
Starting QUAST test
/home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast.py --test

Version: 4.3

System information:
  OS: Linux-4.4.0-45-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64)
  Python version: 2.7.12
  CPUs number: 4

Started: 2016-11-07 15:05:27

Logging to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast.log
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

CWD: /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3
Main parameters: 
  Threads: 1, eukaryotic: true, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000

Reference:
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/reference.fasta.gz ==> reference

Contigs:
  Pre-processing...
  1  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/contigs_1.fasta ==> contigs_1
  2  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/contigs_2.fasta ==> contigs_2

2016-11-07 15:05:28
Running GAGE...
  1  contigs_1...
  1  Logging to files gage_contigs_1.stdout and gage_contigs_1.stderr...
  1  sh quast_libs/gage/getCorrectnessStats.sh quast_libs/E-MEM-linux quast_test_output/quast_corrected_input/reference.fasta \
     quast_test_output/quast_corrected_input/contigs_1.fasta quast_test_output/gage/tmp \
     500 > quast_test_output/gage/gage_contigs_1.stdout 2> quast_test_output/gage/gage_contigs_1.stderr
  1  Done.
  2  contigs_2...
  2  Logging to files gage_contigs_2.stdout and gage_contigs_2.stderr...
  2  sh quast_libs/gage/getCorrectnessStats.sh quast_libs/E-MEM-linux quast_test_output/quast_corrected_input/reference.fasta \
     quast_test_output/quast_corrected_input/contigs_2.fasta quast_test_output/gage/tmp \
     500 > quast_test_output/gage/gage_contigs_2.stdout 2> quast_test_output/gage/gage_contigs_2.stderr
  2  Done.
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/gage_report.txt, gage_report.tsv, and gage_report.tex
  Transposed version of total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/gage_transposed_report.txt, gage_transposed_report.tsv, and gage_transposed_report.tex
Done.

2016-11-07 15:05:42
Running Basic statistics processor...
  Reference genome:
    reference.fasta, Reference length = 10000, Reference GC % = 52.07
  Contig files: 
    1  contigs_1
    2  contigs_2
  Calculating N50 and L50...
    1  contigs_1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp =  0.00
    2  contigs_2, N50 = 3360, L50 = 1, Total length = 5460, GC % = 52.44, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/basic_stats/GC_content_plot.pdf
Done.

2016-11-07 15:05:42
Running Contig analyzer...
  1  contigs_1
  1  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/contigs_report_contigs_1.stdout and contigs_report_contigs_1.stderr...
  1  Aligning contigs to the reference
  1  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/nucmer_output/contigs_1.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/nucmer_output/contigs_1.all_snps.gz
  2  contigs_2
  2  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/contigs_report_contigs_2.stdout and contigs_report_contigs_2.stderr...
  2  Aligning contigs to the reference
  2  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/nucmer_output/contigs_2.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/nucmer_output/contigs_2.all_snps.gz
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Transposed version of total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
  Drawing misassemblies by types plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/contigs_reports/misassemblies_plot.pdf
Done.

2016-11-07 15:05:43
Running NA-NGA calculation...
  1  contigs_1, Largest alignment = 2030, NA50 = 1950, NGA50 = 1610, LA50 = 2, LGA50 = 3
  2  contigs_2, Largest alignment = 2100, NA50 = 1471, NGA50 = 700, LA50 = 2, LGA50 = 4
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/aligned_stats/NGAx_plot.pdf
Done.

2016-11-07 15:05:43
Running Genome analyzer...
  Loaded 10 genes
  Loaded 2 operons
  1  contigs_1
  1  Analysis is finished.
  2  contigs_2
  2  Analysis is finished.
  Drawing genes cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/genome_stats/genes_cumulative_plot.pdf
  Drawing # complete genes histogram...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/genome_stats/complete_genes_histogram.pdf
  Drawing operons cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/genome_stats/operons_cumulative_plot.pdf
  Drawing # complete operons histogram...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/genome_stats/complete_operons_histogram.pdf
  Drawing Genome fraction, % histogram...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/genome_stats/genome_fraction_histogram.pdf
Done.

