adds quast 5.3.0

[Kincekara]

Closes #1099

I forced Jammy in this version. Python 3.10 version of joblib and simplejson are still not compatible with Quast. So, I build tools in focal and then copy them into Jammy.

diff quast/5.2.0/Dockerfile quast/5.3.0/Dockerfile
1c1
< ARG QUAST_VER="5.2.0"
---
> ARG QUAST_VER="5.3.0"
41c41
<     /quast-${QUAST_VER}/setup.py install
---
>     ./setup.py install
47c47
< FROM ubuntu:focal as app
---
> FROM ubuntu:jammy as app
51c51
< LABEL base.image="ubuntu:focal"
---
> LABEL base.image="ubuntu:jammy"
70c70,71
<     python2 \
---
>     python3 \
>     python3-matplotlib \
74c75
<     libidn11 \ 
---
>     libidn12 \ 
78c79,81
<     rm -rf /var/lib/apt/lists/*
---
>     rm -rf /var/lib/apt/lists/* &&\
>     update-alternatives --install /usr/bin/python python /usr/bin/python3 1 &&\
>     ln -s /usr/lib/x86_64-linux-gnu/libidn.so.12 /usr/lib/x86_64-linux-gnu/libidn.so.11
80,83d82
< # python dependencies
< RUN update-alternatives --install /usr/bin/python python /usr/bin/python2 1 &&\
<     wget https://bootstrap.pypa.io/pip/2.7/get-pip.py && python get-pip.py &&\
<     pip install --no-cache matplotlib simplejson joblib
86,87d84
< # copy compiled Time::HiRes perl module
< COPY --from=builder /usr/local/lib/x86_64-linux-gnu/perl/5.30.0/Time/ /usr/local/lib/x86_64-linux-gnu/perl/5.30.0/Time/
89,90c86,87
< ENV LC_ALL=C
< ENV PATH=$PATH:/quast-${QUAST_VER} 
---
> ENV LC_ALL=C \
>     PATH=$PATH:/quast-${QUAST_VER} 
103c100
< RUN metaquast.py --test    
---
> RUN metaquast.py --test-no-ref    
109,110c106,107
< # Note 1: "Warnings are GenMark license related. They disappear when a valid licence is provided."
< # Note 2: "metaquast.py --test-no-ref" throws error related Krona plot (known bug of Quast 5.2.0)
---
> # Note: libidn is required for makeblastdb. libidn.so.11 symlink is a temporary patch for this version.

Pull Request (PR) checklist:

• Include a description of what is in this pull request in this message.
• The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
• Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
  • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
• Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
  • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
• Dockerfile includes the recommended LABELS
• Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
• Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

[erinyoung]

Looks like the tests passed

#18 [test 1/4] RUN quast.py --test-sv && mv ./quast_test_output/ ./quast_test_sv_output/
#18 0.153 /quast-5.3.0/quast.py --test-sv
#18 0.153 
#18 0.153 Version: 5.3.0
#18 0.153 
#18 0.153 System information:
#18 0.155   OS: Linux-6.5.0-1025-azure-x86_64-with-glibc2.35 (linux_64)
#18 0.155   Python version: 3.10.12
#18 0.158   CPUs number: 4
#18 0.158 
#18 0.158 Started: 2024-11-19 11:39:00
#18 0.158 
#18 0.158 Logging to /data/quast_test_output/quast.log
#18 0.158 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#18 0.158 
#18 0.158 CWD: /data
#18 0.159 Main parameters: 
#18 0.159   MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
#18 0.159   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#18 0.808 
#18 0.808 Reference:
#18 0.809   /quast-5.3.0/test_data/reference.fasta.gz ==> reference
#18 0.809 
#18 0.810 Contigs:
#18 0.810   Pre-processing...
#18 0.837   1  /quast-5.3.0/test_data/contigs_1.fasta ==> contigs_1
#18 0.837   2  /quast-5.3.0/test_data/contigs_2.fasta ==> contigs_2
#18 0.848 
#18 0.848 2024-11-19 11:39:01
#18 0.849 Running Reads analyzer...
#18 0.851   Logging to files /data/quast_test_output/reads_stats/reads_stats.log and /data/quast_test_output/reads_stats/reads_stats.err...
#18 0.851   1  Pre-processing reads...
#18 0.851   1  Running BWA...
#18 4.451   1  Done.
#18 4.454   1  Sorting SAM-file...
#18 5.944   1  Analysis is finished.
#18 5.944   2  Pre-processing reads...
#18 5.944   2  Running BWA...
#18 9.501   2  Done.
#18 9.504   2  Sorting SAM-file...
#18 10.95   2  Analysis is finished.
#18 10.95   Pre-processing reads...
