Mercurial > repos > greg > quast
diff test-data/test2.log @ 0:5367786dc871 draft default tip
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| author | greg |
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| date | Tue, 14 Mar 2023 15:21:14 +0000 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.log Tue Mar 14 15:21:14 2023 +0000 @@ -0,0 +1,199 @@ +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat --features /tmp/tmphjbhe4x0/files/3/1/a/dataset_31a7a886-1c84-4423-8fc9-cdfda1537f40.dat --operons /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat --circos --k-mer-stats --k-mer-size 101 --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat --threads 1 + +Version: 5.2.0 + +System information: + OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) + Python version: 3.9.13 + CPUs number: 8 + +Started: 2022-07-07 16:53:46 + +Logging to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log +WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified + +CWD: /tmp/tmphjbhe4x0/job_working_directory/000/12/working +Main parameters: + MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \ + ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 + +Reference: + /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat ==> dataset_adad470c-d758-46ef-afd5-390f178fb362 + +Contigs: + Pre-processing... + 1 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat ==> contig1 + 2 /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat ==> contig2 + +2022-07-07 16:53:55 +Running Basic statistics processor... + Reference genome: + dataset_adad470c-d758-46ef-afd5-390f178fb362.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/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf + Drawing NGx plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf + Drawing cumulative plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf + Drawing GC content plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf + Drawing contig1 GC content plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf + Drawing contig2 GC content plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf +Done. + +2022-07-07 16:53:58 +Running analysis based on unique 101-mers... + Running KMC on reference... +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ +-t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \ +outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc outputdir/k_mer_stats/tmp \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ +-t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ +outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc.histo.txt \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err + Analyzing assemblies completeness... + 1 contig1 +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ +-t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ +outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ +-t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ +outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ +-t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \ +outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc.histo.txt >> \ +outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err + 2 contig2 +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ +-t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \ +outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ +-t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ +outputdir/k_mer_stats/tmp/contig2.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ +-t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \ +outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc.histo.txt >> \ +outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err + Analyzing assemblies correctness... + Downsampling k-mers... +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ +-t1 -hp filter outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ +outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.fasta -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.filtered.fasta \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err + 1 contig1 + /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ + -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ + > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err + 2 contig2 + /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ + -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ + > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err + Creating total report... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex +Done. + +2022-07-07 16:54:01 +Running Contig analyzer... + 1 contig1 + 1 Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... + 1 Aligning contigs to the reference + 1 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ + -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \ + 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \ + outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \ + 2>> outputdir/contigs_reports/contigs_report_contig1.stderr + 1 Analysis is finished. + + 2 contig2 + 2 Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... + 2 Aligning contigs to the reference + 2 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ + -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \ + 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \ + outputdir/quast_corrected_input/contig2 > outputdir/contigs_reports/minimap_output/contig2.coords_tmp \ + 2>> outputdir/contigs_reports/contigs_report_contig2.stderr + 2 Analysis is finished. + + Creating total report... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex + Transposed version of total report... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex + Creating total report... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex + Drawing misassemblies by types plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf + Drawing misassemblies FRCurve plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf +Done. + +2022-07-07 16:54:01 +Running NA-NGA calculation... + 1 contig1, Largest alignment = 2030, NA50 = 1610, NGA50 = 1610, LA50 = 2, LGA50 = 2 + 2 contig2, Largest alignment = 6650, NA50 = 6650, NGA50 = 6650, LA50 = 1, LGA50 = 1 + Drawing cumulative plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf + Drawing NAx plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf + Drawing NGAx plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf +Done. + +2022-07-07 16:54:02 +Running Genome analyzer... + Loaded 14 genomic features of type "ANY" + NOTICE: Reference name in file with genomic features of type "ANY" (NC_000913.3) does not match the name in the reference file (NC_000913.3_1-6650). QUAST will ignore this issue and count as if they match. +WARNING: Incorrect format of operon's file! GFF, NCBI and the plain TXT format accepted. See manual. +WARNING: /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat was skipped + WARNING: No genomic features of type "operon" were loaded. + 1 contig1 + 1 Analysis is finished. + 2 contig2 + 2 Analysis is finished. + Drawing genomic features cumulative plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf + Drawing genomic features FRCurve plot... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf + Drawing # complete genomic features histogram... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf + Drawing Genome fraction, % histogram... + saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf +Done. + +NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. + +2022-07-07 16:54:04 +Creating large visual summaries... +This may take a while: press Ctrl-C to skip this step.. + 1 of 3: Creating PDF with all tables and plots... + 2 of 3: Creating Icarus viewers... + 3 of 3: Creating Circos plot... +/home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/circos \ +-conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err +Done + +2022-07-07 16:54:16 +RESULTS: + Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex + HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.pdf + Circos plot is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf) + Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/icarus.html + Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log + +Finished: 2022-07-07 16:54:16 +Elapsed time: 0:00:30.044753 +NOTICEs: 2; WARNINGs: 4; non-fatal ERRORs: 0 + +Thank you for using QUAST!