# HG changeset patch # User iuc # Date 1759592948 0 # Node ID 1b1cf0c9650190d739126e4fe27e02773010be9e # Parent a3b35edea53a13faf020cfc2fca4d5879ea0f91d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 5b2225491719b922003c69f0394bfc3eb238b360 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 @@ -1,6 +1,6 @@ 5.3.0 - 0 + 1 23.02 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 @@ -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 @@
- + - + @@ -510,7 +514,7 @@ assembly['type'] == 'metagenome' and 'summary' in output_files - assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'none' and 'krona' in output_files + assembly['type'] == 'metagenome' and assembly['ref']['origin'] == 'silva' and 'krona' in output_files @@ -1001,7 +1005,7 @@ - + @@ -1036,7 +1040,7 @@ - + @@ -1080,7 +1084,7 @@ - + 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 @@ -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 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 @@ -1,34 +1,34 @@ -/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 +/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 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 11:21:53 +Started: 2025-09-26 14:26:15 -Logging to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log +Logging to /tmp/tmpq9nvn3a2/job_working_directory/000/6/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/000/12/working +CWD: /tmp/tmpq9nvn3a2/job_working_directory/000/6/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/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39 + /tmp/tmpq9nvn3a2/files/a/e/5/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat ==> dataset_ae5c9f35-24a9-480d-913f-29f428c81140 Contigs: Pre-processing... - 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 + 1 /tmp/tmpq9nvn3a2/files/2/3/6/dataset_236c1256-0b90-4170-989f-3e12c0513907.dat ==> contig1 + 2 /tmp/tmpq9nvn3a2/files/0/9/f/dataset_09f43799-9fb9-40e4-930c-f5c1bf60b4f3.dat ==> contig2 -2024-11-12 11:21:54 +2025-09-26 14:26:16 Running Basic statistics processor... Reference genome: - dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat, length = 6650, num fragments = 1, GC % = 52.00 + dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat, length = 6650, num fragments = 1, GC % = 52.00 Contig files: 1 contig1 2 contig2 @@ -36,61 +36,61 @@ 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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/Nx_plot.pdf Drawing NGx plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/NGx_plot.pdf Drawing cumulative plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/GC_content_plot.pdf Drawing contig1 GC content plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/contig1_GC_content_plot.pdf Drawing contig2 GC content plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/contig2_GC_content_plot.pdf Done. -2024-11-12 11:21:54 +2025-09-26 14:26:16 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 +NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/kmc. KMC will be downloaded to home directory /tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast Downloading KMC (file: kmc)... KMC successfully downloaded! Downloading KMC (file: kmc_tools)... KMC successfully downloaded! Running KMC on reference... -/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 \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat \ +outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat.kmc outputdir/k_mer_stats/tmp \ >> 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-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc.histo.txt \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat.kmc outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat.kmc.histo.txt \ >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err Analyzing assemblies completeness... 1 contig1 -/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/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 -/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 >> \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast/kmc/kmc_tools -t1 -hp simple \ +outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \ +intersect outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913_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 \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913_contig1.kmc outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913_contig1.kmc.histo.txt \ >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 2 contig2 -/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/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 -/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 >> \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast/kmc/kmc_tools -t1 -hp simple \ +outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \ +intersect outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913_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 \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913_contig2.kmc outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913_contig2.kmc.histo.txt \ >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err Analyzing assemblies correctness... Downsampling k-mers... -/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 \ +/tmp/tmpq9nvn3a2/job_working_directory/000/6/home/.quast/kmc/kmc_tools -t1 -hp filter \ +outputdir/k_mer_stats/tmp/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.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 @@ -102,77 +102,77 @@ 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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex Done. -2024-11-12 11:21:55 +2025-09-26 14:26:19 Running Contig analyzer... 1 contig1 - 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 Logging to files /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... 1 Aligning contigs to the reference 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 \ + 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... + 2 Logging to files /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... 2 Aligning contigs to the reference 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 \ + 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... - 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 + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Drawing misassemblies by types plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf Done. -2024-11-12 11:21:55 +2025-09-26 14:26:20 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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/aligned_stats/cumulative_plot.pdf Drawing NAx plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/aligned_stats/NAx_plot.pdf Drawing NGAx plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/aligned_stats/NGAx_plot.pdf Done. -2024-11-12 11:21:56 +2025-09-26 14:26:20 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/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat was skipped +WARNING: /tmp/tmpq9nvn3a2/files/9/d/7/dataset_9d73dece-daed-4cb5-aa43-3d6af6987252.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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/features_cumulative_plot.pdf Drawing genomic features FRCurve plot... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/features_frcurve_plot.pdf Drawing # complete genomic features histogram... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/complete_features_histogram.pdf Drawing Genome fraction, % histogram... - saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf + saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/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. -2024-11-12 11:21:56 +2025-09-26 14:26:21 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... @@ -182,18 +182,18 @@ 2> outputdir/circos/circos.err Done -2024-11-12 11:22:00 +2025-09-26 14:26:29 RESULTS: - 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 + Text versions of total report are saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/report.txt, report.tsv, and report.tex + 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 + HTML version (interactive tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/report.pdf + 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) + Icarus (contig browser) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/icarus.html + Log is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/quast.log -Finished: 2024-11-12 11:22:00 -Elapsed time: 0:00:07.048981 +Finished: 2025-09-26 14:26:29 +Elapsed time: 0:00:13.957566 NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0 Thank you for using QUAST! 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 @@ -4638,7 +4638,7 @@
- {"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":" # 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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":"# 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}
{{ qualities }} diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test2_report.pdf Binary file test-data/test2_report.pdf has changed 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 @@ -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 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 @@ -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! 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 @@ -4638,7 +4638,7 @@
- {"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}
{{ qualities }} diff -r a3b35edea53a -r 1b1cf0c96501 test-data/test3_report.pdf Binary file test-data/test3_report.pdf has changed 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 @@ -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 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 @@ -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 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 @@ -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