comparison test-data/test2.log @ 14:3061c8b029e5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124

13:675488238c96

/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat --features /tmp/tmpmqu3v_ze/files/2/a/f/dataset_2afd5bcc-2ff5-46bc-83cd-0690bcbd9c67.dat --operons /tmp/tmpmqu3v_ze/files/f/f/a/dataset_ffa07559-8af9-4a08-8719-807dc3575dc8.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat --threads 1

Version: 5.0.2

System information:
  OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64)
  Python version: 3.7.12
  CPUs number: 8

Started: 2022-02-06 19:54:35

Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log
NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified

CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/12/working
Main parameters: 
  MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \
  ambiguity: all, threshold for extensive misassembly size: 1000

Reference:
  /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat ==> dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039

Contigs:
  Pre-processing...
  1  /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat ==> contig1
  2  /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat ==> contig2

2022-02-06 19:54:39
Running Basic statistics processor...
  Reference genome:
    dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.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/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing contig1 GC content plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf
  Drawing contig2 GC content plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf
Done.

2022-02-06 19:54:40
Running analysis based on unique 101-mers...
  Running KMC on reference...
/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc \
-t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat \
outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
-t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \
outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
-t1 -hp simple outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \
outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc \
>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
-t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc \
outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc.histo.txt >> \
outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
    2  contig2
/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
-t1 -hp simple outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \
outputdir/k_mer_stats/tmp/contig2.kmc intersect outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc \
>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
-t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc \
outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
-t1 -hp filter outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/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/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex
Done.

2022-02-06 19:54:41
Running Contig analyzer...
  1  contig1
  1  Logging to files /tmp/tmpmqu3v_ze/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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/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_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.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/tmpmqu3v_ze/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-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/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_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.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/tmpmqu3v_ze/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/tmpmqu3v_ze/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/tmpmqu3v_ze/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/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf
  Drawing misassemblies FRCurve plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf
Done.

2022-02-06 19:54:41
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/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf
Done.

2022-02-06 19:54:42
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/tmpmqu3v_ze/files/f/f/a/dataset_ffa07559-8af9-4a08-8719-807dc3575dc8.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/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf
  Drawing genomic features FRCurve plot...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf
  Drawing # complete genomic features histogram...
    saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf
  Drawing Genome fraction, % histogram...
    saved to /tmp/tmpmqu3v_ze/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.

2022-02-06 19:54:42
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...
/home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/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

2022-02-06 19:54:46
RESULTS:
  Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/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/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.pdf
  Circos plot is saved to /tmp/tmpmqu3v_ze/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/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/icarus.html
  Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log

Finished: 2022-02-06 19:54:46
Elapsed time: 0:00:11.313989
NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0

Thank you for using QUAST!

14:3061c8b029e5

/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!