#18 10.95   Running BWA for reference...
#18 14.36   Done.
#18 14.36   Sorting SAM-file for reference...
#18 15.92   Analysis for reference is finished.
#18 15.92   Creating total report...
#18 15.94     saved to /data/quast_test_output/reads_stats/reads_report.txt, reads_report.tsv, and reads_report.tex
#18 18.16   Calculating reads coverage...
#18 18.33   Calculating physical coverage...
#18 20.85   Looking for trivial deletions (long zero-covered fragments)...
#18 20.98   Trivial deletions: 0 found
#18 20.98     Saving to: /data/quast_test_output/reads_stats/temp_output/trivial_deletions.bed
#18 20.98   Searching structural variations with GRIDSS...
#18 25.09     Saving to: /data/quast_test_output/reads_stats/temp_output/reference_structural_variations.bed
#18 25.09   Structural variations are in /data/quast_test_output/reads_stats/reference.bed
#18 25.09   Coverage distribution along the reference genome is in /data/quast_test_output/reads_stats/reference.cov
#18 25.13 Done.
#18 25.15 
#18 25.15 2024-11-19 11:39:25
#18 25.15 Running Basic statistics processor...
#18 25.15   Reference genome:
#18 25.15     reference.fasta, length = 10000, num fragments = 1, GC % = 52.07
#18 25.15   Contig files: 
#18 25.15     1  contigs_1
#18 25.15     2  contigs_2
#18 25.17   Calculating N50 and L50...
#18 25.17     1  contigs_1, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp =  0.00
#18 25.17     2  contigs_2, N50 = 3360, L50 = 1, auN = 2875.4, Total length = 5460, GC % = 52.44, # N's per 100 kbp =  0.00
#18 25.17   Drawing Nx plot...
#18 25.33     saved to /data/quast_test_output/basic_stats/Nx_plot.pdf
#18 25.33   Drawing NGx plot...
#18 25.43     saved to /data/quast_test_output/basic_stats/NGx_plot.pdf
#18 25.43   Drawing cumulative plot...
#18 25.53     saved to /data/quast_test_output/basic_stats/cumulative_plot.pdf
#18 25.53   Drawing GC content plot...
#18 25.66     saved to /data/quast_test_output/basic_stats/GC_content_plot.pdf
#18 25.66   Drawing contigs_1 GC content plot...
#18 25.81     saved to /data/quast_test_output/basic_stats/contigs_1_GC_content_plot.pdf
#18 25.81   Drawing contigs_2 GC content plot...
#18 25.92     saved to /data/quast_test_output/basic_stats/contigs_2_GC_content_plot.pdf
#18 25.92 Done.
#18 25.93 
#18 25.93 2024-11-19 11:39:26
#18 25.93 Running Contig analyzer...
#18 25.94   1  contigs_1
#18 25.94   1  Logging to files /data/quast_test_output/contigs_reports/contigs_report_contigs_1.stdout and contigs_report_contigs_1.stderr...
#18 25.94   1  Aligning contigs to the reference
#18 25.94   1  Analysis is finished.
#18 25.95   2  contigs_2
#18 25.95   2  Logging to files /data/quast_test_output/contigs_reports/contigs_report_contigs_2.stdout and contigs_report_contigs_2.stderr...
#18 25.95   2  Aligning contigs to the reference
#18 25.95   2  Analysis is finished.
#18 25.95   Creating total report...
#18 25.97     saved to /data/quast_test_output/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#18 25.97   Transposed version of total report...
#18 25.97     saved to /data/quast_test_output/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#18 25.97   Creating total report...
#18 25.98     saved to /data/quast_test_output/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#18 25.98   Drawing misassemblies by types plot...
#18 26.06     saved to /data/quast_test_output/contigs_reports/misassemblies_plot.pdf
#18 26.06   Drawing misassemblies FRCurve plot...
#18 26.16     saved to /data/quast_test_output/contigs_reports/misassemblies_frcurve_plot.pdf
#18 26.16 Done.
#18 26.16 
#18 26.16 2024-11-19 11:39:26
#18 26.16 Running NA-NGA calculation...
#18 26.16   1  contigs_1, Largest alignment = 2030, NA50 = 1950, NGA50 = 1610, LA50 = 2, LGA50 = 3
#18 26.16   2  contigs_2, Largest alignment = 2100, NA50 = 1471, NGA50 = 700, LA50 = 2, LGA50 = 4
#18 26.16   Drawing cumulative plot...
#18 26.26     saved to /data/quast_test_output/aligned_stats/cumulative_plot.pdf
#18 26.26   Drawing NAx plot...
#18 26.36     saved to /data/quast_test_output/aligned_stats/NAx_plot.pdf
#18 26.36   Drawing NGAx plot...
