Mercurial > repos > iuc > quast
diff test-data/test2.log @ 9:45924fa8d8c5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
| author | iuc |
|---|---|
| date | Mon, 08 Nov 2021 09:03:00 +0000 |
| parents | |
| children | 875d0f36d66f |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test2.log Mon Nov 08 09:03:00 2021 +0000 @@ -0,0 +1,198 @@ +/usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat --features /tmp/tmpfgnwy_vl/files/4/0/6/dataset_406c3bca-dfac-498b-954d-476186610bc9.dat --operons /tmp/tmpfgnwy_vl/files/e/5/8/dataset_e5851e9e-28d2-42f8-9a7a-0d05d0770635.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat --threads 1 + +Version: 5.0.2 + +System information: + OS: Linux-5.11.0-37-generic-x86_64-with-debian-10.9 (linux_64) + Python version: 3.7.12 + CPUs number: 8 + +Started: 2021-11-07 18:59:01 + +Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log + +CWD: /tmp/tmpfgnwy_vl/job_working_directory/000/12/working +Main parameters: + MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \ + ambiguity: one, threshold for extensive misassembly size: 1000 + +Reference: + /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat ==> dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74 + +Contigs: + Pre-processing... + 1 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat ==> contig1 + 2 /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat ==> contig2 + +2021-11-07 18:59:01 +Running Basic statistics processor... + Reference genome: + dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.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, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 + 2 contig2, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 + Drawing Nx plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf + Drawing NGx plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf + Drawing cumulative plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf + Drawing GC content plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf + Drawing contig1 GC content plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf + Drawing contig2 GC content plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf +Done. + +2021-11-07 18:59:02 +Running analysis based on unique 101-mers... +NOTICE: Permission denied accessing /usr/local/lib/python3.7/site-packages/quast_libs/kmc. KMC will be downloaded to home directory /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast +Downloading KMC (file: kmc)... +KMC successfully downloaded! +Downloading KMC (file: kmc_tools)... +KMC successfully downloaded! + Running KMC on reference... +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat \ +outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc.histo.txt \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err + Analyzing assemblies completeness... + 1 contig1 +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ +outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ +outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \ +intersect outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc >> \ +outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc.histo.txt \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err + 2 contig2 +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ +-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \ +outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ +outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \ +intersect outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc >> \ +outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ +outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc.histo.txt \ +>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err + Analyzing assemblies correctness... + Downsampling k-mers... +/tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \ +outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.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/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex +Done. + +2021-11-07 18:59:04 +Running Contig analyzer... + 1 contig1 + 1 Logging to files /tmp/tmpfgnwy_vl/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 /usr/local/bin/minimap2 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -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_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.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/tmpfgnwy_vl/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 /usr/local/bin/minimap2 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -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_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.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/tmpfgnwy_vl/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/tmpfgnwy_vl/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/tmpfgnwy_vl/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/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf + Drawing misassemblies FRCurve plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf +Done. + +2021-11-07 18:59:04 +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/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf + Drawing NAx plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf + Drawing NGAx plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf +Done. + +2021-11-07 18:59:05 +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/tmpfgnwy_vl/files/e/5/8/dataset_e5851e9e-28d2-42f8-9a7a-0d05d0770635.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/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf + Drawing genomic features FRCurve plot... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf + Drawing # complete genomic features histogram... + saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf + Drawing Genome fraction, % histogram... + saved to /tmp/tmpfgnwy_vl/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. + +2021-11-07 18:59:05 +Creating large visual summaries... +This may take a while: press Ctrl-C to skip this step.. + 1 of 3: Creating Icarus viewers... + 2 of 3: Creating Circos plot... +/usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \ +2> outputdir/circos/circos.err + 3 of 3: Creating PDF with all tables and plots... +Done + +2021-11-07 18:59:15 +RESULTS: + Text versions of total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex + Text versions of transposed total report are saved to /tmp/tmpfgnwy_vl/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/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.html + PDF version (tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.pdf + Circos plot is saved to /tmp/tmpfgnwy_vl/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/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/icarus.html + Log is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log + +Finished: 2021-11-07 18:59:15 +Elapsed time: 0:00:13.941680 +NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0 + +Thank you for using QUAST!