/mnt/src/quast-2.2/quast.py -R /mnt/galaxy/galaxy-dist/database/files/000/dataset_35.dat -o /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files /mnt/galaxy/galaxy-dist/database/files/001/dataset_1232.dat

Version 2.2, build 31.07.2013 02:04


System information:
  OS: Linux-3.2.0-40-virtual-x86_64-with-Ubuntu-12.04-precise
  Python version: 2.7.3
  CPUs number: 1

Started: 2014-09-23 16:17:55

Logging to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/quast.log

NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

Reference:
  /mnt/galaxy/galaxy-dist/database/files/000/dataset_35.dat ==> dataset_35

Contigs:
  /mnt/galaxy/galaxy-dist/database/files/001/dataset_1232.dat ==> dataset_1232.dat

2014-09-23 16:17:58
Running Basic statistics processor...
  Reference genome:
    dataset_35.dat, Reference length = 136376, Reference GC % = 67.53
  Contig files: 
    dataset_1232.dat
  Calculating N50 and L50...
    dataset_1232.dat, N50 = 117687, L50 = 1, Total length = 136129, GC % = 67.38, # N's per 100 kbp =  370.24
  Drawing cumulative plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/basic_stats/GC_content_plot.pdf
  Drawing Nx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/basic_stats/NGx_plot.pdf
Done.

2014-09-23 16:18:03
Running Contig analyzer...
  dataset_1232.dat
  Logging to files /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/contigs_reports/contigs_report_dataset_1232.stdout and contigs_report_dataset_1232.stderr...
  Running Nucmer... 
/mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/contigs_reports/alignments_dataset_1232.tsv
  Analysis is finished.
  Creating total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Creating total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
Done.

2014-09-23 16:18:06
Running NA-NGA calculation...
  Calculating NA50 and NGA50...
    dataset_1232.dat, Largest alignment = 107859, NA50 = 107859, NGA50 = 107859, LA50 = 1, LGA50 = 1
  Drawing cumulative plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/aligned_stats/NGAx_plot.pdf
  Done.

2014-09-23 16:18:09
Running Genome analyzer...
  NOTICE: Annotated genes file was not provided. Use -G option to specify it.
  NOTICE: Annotated operons file was not provided. Use -O option to specify it.
  dataset_1232.dat
  Drawing Genome fraction, % histogram...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/genome_stats/genome_fraction_histogram.pdf
Done.

NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it.

2014-09-23 16:18:10
Summarizing...
  Creating total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/report.txt, report.tsv, and report.tex
  Transposed version of total report...
    saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/report.html
  All pdf files are merged to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/plots.pdf
Log saved to /mnt/galaxy/galaxy-dist/database/job_working_directory/000/586/dataset_1233_files/quast.log

Finished: 2014-09-23 16:18:10
Elapsed time: 0:00:14.295187