2016-11-07 15:05:44
Running GlimmerHMM...
  1  contigs_1
  1    Genes = 7 unique, 7 total
  1    Predicted genes (GFF): /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/predicted_genes/contigs_1_glimmer_genes.gff.gz
  2  contigs_2
  2    Genes = 6 unique, 6 total
  2    Predicted genes (GFF): /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/predicted_genes/contigs_2_glimmer_genes.gff.gz
Done.

2016-11-07 15:05:44
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2016-11-07 15:05:45
RESULTS:
  Text versions of total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/report.html
  PDF version (tables and plots) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/report.pdf
  Icarus (contig browser) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/icarus.html
  Log saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast.log

Finished: 2016-11-07 15:05:45
Elapsed time: 0:00:18.602966
NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using QUAST!

TEST PASSED!

Starting MetaQUAST test
/home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/metaquast.py --test

Version: 4.3

System information:
  OS: Linux-4.4.0-45-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64)
  Python version: 2.7.12
  CPUs number: 4

Started: 2016-11-07 15:05:46

Logging to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/metaquast.log
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

Reference(s):
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_ref_1.fasta ==> meta_ref_1
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_ref_2.fasta ==> meta_ref_2
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_ref_3.fasta ==> meta_ref_3
  All references combined in combined_reference.fasta

Contigs:
  Pre-processing...
  1  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_contigs_1.fasta ==> meta_contigs_1
  2  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_contigs_2.fasta ==> meta_contigs_2

Starting quast.py for the combined reference...
/home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast.pyc --meta --combined-ref --colors #E31A1C,#1F78B4 --ls solid,solid --ambiguity-usage all /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_contigs_1.fasta /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_contigs_2.fasta -R /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/combined_reference.fasta -o /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference --labels "meta_contigs_1, meta_contigs_2"

Started: 2016-11-07 15:05:46

Logging to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/quast.log
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

CWD: /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3
Main parameters: 
  Threads: 1, meta: true, minimum contig length: 500, ambiguity: all, threshold for extensive misassembly size: 1000

Reference:
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/combined_reference.fasta ==> combined_reference

Contigs:
  Pre-processing...
  1  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_contigs_1.fasta ==> meta_contigs_1
  2  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/test_data/meta_contigs_2.fasta ==> meta_contigs_2

2016-11-07 15:05:46
Running Basic statistics processor...
  Reference genome:
    combined_reference.fasta, Reference length = 179997, Reference GC % = 45.50
  Contig files: 
    1  meta_contigs_1
    2  meta_contigs_2
  Calculating N50 and L50...
    1  meta_contigs_1, N50 = 49658, L50 = 2, Total length = 180875, GC % = 45.35, # N's per 100 kbp =  7.74
    2  meta_contigs_2, N50 = 49658, L50 = 2, Total length = 173140, GC % = 45.15, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/basic_stats/cumulative_plot.pdf
  Drawing Coverage histogram (bin size: 226x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/basic_stats/coverage_histogram.pdf
  Drawing meta_contigs_1 coverage histogram (bin size: 226x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/basic_stats/meta_contigs_1_coverage_histogram.pdf
  Drawing meta_contigs_2 coverage histogram (bin size: 269x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/basic_stats/meta_contigs_2_coverage_histogram.pdf
Done.

2016-11-07 15:05:46
Running Contig analyzer...
  1  meta_contigs_1
  1  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
  1  Aligning contigs to the reference
  1  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/nucmer_output/meta_contigs_1.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/nucmer_output/meta_contigs_1.all_snps.gz
  2  meta_contigs_2
  2  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
  2  Aligning contigs to the reference
  2  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/nucmer_output/meta_contigs_2.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/nucmer_output/meta_contigs_2.all_snps.gz
  Information about interspecies translocations by references for meta_contigs_1 is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/interspecies_translocations_by_refs_meta_contigs_1.info
  Information about interspecies translocations by references for meta_contigs_2 is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/interspecies_translocations_by_refs_meta_contigs_2.info
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Transposed version of total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
  Drawing misassemblies by types plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/contigs_reports/misassemblies_plot.pdf
Done.