#18 26.46     saved to /data/quast_test_output/aligned_stats/NGAx_plot.pdf
#18 26.46 Done.
#18 26.47 
#18 26.47 2024-11-19 11:39:26
#18 26.47 Running Genome analyzer...
#18 26.47   Loaded 10 genomic features of type "gene"
#18 26.47   Loaded 2 genomic features of type "operon"
#18 26.47   1  contigs_1
#18 26.47   1  Analysis is finished.
#18 26.47   2  contigs_2
#18 26.47   2  Analysis is finished.
#18 26.48   Drawing genomic features cumulative plot...
#18 26.58     saved to /data/quast_test_output/genome_stats/features_cumulative_plot.pdf
#18 26.58   Drawing genomic features FRCurve plot...
#18 26.72     saved to /data/quast_test_output/genome_stats/features_frcurve_plot.pdf
#18 26.72   Drawing # complete genomic features histogram...
#18 26.79     saved to /data/quast_test_output/genome_stats/complete_features_histogram.pdf
#18 26.79   Drawing operons cumulative plot...
#18 26.89     saved to /data/quast_test_output/genome_stats/operons_cumulative_plot.pdf
#18 26.89   Drawing operons FRCurve plot...
#18 26.98     saved to /data/quast_test_output/genome_stats/operons_frcurve_plot.pdf
#18 26.98   Drawing # complete operons histogram...
#18 27.04     saved to /data/quast_test_output/genome_stats/complete_operons_histogram.pdf
#18 27.04   Drawing Genome fraction, % histogram...
#18 27.10     saved to /data/quast_test_output/genome_stats/genome_fraction_histogram.pdf
#18 27.10 Done.
#18 27.11 
#18 27.11 2024-11-19 11:39:27
#18 27.11 Running GlimmerHMM...
#18 27.11   1  contigs_1
#18 27.17   1    Genes = 7 unique, 7 total
#18 27.17   1    Predicted genes (GFF): /data/quast_test_output/predicted_genes/contigs_1_glimmer_genes.gff
#18 27.17   2  contigs_2
#18 27.21   2    Genes = 6 unique, 6 total
#18 27.21   2    Predicted genes (GFF): /data/quast_test_output/predicted_genes/contigs_2_glimmer_genes.gff
#18 27.21 Done.
#18 27.21 
#18 27.21 2024-11-19 11:39:27
#18 27.21 Running GeneMarkS...
#18 27.21   1  contigs_1
#18 27.25   1    Genes = 8 unique, 8 total
#18 27.25   1    Predicted genes (GFF): /data/quast_test_output/predicted_genes/contigs_1_genemark_genes.gff
#18 27.25   2  contigs_2
#18 27.30   2    Genes = 7 unique, 7 total
#18 27.30   2    Predicted genes (GFF): /data/quast_test_output/predicted_genes/contigs_2_genemark_genes.gff
#18 27.30 Done.
#18 27.33 
#18 27.33 2024-11-19 11:39:27
#18 27.33 Creating large visual summaries...
#18 27.33 This may take a while: press Ctrl-C to skip this step..
#18 27.33   1 of 2: Creating PDF with all tables and plots...
#18 29.48   2 of 2: Creating Icarus viewers...
#18 29.52 Done
#18 29.52 
#18 29.52 2024-11-19 11:39:29
#18 29.52 RESULTS:
#18 29.52   Text versions of total report are saved to /data/quast_test_output/report.txt, report.tsv, and report.tex
#18 29.52   Text versions of transposed total report are saved to /data/quast_test_output/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#18 29.53   HTML version (interactive tables and plots) is saved to /data/quast_test_output/report.html
#18 29.53   PDF version (tables and plots) is saved to /data/quast_test_output/report.pdf
#18 29.53   Icarus (contig browser) is saved to /data/quast_test_output/icarus.html
#18 29.53   Log is saved to /data/quast_test_output/quast.log
#18 29.53 
#18 29.53 Finished: 2024-11-19 11:39:29
#18 29.53 Elapsed time: 0:00:29.370492
#18 29.53 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0
#18 29.53 
#18 29.53 Thank you for using QUAST!
#18 29.53 
#18 29.53 TEST PASSED!
