 bp)","quality":"Equal","values":[0,1],"isMain":false},{"metricName":"# contigs (>= 10000 bp)","quality":"Equal","values":[0,0],"isMain":false},{"metricName":"# contigs (>= 25000 bp)","quality":"Equal","values":[0,0],"isMain":false},{"metricName":"# contigs (>= 50000 bp)","quality":"Equal","values":[0,0],"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 (>= 5000 bp)","quality":"More is better","values":[0,6650],"isMain":false},{"metricName":"Total length (>= 10000 bp)","quality":"More is better","values":[0,0],"isMain":true},{"metricName":"Total length (>= 25000 bp)","quality":"More is better","values":[0,0],"isMain":false},{"metricName":"Total length (>= 50000 bp)","quality":"More is better","values":[0,0],"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 a3b35edea53a -r 1b1cf0c96501 test-data/test2_report.pdf |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test2_report.tab --- a/test-data/test2_report.tab Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test2_report.tab Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -1,8 +1,16 @@ Assembly contig1 contig2 # contigs (>= 0 bp) 3 1 # contigs (>= 1000 bp) 3 1 +# contigs (>= 5000 bp) 0 1 +# contigs (>= 10000 bp) 0 0 +# contigs (>= 25000 bp) 0 0 +# contigs (>= 50000 bp) 0 0 Total length (>= 0 bp) 6710 6650 Total length (>= 1000 bp) 6710 6650 +Total length (>= 5000 bp) 0 6650 +Total length (>= 10000 bp) 0 0 +Total length (>= 25000 bp) 0 0 +Total length (>= 50000 bp) 0 0 # contigs 3 1 Largest contig 3980 6650 Total length 6710 6650 |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test3.log --- a/test-data/test3.log Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test3.log Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -1,62 +1,62 @@ -/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 +/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/tmpq9nvn3a2/files/9/1/e/dataset_91ea48a6-22ee-45b1-9f7f-206c94f14ba8.dat --threads 1 --no-krona Version: 5.3.0 System information: - OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64) + OS: Linux-6.8.0-83-generic-x86_64-with-glibc2.36 (linux_64) Python version: 3.12.3 - CPUs number: 12 + CPUs number: 8 -Started: 2024-11-12 11:22:10 +Started: 2025-09-26 14:27:05 -Logging to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log +Logging to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/quast.log WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified -CWD: /tmp/tmplvd_uy2v/job_working_directory/000/14/working +CWD: /tmp/tmpq9nvn3a2/job_working_directory/000/8/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... - /tmp/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat ==> contigs1_fna + /tmp/tmpq9nvn3a2/files/9/1/e/dataset_91ea48a6-22ee-45b1-9f7f-206c94f14ba8.dat ==> contigs1_fna -2024-11-12 11:22:11 +2025-09-26 14:27:06 Running Basic statistics processor... Contig files: contigs1_fna Calculating N50 and L50... 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/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/basic_stats/Nx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contigs1_fna GC content plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/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. -2024-11-12 11:22:11 +2025-09-26 14:27:06 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 -2024-11-12 11:22:11 +2025-09-26 14:27:07 RESULTS: - 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 + Text versions of total report are saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex + HTML version (interactive tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/report.pdf + Icarus (contig browser) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/icarus.html + Log is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/quast.log -Finished: 2024-11-12 11:22:11 -Elapsed time: 0:00:01.104288 +Finished: 2025-09-26 14:27:07 +Elapsed time: 0:00:01.640426 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST! |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test3_report.html --- a/test-data/test3_report.html Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test3_report.html Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -4638,7 +4638,7 @@ <div class='json-code'> <div id='total-report-json'> - {"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":"# contigs (>= 500 bp)","quality":"Equal","values":[3],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28"],"isMain":false}]],["K-mer-based statistics",[]],["BUSCO completeness",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500} + {"date":"26 September 2025, Friday, 14:27:07","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":"# contigs (>= 500 bp)","quality":"Equal","values":[3],"isMain":false},{"metricName":"Largest contig","quality":"More is better","values":[3980],"isMain":true},{"metricName":"Total length","quality":"More is better","values":[6710],"isMain":true},{"metricName":"Total length (>= 0 bp)","quality":"More is better","values":[6710],"isMain":false},{"metricName":"Total length (>= 1000 bp)","quality":"More is better","values":[6710],"isMain":true},{"metricName":"Total length (>= 500 bp)","quality":"More is better","values":[6710],"isMain":false},{"metricName":"N50","quality":"More is better","values":[3980],"isMain":false},{"metricName":"N90","quality":"More is better","values":[1120],"isMain":false},{"metricName":"auN","quality":"More is better","values":["2934.0"],"isMain":false},{"metricName":"L50","quality":"Less is better","values":[1],"isMain":false},{"metricName":"L90","quality":"Less is better","values":[3],"isMain":false},{"metricName":"GC (%)","quality":"Equal","values":["51.28"],"isMain":false}]],["K-mer-based statistics",[]],["BUSCO completeness",[]],["Predicted genes",[]],["Similarity statistics",[]],["Reference statistics",[]]],"subreferences":[],"subreports":[],"minContig":500} </div> <div id='qualities-json'> {{ qualities }} |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test5.tab --- a/test-data/test5.tab Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test5.tab Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -1,8 +1,16 @@ Assembly contig1 contig2 # contigs (>= 0 bp) 3 1 # contigs (>= 1000 bp) 3 1 +# contigs (>= 5000 bp) 0 1 +# contigs (>= 10000 bp) 0 0 +# contigs (>= 25000 bp) 0 0 +# contigs (>= 50000 bp) 0 0 Total length (>= 0 bp) 6710 6650 Total length (>= 1000 bp) 6710 6650 +Total length (>= 5000 bp) 0 6650 +Total length (>= 10000 bp) 0 0 +Total length (>= 25000 bp) 0 0 +Total length (>= 50000 bp) 0 0 # contigs 3 1 Largest contig 3980 6650 Total length 6710 6650 |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test6.tab --- a/test-data/test6.tab Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test6.tab Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -1,8 +1,16 @@ Assembly contig1 contig2 # contigs (>= 0 bp) 3 1 # contigs (>= 1000 bp) 3 1 +# contigs (>= 5000 bp) 0 1 +# contigs (>= 10000 bp) 0 0 +# contigs (>= 25000 bp) 0 0 +# contigs (>= 50000 bp) 0 0 Total length (>= 0 bp) 6710 6650 Total length (>= 1000 bp) 6710 6650 +Total length (>= 5000 bp) 0 6650 +Total length (>= 10000 bp) 0 0 +Total length (>= 25000 bp) 0 0 +Total length (>= 50000 bp) 0 0 # contigs 3 1 Largest contig 3980 6650 Total length 6710 6650 |
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| diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test7.tab --- a/test-data/test7.tab Tue Nov 12 12:46:19 2024 +0000 +++ b/test-data/test7.tab Sat Oct 04 15:49:08 2025 +0000 |
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| @@ -1,8 +1,16 @@ Assembly contig1 contig2 # contigs (>= 0 bp) 3 1 # contigs (>= 1000 bp) 3 1 +# contigs (>= 5000 bp) 0 1 +# contigs (>= 10000 bp) 0 0 +# contigs (>= 25000 bp) 0 0 +# contigs (>= 50000 bp) 0 0 Total length (>= 0 bp) 6710 6650 Total length (>= 1000 bp) 6710 6650 +Total length (>= 5000 bp) 0 6650 +Total length (>= 10000 bp) 0 0 +Total length (>= 25000 bp) 0 0 +Total length (>= 50000 bp) 0 0 # contigs 3 1 Largest contig 3980 6650 Total length 6710 6650 |