2016-11-07 15:05:47
Running NA-NGA calculation...
  1  meta_contigs_1, Largest alignment = 55106, NA50 = 49658, LA50 = 2
  2  meta_contigs_2, Largest alignment = 55421, NA50 = 49658, LA50 = 2
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/aligned_stats/NAx_plot.pdf
Done.

2016-11-07 15:05:47
Running Genome analyzer...
  NOTICE: No file with genes provided. Use the -G option if you want to specify it.
  NOTICE: No file with operons provided. Use the -O option if you want to specify it.
  1  meta_contigs_1
  1  Analysis is finished.
  2  meta_contigs_2
  2  Analysis is finished.
  Drawing Genome fraction, % histogram...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/genome_stats/genome_fraction_histogram.pdf
Done.

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

2016-11-07 15:05:47
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2016-11-07 15:05:48
RESULTS:
  Text versions of total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/report.html
  PDF version (tables and plots) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/report.pdf
  Icarus (contig browser) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/combined_reference/icarus.html

Partitioning contigs into bins aligned to each reference..
  processing meta_contigs_1
  processing meta_contigs_2

Starting quast.py for the contigs aligned to meta_ref_1
/home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast.pyc --meta --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_1.fasta /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_1.fasta -R /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_ref_1.fasta -o /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1 --labels "meta_contigs_1, meta_contigs_2"

Started: 2016-11-07 15:05:48

Logging to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/quast.log
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

CWD: /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3
Main parameters: 
  Threads: 1, meta: true, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000

Reference:
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_ref_1.fasta ==> meta_ref_1

Contigs:
  Pre-processing...
  1  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_1.fasta ==> meta_contigs_1
  2  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_1.fasta ==> meta_contigs_2

2016-11-07 15:05:48
Running Basic statistics processor...
  Reference genome:
    meta_ref_1.fasta, Reference length = 54999, Reference GC % = 45.96
  Contig files: 
    1  meta_contigs_1
    2  meta_contigs_2
  Calculating N50 and L50...
    1  meta_contigs_1, N50 = 49658, L50 = 1, Total length = 50372, GC % = 45.67, # N's per 100 kbp =  0.00
    2  meta_contigs_2, N50 = 49658, L50 = 1, Total length = 50372, GC % = 45.67, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/basic_stats/GC_content_plot.pdf
  Drawing Coverage histogram (bin size: 1x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/basic_stats/coverage_histogram.pdf
  Drawing meta_contigs_1 coverage histogram (bin size: 1x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/basic_stats/meta_contigs_1_coverage_histogram.pdf
  Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/basic_stats/meta_contigs_2_coverage_histogram.pdf
Done.

2016-11-07 15:05:49
Running Contig analyzer...
  1  meta_contigs_1
  1  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
  1  Aligning contigs to the reference
  1  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/nucmer_output/meta_contigs_1.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/nucmer_output/meta_contigs_1.all_snps.gz
  2  meta_contigs_2
  2  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
  2  Aligning contigs to the reference
  2  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/nucmer_output/meta_contigs_2.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/nucmer_output/meta_contigs_2.all_snps.gz
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Transposed version of total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
  Drawing misassemblies by types plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/contigs_reports/misassemblies_plot.pdf
Done.

2016-11-07 15:05:50
Running NA-NGA calculation...
  1  meta_contigs_1, Largest alignment = 49658, NA50 = 49658, NGA50 = 49658, LA50 = 1, LGA50 = 1
  2  meta_contigs_2, Largest alignment = 49658, NA50 = 49658, NGA50 = 49658, LA50 = 1, LGA50 = 1
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/aligned_stats/NGAx_plot.pdf
Done.