#18 DONE 29.6s

#19 [test 2/4] RUN quast-lg.py --test && mv ./quast_test_output/ ./quast_test_lg_output/
#19 0.125 /quast-5.3.0/quast-lg.py --test
#19 0.125 
#19 0.125 Version: 5.3.0
#19 0.125 
#19 0.125 System information:
#19 0.127   OS: Linux-6.5.0-1025-azure-x86_64-with-glibc2.35 (linux_64)
#19 0.127   Python version: 3.10.12
#19 0.129   CPUs number: 4
#19 0.129 
#19 0.129 Started: 2024-11-19 11:39:29
#19 0.129 
#19 0.130 Logging to /data/quast_test_output/quast.log
#19 0.130 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#19 0.130 
#19 0.130 CWD: /data
#19 0.130 Main parameters: 
#19 0.130   MODE: large, threads: 1, eukaryotic: true, min contig length: 3000, min alignment length: 500, \
#19 0.130   min alignment IDY: 95.0, ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 7000
#19 0.641 
#19 0.641 Reference:
#19 0.643   /quast-5.3.0/test_data/reference.fasta.gz ==> reference
#19 0.643 
#19 0.643 Contigs:
#19 0.643   Pre-processing...
#19 0.653   1  /quast-5.3.0/test_data/contigs_1.fasta ==> contigs_1
#19 0.653   2  /quast-5.3.0/test_data/contigs_2.fasta ==> contigs_2
#19 0.659 
#19 0.659 2024-11-19 11:39:30
#19 0.659 Running Basic statistics processor...
#19 0.660   Reference genome:
#19 0.660     reference.fasta, length = 10000, num fragments = 1, GC % = 52.07
#19 0.660   Contig files: 
#19 0.660     1  contigs_1
#19 0.660     2  contigs_2
#19 0.675   Calculating N50 and L50...
#19 0.675     1  contigs_1, N50 = 3980, L50 = 1, auN = 3980.0, Total length = 3980, GC % = 50.83, # N's per 100 kbp =  0.00
#19 0.676     2  contigs_2, N50 = 3360, L50 = 1, auN = 3360.0, Total length = 3360, GC % = 52.35, # N's per 100 kbp =  0.00
#19 0.679   Drawing Nx plot...
#19 0.848     saved to /data/quast_test_output/basic_stats/Nx_plot.pdf
#19 0.849   Drawing NGx plot...
#19 0.971     saved to /data/quast_test_output/basic_stats/NGx_plot.pdf
#19 0.972   Drawing cumulative plot...
#19 1.086     saved to /data/quast_test_output/basic_stats/cumulative_plot.pdf
#19 1.087   Drawing GC content plot...
#19 1.212     saved to /data/quast_test_output/basic_stats/GC_content_plot.pdf
#19 1.213   Drawing contigs_1 GC content plot...
#19 1.353     saved to /data/quast_test_output/basic_stats/contigs_1_GC_content_plot.pdf
#19 1.354   Drawing contigs_2 GC content plot...
#19 1.510     saved to /data/quast_test_output/basic_stats/contigs_2_GC_content_plot.pdf
#19 1.510 Done.
#19 1.512 
#19 1.512 2024-11-19 11:39:31
#19 1.512 Running Contig analyzer...
#19 1.515   1  contigs_1
#19 1.515   1  Logging to files /data/quast_test_output/contigs_reports/contigs_report_contigs_1.stdout and contigs_report_contigs_1.stderr...
#19 1.515   1  Aligning contigs to the reference
#19 1.525   1  Analysis is finished.
#19 1.526   2  contigs_2
#19 1.526   2  Logging to files /data/quast_test_output/contigs_reports/contigs_report_contigs_2.stdout and contigs_report_contigs_2.stderr...
#19 1.526   2  Aligning contigs to the reference
#19 1.536   2  Analysis is finished.
#19 1.537   Creating total report...
#19 1.555     saved to /data/quast_test_output/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#19 1.555   Transposed version of total report...
#19 1.555     saved to /data/quast_test_output/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#19 1.555   Creating total report...
#19 1.566     saved to /data/quast_test_output/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#19 1.566   Drawing misassemblies by types plot...
#19 1.641     saved to /data/quast_test_output/contigs_reports/misassemblies_plot.pdf
#19 1.642   Drawing misassemblies FRCurve plot...
#19 1.757     saved to /data/quast_test_output/contigs_reports/misassemblies_frcurve_plot.pdf
#19 1.759 Done.
#19 1.759 
#19 1.759 2024-11-19 11:39:31
#19 1.759 Running NA-NGA calculation...
#19 1.759   1  contigs_1, Largest alignment = 3980, NA50 = 3980, LA50 = 1
#19 1.759   2  contigs_2, Largest alignment = 2660, NA50 = 2660, LA50 = 1
#19 1.763   Drawing cumulative plot...
#19 1.879     saved to /data/quast_test_output/aligned_stats/cumulative_plot.pdf
#19 1.881   Drawing NAx plot...
#19 2.002     saved to /data/quast_test_output/aligned_stats/NAx_plot.pdf
#19 2.004   Drawing NGAx plot...
#19 2.125     saved to /data/quast_test_output/aligned_stats/NGAx_plot.pdf
#19 2.127 Done.
