comparison test-data/test2.log @ 9:45924fa8d8c5 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"

9:45924fa8d8c5

/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!