2016-11-07 15:05:50
Running Genome analyzer...
  NOTICE: No file with genes provided. Use the -G option if you want to specify it.
  NOTICE: No file with operons provided. Use the -O option if you want to specify it.
  1  meta_contigs_1
  1  Analysis is finished.
  2  meta_contigs_2
  2  Analysis is finished.
  Drawing Genome fraction, % histogram...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/genome_stats/genome_fraction_histogram.pdf
Done.

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

2016-11-07 15:05:50
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2016-11-07 15:05:51
RESULTS:
  Text versions of total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/report.html
  PDF version (tables and plots) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/report.pdf
  Icarus (contig browser) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_1/icarus.html

Starting quast.py for the contigs aligned to meta_ref_2
/home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast.pyc --meta --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_2.fasta /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_2.fasta -R /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_ref_2.fasta -o /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2 --labels "meta_contigs_1, meta_contigs_2"

Started: 2016-11-07 15:05:51

Logging to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/quast.log
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

CWD: /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3
Main parameters: 
  Threads: 1, meta: true, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000

Reference:
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_ref_2.fasta ==> meta_ref_2

Contigs:
  Pre-processing...
  1  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_2.fasta ==> meta_contigs_1
  2  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_2.fasta ==> meta_contigs_2

2016-11-07 15:05:51
Running Basic statistics processor...
  Reference genome:
    meta_ref_2.fasta, Reference length = 59999, Reference GC % = 50.25
  Contig files: 
    1  meta_contigs_1
    2  meta_contigs_2
  Calculating N50 and L50...
    1  meta_contigs_1, N50 = 55106, L50 = 1, Total length = 58663, GC % = 50.17, # N's per 100 kbp =  1.70
    2  meta_contigs_2, N50 = 55421, L50 = 1, Total length = 58868, GC % = 50.19, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/basic_stats/GC_content_plot.pdf
  Drawing Coverage histogram (bin size: 1x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/basic_stats/coverage_histogram.pdf
  Drawing meta_contigs_1 coverage histogram (bin size: 1x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/basic_stats/meta_contigs_1_coverage_histogram.pdf
  Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/basic_stats/meta_contigs_2_coverage_histogram.pdf
Done.

2016-11-07 15:05:52
Running Contig analyzer...
  1  meta_contigs_1
  1  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
  1  Aligning contigs to the reference
  1  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/nucmer_output/meta_contigs_1.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/nucmer_output/meta_contigs_1.all_snps.gz
  2  meta_contigs_2
  2  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
  2  Aligning contigs to the reference
  2  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/nucmer_output/meta_contigs_2.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/nucmer_output/meta_contigs_2.all_snps.gz
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Transposed version of total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
  Drawing misassemblies by types plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/contigs_reports/misassemblies_plot.pdf
Done.

2016-11-07 15:05:53
Running NA-NGA calculation...
  1  meta_contigs_1, Largest alignment = 55106, NA50 = 55106, NGA50 = 55106, LA50 = 1, LGA50 = 1
  2  meta_contigs_2, Largest alignment = 55421, NA50 = 55421, NGA50 = 55421, LA50 = 1, LGA50 = 1
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/aligned_stats/NGAx_plot.pdf
Done.

2016-11-07 15:05:53
Running Genome analyzer...
  NOTICE: No file with genes provided. Use the -G option if you want to specify it.
  NOTICE: No file with operons provided. Use the -O option if you want to specify it.
  1  meta_contigs_1
  1  Analysis is finished.
  2  meta_contigs_2
  2  Analysis is finished.
  Drawing Genome fraction, % histogram...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/genome_stats/genome_fraction_histogram.pdf
Done.