#19 2.130 
#19 2.130 2024-11-19 11:39:31
#19 2.130 Running Genome analyzer...
#19 2.132   Loaded 10 genomic features of type "gene"
#19 2.132   Loaded 2 genomic features of type "operon"
#19 2.132   1  contigs_1
#19 2.133   1  Analysis is finished.
#19 2.133   2  contigs_2
#19 2.134   2  Analysis is finished.
#19 2.141   Drawing genomic features cumulative plot...
#19 2.260     saved to /data/quast_test_output/genome_stats/features_cumulative_plot.pdf
#19 2.262   Drawing genomic features FRCurve plot...
#19 2.389     saved to /data/quast_test_output/genome_stats/features_frcurve_plot.pdf
#19 2.390   Drawing # complete genomic features histogram...
#19 2.481     saved to /data/quast_test_output/genome_stats/complete_features_histogram.pdf
#19 2.482   Drawing operons cumulative plot...
#19 2.631     saved to /data/quast_test_output/genome_stats/operons_cumulative_plot.pdf
#19 2.633   Drawing operons FRCurve plot...
#19 2.747     saved to /data/quast_test_output/genome_stats/operons_frcurve_plot.pdf
#19 2.748   Drawing # complete operons histogram...
#19 2.825     saved to /data/quast_test_output/genome_stats/complete_operons_histogram.pdf
#19 2.825   Drawing Genome fraction, % histogram...
#19 2.903     saved to /data/quast_test_output/genome_stats/genome_fraction_histogram.pdf
#19 2.904 Done.
#19 2.905 
#19 2.905 2024-11-19 11:39:32
#19 2.905 Running GlimmerHMM...
#19 2.905   1  contigs_1
#19 2.942   1    Genes = 4 unique, 4 total
#19 2.942   1    Predicted genes (GFF): /data/quast_test_output/predicted_genes/contigs_1_glimmer_genes.gff
#19 2.943   2  contigs_2
#19 2.974   2    Genes = 4 unique, 4 total
#19 2.974   2    Predicted genes (GFF): /data/quast_test_output/predicted_genes/contigs_2_glimmer_genes.gff
#19 2.974 Done.
#19 3.006 
#19 3.006 2024-11-19 11:39:32
#19 3.006 Creating large visual summaries...
#19 3.006 This may take a while: press Ctrl-C to skip this step..
#19 3.006   1 of 2: Creating PDF with all tables and plots...
#19 4.617   2 of 2: Creating Icarus viewers...
#19 4.651 Done
#19 4.651 
#19 4.651 2024-11-19 11:39:34
#19 4.652 RESULTS:
#19 4.652   Text versions of total report are saved to /data/quast_test_output/report.txt, report.tsv, and report.tex
#19 4.652   Text versions of transposed total report are saved to /data/quast_test_output/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#19 4.659   HTML version (interactive tables and plots) is saved to /data/quast_test_output/report.html
#19 4.659   PDF version (tables and plots) is saved to /data/quast_test_output/report.pdf
#19 4.660   Icarus (contig browser) is saved to /data/quast_test_output/icarus.html
#19 4.660   Log is saved to /data/quast_test_output/quast.log
#19 4.660 
#19 4.660 Finished: 2024-11-19 11:39:34
#19 4.660 Elapsed time: 0:00:04.530653
#19 4.660 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0
#19 4.660 
#19 4.660 Thank you for using QUAST!
#19 4.660 
#19 4.660 TEST PASSED!
#19 DONE 4.8s

#20 [test 3/4] RUN metaquast.py --test-no-ref
#20 0.139 /quast-5.3.0/metaquast.py --test-no-ref
#20 0.139 
#20 0.139 Version: 5.3.0
#20 0.140 
#20 0.140 System information:
#20 0.141   OS: Linux-6.5.0-1025-azure-x86_64-with-glibc2.35 (linux_64)
#20 0.141   Python version: 3.10.12
#20 0.144   CPUs number: 4
#20 0.144 
#20 0.144 Started: 2024-11-19 11:39:34
#20 0.144 
#20 0.144 Logging to /data/quast_test_output/metaquast.log
#20 0.144 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 0.668 
#20 0.668 Contigs:
#20 0.668   Pre-processing...
#20 0.686   1  /quast-5.3.0/test_data/meta_contigs_1.fasta ==> meta_contigs_1
#20 0.686   2  /quast-5.3.0/test_data/meta_contigs_2.fasta ==> meta_contigs_2
#20 0.687 
#20 0.687 No references are provided, starting to search for reference genomes in SILVA 16S rRNA database and to download them from NCBI...
#20 0.687 
#20 0.687 2024-11-19 11:39:35
#20 0.688 Downloading blast (file: makeblastdb)...
