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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 5b2225491719b922003c69f0394bfc3eb238b360
| author | iuc |
|---|---|
| date | Sat, 04 Oct 2025 15:48:40 +0000 |
| parents | 2f0ede3447fb |
| children |
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/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-6.8.0-83-generic-x86_64-with-glibc2.36 (linux_64) Python version: 3.12.3 CPUs number: 8 Started: 2025-09-26 14:26:15 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/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/tmpq9nvn3a2/files/a/e/5/dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat ==> dataset_ae5c9f35-24a9-480d-913f-29f428c81140 Contigs: Pre-processing... 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 2025-09-26 14:26:16 Running Basic statistics processor... Reference genome: dataset_ae5c9f35-24a9-480d-913f-29f428c81140.dat, length = 6650, num fragments = 1, GC % = 52.00 Contig files: 1 contig1 2 contig2 Calculating N50 and L50... 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/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/Nx_plot.pdf Drawing NGx plot... saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/NGx_plot.pdf Drawing cumulative plot... saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/cumulative_plot.pdf Drawing GC content plot... 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/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/contig1_GC_content_plot.pdf Drawing contig2 GC content plot... saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/basic_stats/contig2_GC_content_plot.pdf Done. 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/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/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/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/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/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/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/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/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/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/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 /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 /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/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex Done. 2025-09-26 14:26:19 Running Contig analyzer... 1 contig1 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_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/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_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/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/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/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/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf Done. 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/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/aligned_stats/cumulative_plot.pdf Drawing NAx plot... saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/aligned_stats/NAx_plot.pdf Drawing NGAx plot... saved to /tmp/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/aligned_stats/NGAx_plot.pdf Done. 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/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/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/features_cumulative_plot.pdf Drawing genomic features FRCurve plot... 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/tmpq9nvn3a2/job_working_directory/000/6/working/outputdir/genome_stats/complete_features_histogram.pdf Drawing Genome fraction, % histogram... 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. 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... 2 of 3: Creating Icarus viewers... 3 of 3: Creating Circos plot... /usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \ 2> outputdir/circos/circos.err Done 2025-09-26 14:26:29 RESULTS: 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: 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!