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

2016-11-07 15:05:53
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2016-11-07 15:05:54
RESULTS:
  Text versions of total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/report.html
  PDF version (tables and plots) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/report.pdf
  Icarus (contig browser) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_2/icarus.html

Starting quast.py for the contigs aligned to meta_ref_3
/home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast.pyc --meta --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_3.fasta /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_3.fasta -R /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_ref_3.fasta -o /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3 --labels "meta_contigs_1, meta_contigs_2"

Started: 2016-11-07 15:05:54

Logging to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/quast.log
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

CWD: /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3
Main parameters: 
  Threads: 1, meta: true, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000

Reference:
  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_ref_3.fasta ==> meta_ref_3

Contigs:
  Pre-processing...
  1  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_to_meta_ref_3.fasta ==> meta_contigs_1
  2  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_to_meta_ref_3.fasta ==> meta_contigs_2

2016-11-07 15:05:54
Running Basic statistics processor...
  Reference genome:
    meta_ref_3.fasta, Reference length = 64999, Reference GC % = 40.73
  Contig files: 
    1  meta_contigs_1
    2  meta_contigs_2
  Calculating N50 and L50...
    1  meta_contigs_1, N50 = 17535, L50 = 2, Total length = 69110, GC % = 40.75, # N's per 100 kbp =  18.81
    2  meta_contigs_2, N50 = 16099, L50 = 2, Total length = 63015, GC % = 40.67, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/Nx_plot.pdf
  Drawing NGx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/NGx_plot.pdf
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/GC_content_plot.pdf
  Drawing Coverage histogram (bin size: 7x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/coverage_histogram.pdf
  Drawing meta_contigs_1 coverage histogram (bin size: 7x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/meta_contigs_1_coverage_histogram.pdf
  Drawing meta_contigs_2 coverage histogram (bin size: 7x)...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/basic_stats/meta_contigs_2_coverage_histogram.pdf
Done.

2016-11-07 15:05:56
Running Contig analyzer...
  1  meta_contigs_1
  1  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
  1  Aligning contigs to the reference
  1  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/nucmer_output/meta_contigs_1.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/nucmer_output/meta_contigs_1.all_snps.gz
  2  meta_contigs_2
  2  Logging to files /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
  2  Aligning contigs to the reference
  2  Analysis is finished.
  Gzipping /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/nucmer_output/meta_contigs_2.all_snps to reduce disk space usage...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/nucmer_output/meta_contigs_2.all_snps.gz
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
  Transposed version of total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
  Creating total report...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
  Drawing misassemblies by types plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/contigs_reports/misassemblies_plot.pdf
Done.

2016-11-07 15:05:56
Running NA-NGA calculation...
  1  meta_contigs_1, Largest alignment = 27969, NA50 = 17534, NGA50 = 17534, LA50 = 2, LGA50 = 2
  2  meta_contigs_2, Largest alignment = 27260, NA50 = 16099, NGA50 = 16099, LA50 = 2, LGA50 = 2
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/aligned_stats/cumulative_plot.pdf
  Drawing NAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/aligned_stats/NAx_plot.pdf
  Drawing NGAx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/aligned_stats/NGAx_plot.pdf
Done.

2016-11-07 15:05:56
Running Genome analyzer...
  NOTICE: No file with genes provided. Use the -G option if you want to specify it.
  NOTICE: No file with operons provided. Use the -O option if you want to specify it.
  1  meta_contigs_1
  1  Analysis is finished.
  2  meta_contigs_2
  2  Analysis is finished.
  Drawing Genome fraction, % histogram...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/genome_stats/genome_fraction_histogram.pdf
Done.