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#20 1.317 blast successfully downloaded!
#20 1.317 Downloading blast (file: blastn)...
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#20 2.034  99.0% of 39777200 bytes
#20 2.034 blast successfully downloaded!
#20 2.035 
#20 2.035 Downloading SILVA 16S ribosomal RNA gene database (version 138.1)...
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#20 12.07 Processing downloaded file. Logging to /quast-5.3.0/quast_libs/silva/blastdb.log...
#20 12.07 Unpacking and replacing " " with "_"...
#20 19.98 Making BLAST database...
#20 34.44 Running BlastN..
#20 34.44   processing meta_contigs_1
#20 72.21   BLAST results for meta_contigs_1 are saved to /data/quast_test_output/quast_downloaded_references/blast.res_meta_contigs_1...
#20 72.21   processing meta_contigs_2
#20 99.73   BLAST results for meta_contigs_2 are saved to /data/quast_test_output/quast_downloaded_references/blast.res_meta_contigs_2...
#20 99.73 
#20 99.74 
#20 99.74 2024-11-19 11:41:14
#20 99.74 Trying to download found references from NCBI. Totally 11 organisms to try.
#20 100.9   Streptococcus_pneumoniae                    | successfully downloaded (total 1, 10 more to go)
#20 103.7   Streptococcus_agalactiae_SS1219             | successfully downloaded (total 2, 9 more to go)
#20 103.8   Lactobacillus_sp._NBRC_14513                | not found in the NCBI database
#20 103.8   Lactobacillus_sp._NBRC_14513 was not found in NCBI database, trying to download the next best match
#20 103.9   Lactobacillus_sp._NBRC_14511                | not found in the NCBI database
#20 103.9   Lactobacillus_sp._NBRC_14511 was not found in NCBI database, trying to download the next best match
#20 104.0   Lactobacillus_sp._NBRC_14512                | not found in the NCBI database
#20 105.2   Lactobacillus_sp._L0(2016)                  | not found in the NCBI database
#20 105.2   Lactobacillus_sp._L0(2016) was not found in NCBI database, trying to download the next best match
#20 105.2   Lactobacillus_sp._NBRC_14511                | not found in the NCBI database
#20 105.2   Lactobacillus_sp._NBRC_14511 was not found in NCBI database, trying to download the next best match
#20 105.2   Lactobacillus_sp._NBRC_14512                | not found in the NCBI database
#20 107.1   Lactobacillus_reuteri_TD1                   | successfully downloaded (total 3, 6 more to go)
#20 109.2   Lactobacillus_reuteri                       | successfully downloaded (total 4, 5 more to go)
#20 112.0   Lactobacillus_psittaci                      | successfully downloaded (total 5, 4 more to go)
#20 112.1   Lactobacillus_plantarum                     | not found in the NCBI database
#20 112.1   Lactobacillus_plantarum was not found in NCBI database, trying to download the next best match
#20 117.3   Lactobacillus_pentosus                      | successfully downloaded (total 6, 3 more to go)
#20 121.5   Lactobacillus_modestisalitolerans           | successfully downloaded (total 7, 2 more to go)
#20 125.5   Lactobacillus_delbrueckii_subsp._bulgaricus | successfully downloaded (total 8, 1 more to go)
#20 127.2   Lactobacillus_brantae                       | successfully downloaded (total 9, 0 more to go)
#20 127.2 
#20 127.2 Downloaded reference(s):
#20 127.2   /data/quast_test_output/quast_downloaded_references/Lactobacillus_brantae.fasta ==> Lactobacillus_brantae
#20 127.2   /data/quast_test_output/quast_downloaded_references/Lactobacillus_delbrueckii_subsp._bulgaricus.fasta ==> Lactobacillus_delbrueckii_subsp._bulgaricus
#20 127.3   /data/quast_test_output/quast_downloaded_references/Lactobacillus_modestisalitolerans.fasta ==> Lactobacillus_modestisalitolerans
#20 127.4   /data/quast_test_output/quast_downloaded_references/Lactobacillus_pentosus.fasta ==> Lactobacillus_pentosus
#20 127.5   /data/quast_test_output/quast_downloaded_references/Lactobacillus_psittaci.fasta ==> Lactobacillus_psittaci
#20 127.5   /data/quast_test_output/quast_downloaded_references/Lactobacillus_reuteri.fasta ==> Lactobacillus_reuteri
#20 127.6   /data/quast_test_output/quast_downloaded_references/Lactobacillus_reuteri_TD1.fasta ==> Lactobacillus_reuteri_TD1
#20 127.6   /data/quast_test_output/quast_downloaded_references/Streptococcus_agalactiae_SS1219.fasta ==> Streptococcus_agalactiae_SS1219
#20 127.7   /data/quast_test_output/quast_downloaded_references/Streptococcus_pneumoniae.fasta ==> Streptococcus_pneumoniae
#20 127.7   All references were combined in combined_reference.fasta
#20 127.7 
#20 127.7 Starting quast.py for the combined reference...
