/usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat --features /tmp/tmplvd_uy2v/files/a/3/1/dataset_a314adcb-6b74-48ce-9b09-e2eba7a43bd1.dat --operons /tmp/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.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/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat --threads 1

Version: 5.3.0

System information:
  OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64)
  Python version: 3.12.3
  CPUs number: 12

Started: 2024-11-12 11:21:53

Logging to /tmp/tmplvd_uy2v/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/tmplvd_uy2v/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/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39

Contigs:
  Pre-processing...
  1  /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat ==> contig1
  2  /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat ==> contig2

2024-11-12 11:21:54
Running Basic statistics processor...
  Reference genome:
    dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf
  Drawing contig1 GC content plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf
  Drawing contig2 GC content plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf
Done.

2024-11-12 11:21:54
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/tmplvd_uy2v/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/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
-k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp \
>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc.histo.txt \
>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
  Analyzing assemblies completeness...
    1  contig1
/tmp/tmplvd_uy2v/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/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \
intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc >> \
outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc.histo.txt \
>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
    2  contig2
/tmp/tmplvd_uy2v/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/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \
intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc >> \
outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc.histo.txt \
>> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
  Analyzing assemblies correctness...
    Downsampling k-mers...
/tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \
outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex
Done.

2024-11-12 11:21:55
Running Contig analyzer...
  1  contig1
  1  Logging to files /tmp/tmplvd_uy2v/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 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_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.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/tmplvd_uy2v/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 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_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.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/tmplvd_uy2v/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/tmplvd_uy2v/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/tmplvd_uy2v/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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf
  Drawing misassemblies FRCurve plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf
Done.

2024-11-12 11:21:55
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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf
Done.

2024-11-12 11:21:56
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/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf
  Drawing genomic features FRCurve plot...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf
  Drawing # complete genomic features histogram...
    saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf
  Drawing Genome fraction, % histogram...
    saved to /tmp/tmplvd_uy2v/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.

2024-11-12 11:21:56
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

2024-11-12 11:22:00
RESULTS:
  Text versions of total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /tmp/tmplvd_uy2v/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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.html
  PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.pdf
  Circos plot is saved to /tmp/tmplvd_uy2v/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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/icarus.html
  Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log

Finished: 2024-11-12 11:22:00
Elapsed time: 0:00:07.048981
NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0

Thank you for using QUAST!