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

2016-11-07 15:05:57
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2016-11-07 15:05:58
RESULTS:
  Text versions of total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/report.html
  PDF version (tables and plots) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/report.pdf
  Icarus (contig browser) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/runs_per_reference/meta_ref_3/icarus.html

Starting quast.py for the contigs not aligned anywhere...
/home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast.pyc --meta --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_not_aligned_anywhere.fasta /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_not_aligned_anywhere.fasta -o /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned --labels "meta_contigs_1, meta_contigs_2"

Started: 2016-11-07 15:05:58

Logging to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/quast.log
NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)

CWD: /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3
Main parameters: 
  Threads: 1, meta: true, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000

Contigs:
  Pre-processing...
  1  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_1_not_aligned_anywhere.fasta ==> meta_contigs_1
  2  /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/quast_corrected_input/meta_contigs_2_not_aligned_anywhere.fasta ==> meta_contigs_2

2016-11-07 15:05:58
Running Basic statistics processor...
  Contig files: 
    1  meta_contigs_1
    2  meta_contigs_2
  Calculating N50 and L50...
    1  meta_contigs_1, N50 = 1610, L50 = 1, Total length = 2730, GC % = 51.94, # N's per 100 kbp =  0.00
    2  meta_contigs_2, N50 = 885, L50 = 1, Total length = 885, GC % = 0.00, # N's per 100 kbp =  0.00
  Drawing Nx plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/basic_stats/Nx_plot.pdf
  Drawing cumulative plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/basic_stats/cumulative_plot.pdf
  Drawing GC content plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/basic_stats/GC_content_plot.pdf
Done.

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

2016-11-07 15:05:58
Creating large visual summaries...
This may take a while: press Ctrl-C to skip this step..
  1 of 2: Creating Icarus viewers...
  2 of 2: Creating PDF with all tables and plots...
Done

2016-11-07 15:05:59
RESULTS:
  Text versions of total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/report.txt, report.tsv, and report.tex
  Text versions of transposed total report are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
  HTML version (interactive tables and plots) saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/report.html
  PDF version (tables and plots) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/report.pdf
  Icarus (contig browser) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/not_aligned/icarus.html

2016-11-07 15:05:59
Summarizing results...
  Drawing # contigs metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/#_contigs.pdf
  Drawing Largest contig metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Largest_contig.pdf
  Drawing Total length metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Total_length.pdf
  Drawing Largest alignment metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Largest_alignment.pdf
  Drawing Total aligned length metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Total_aligned_length.pdf
  Drawing Total length (>= 1000 bp) metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Total_length_(>=_1000_bp).pdf
  Drawing Total length (>= 10000 bp) metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Total_length_(>=_10000_bp).pdf
  Drawing Total length (>= 50000 bp) metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Total_length_(>=_50000_bp).pdf
  Drawing # misassemblies metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/#_misassemblies.pdf
  Drawing metaQUAST summary misassemblies plot for meta_contigs_1...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/meta_contigs_1_misassemblies.pdf
  Drawing metaQUAST summary misassemblies plot for meta_contigs_2...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/meta_contigs_2_misassemblies.pdf
  Drawing Misassembled contigs length metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Misassembled_contigs_length.pdf
  Drawing # mismatches per 100 kbp metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/#_mismatches_per_100_kbp.pdf
  Drawing # indels per 100 kbp metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/#_indels_per_100_kbp.pdf
  Drawing # N's per 100 kbp metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/#_N's_per_100_kbp.pdf
  Drawing Genome fraction (%) metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Genome_fraction_(%).pdf
  Drawing Duplication ratio metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/Duplication_ratio.pdf
  Drawing NGA50 metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/NGA50.pdf
  Drawing LGA50 metaQUAST summary plot...
    saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/PDF/LGA50.pdf

  Text versions of reports and plots for each metric (for all references and assemblies) are saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/summary/
  Icarus (contig browser) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/icarus.html
  Extended version of HTML-report (for all references and assemblies) is saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/report.html

MetaQUAST finished.
  Log saved to /home/lorinc/bioinfo/Gyakorlat/Assembly/programs/quast-4.3/quast_test_output/metaquast.log

Finished: 2016-11-07 15:06:01
Elapsed time: 0:00:15.576066
Total NOTICEs: 12; WARNINGs: 0; non-fatal ERRORs: 0

Thank you for using QUAST!

TEST PASSED!