#20 127.7 /quast-5.3.0/quast.py --min-identity 90.0 --combined-ref --colors #E31A1C,#1F78B4 --ls solid,solid --ambiguity-usage all /quast-5.3.0/test_data/meta_contigs_1.fasta /quast-5.3.0/test_data/meta_contigs_2.fasta -R /data/quast_test_output/quast_corrected_input/combined_reference.fasta -o /data/quast_test_output/combined_reference --labels "meta_contigs_1, meta_contigs_2"
#20 127.7 
#20 127.7 Started: 2024-11-19 11:41:42
#20 127.7 
#20 127.7 Logging to /data/quast_test_output/combined_reference/quast.log
#20 127.7 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 127.7 
#20 127.7 CWD: /data
#20 127.7 Main parameters: 
#20 127.7   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 127.7   ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000
#20 127.7 
#20 127.7 Reference:
#20 127.7   /data/quast_test_output/quast_corrected_input/combined_reference.fasta ==> combined_reference
#20 127.7 
#20 127.7 Contigs:
#20 127.7   Pre-processing...
#20 127.7   1  /quast-5.3.0/test_data/meta_contigs_1.fasta ==> meta_contigs_1
#20 127.7   2  /quast-5.3.0/test_data/meta_contigs_2.fasta ==> meta_contigs_2
#20 127.7 
#20 127.7 2024-11-19 11:41:42
#20 127.7 Running Basic statistics processor...
#20 128.6   Reference genome:
#20 128.6     combined_reference.fasta, length = 19831134, num fragments = 150, GC % = 42.95
#20 128.6 WARNING:   Reference genome is fragmented. You may consider rerunning QUAST using --fragmented option. QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from # misassemblies).
#20 128.6   Contig files: 
#20 128.6     1  meta_contigs_1
#20 128.6     2  meta_contigs_2
#20 128.6   Calculating N50 and L50...
#20 128.6     1  meta_contigs_1, N50 = 48458, L50 = 2, auN = 36838.5, Total length = 180190, GC % = 45.35, # N's per 100 kbp =  18.87
#20 128.6     2  meta_contigs_2, N50 = 49658, L50 = 2, auN = 38106.6, Total length = 172703, GC % = 45.11, # N's per 100 kbp =  0.00
#20 128.6   Drawing Nx plot...
#20 128.8     saved to /data/quast_test_output/combined_reference/basic_stats/Nx_plot.pdf
#20 128.8   Drawing cumulative plot...
#20 129.2     saved to /data/quast_test_output/combined_reference/basic_stats/cumulative_plot.pdf
#20 129.2   Drawing GC content plot...
#20 129.4     saved to /data/quast_test_output/combined_reference/basic_stats/GC_content_plot.pdf
#20 129.4   Drawing meta_contigs_1 GC content plot...
#20 129.7     saved to /data/quast_test_output/combined_reference/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 129.7   Drawing meta_contigs_2 GC content plot...
#20 129.9     saved to /data/quast_test_output/combined_reference/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 129.9   Drawing Coverage histogram (bin size: 97x)...
#20 130.2     saved to /data/quast_test_output/combined_reference/basic_stats/coverage_histogram.pdf
#20 130.2   Drawing meta_contigs_1 coverage histogram (bin size: 63x)...
#20 130.4     saved to /data/quast_test_output/combined_reference/basic_stats/meta_contigs_1_coverage_histogram.pdf
#20 130.4   Drawing meta_contigs_2 coverage histogram (bin size: 97x)...
#20 130.6     saved to /data/quast_test_output/combined_reference/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 130.6 Done.
#20 130.6 
#20 130.6 2024-11-19 11:41:45
#20 130.6 Running Contig analyzer...
#20 131.6   1  meta_contigs_1
#20 131.6   1  Logging to files /data/quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
#20 131.6   1  Aligning contigs to the reference
#20 132.7   1  Analysis is finished.
#20 132.7   2  meta_contigs_2
#20 132.7   2  Logging to files /data/quast_test_output/combined_reference/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 132.7   2  Aligning contigs to the reference
#20 133.8   2  Analysis is finished.
#20 133.8   Information about interspecies translocations by references for meta_contigs_1 is saved to /data/quast_test_output/combined_reference/contigs_reports/interspecies_translocations_by_refs_meta_contigs_1.info
#20 133.8   Information about interspecies translocations by references for meta_contigs_2 is saved to /data/quast_test_output/combined_reference/contigs_reports/interspecies_translocations_by_refs_meta_contigs_2.info
#20 133.8   Drawing Intergenomic misassemblies (found and supposed) metaQUAST summary plot...
#20 134.1     saved to /data/quast_test_output/combined_reference/contigs_reports/intergenomic_misassemblies.pdf
#20 134.1   Creating total report...
#20 134.1     saved to /data/quast_test_output/combined_reference/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 134.1   Transposed version of total report...
#20 134.1     saved to /data/quast_test_output/combined_reference/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 134.1   Creating total report...
#20 134.1     saved to /data/quast_test_output/combined_reference/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 134.1   Drawing misassemblies by types plot...
#20 134.4     saved to /data/quast_test_output/combined_reference/contigs_reports/misassemblies_plot.pdf
#20 134.4   Drawing misassemblies FRCurve plot...
#20 134.7     saved to /data/quast_test_output/combined_reference/contigs_reports/misassemblies_frcurve_plot.pdf
#20 134.7 Done.
#20 134.7 
#20 134.7 2024-11-19 11:41:49
#20 134.7 Running NA-NGA calculation...
#20 134.8   1  meta_contigs_1, Largest alignment = 25033, NA50 = 4832, LA50 = 8
#20 134.8   2  meta_contigs_2, Largest alignment = 25033, NA50 = 5305, LA50 = 8
#20 134.8   Drawing cumulative plot...
#20 135.2     saved to /data/quast_test_output/combined_reference/aligned_stats/cumulative_plot.pdf
#20 135.2   Drawing NAx plot...
#20 135.4     saved to /data/quast_test_output/combined_reference/aligned_stats/NAx_plot.pdf
#20 135.4 Done.
#20 135.4 
#20 135.4 2024-11-19 11:41:50
#20 135.4 Running Genome analyzer...
#20 136.4   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 136.4 
#20 136.4   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 136.4   1  meta_contigs_1
#20 138.4   1  Analysis is finished.
#20 138.4   2  meta_contigs_2
#20 140.3   2  Analysis is finished.
#20 140.3   Drawing Genome fraction, % histogram...
#20 140.5     saved to /data/quast_test_output/combined_reference/genome_stats/genome_fraction_histogram.pdf
#20 140.5 Done.
#20 140.5 
#20 140.5 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 140.5 
#20 140.5 2024-11-19 11:41:55
#20 140.5 Creating large visual summaries...
#20 140.5 This may take a while: press Ctrl-C to skip this step..
#20 140.5   1 of 2: Creating PDF with all tables and plots...
#20 142.1   2 of 2: Creating Icarus viewers...
#20 142.5 Done
#20 142.5 
#20 142.5 2024-11-19 11:41:57
#20 142.5 RESULTS:
#20 142.5   Text versions of total report are saved to /data/quast_test_output/combined_reference/report.txt, report.tsv, and report.tex
#20 142.5   Text versions of transposed total report are saved to /data/quast_test_output/combined_reference/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 142.5   HTML version (interactive tables and plots) is saved to /data/quast_test_output/combined_reference/report.html
#20 142.5   PDF version (tables and plots) is saved to /data/quast_test_output/combined_reference/report.pdf
#20 142.5   Icarus (contig browser) is saved to /data/quast_test_output/combined_reference/icarus.html
#20 142.5 
#20 142.5 Excluding downloaded references with low genome fraction from further analysis..
#20 142.5 All downloaded references have low genome fraction. Nothing was excluded for now.
#20 142.5 
#20 142.5 Partitioning contigs into bins aligned to each reference..
#20 142.5   processing meta_contigs_1
#20 142.5   processing meta_contigs_2
#20 142.5 
#20 142.5 Starting quast.py for the contigs aligned to Lactobacillus_brantae... (logging to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/quast.log)
#20 142.5 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_brantae.fasta -R /data/quast_test_output/quast_corrected_input/Lactobacillus_brantae.fasta -o /data/quast_test_output/runs_per_reference/Lactobacillus_brantae --labels meta_contigs_2
#20 142.5 
#20 142.5 Started: 2024-11-19 11:41:57
#20 142.5 
#20 142.5 Logging to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/quast.log
#20 142.5 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 142.5 
#20 142.5 CWD: /data
#20 142.5 Main parameters: 
#20 142.5   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 142.5   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 142.5 
#20 142.5 Reference:
#20 142.5   /data/quast_test_output/quast_corrected_input/Lactobacillus_brantae.fasta ==> Lactobacillus_brantae
#20 142.5 
#20 142.5 Contigs:
#20 142.5   Pre-processing...
#20 142.5   /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_brantae.fasta ==> meta_contigs_2
#20 142.5 
#20 142.5 2024-11-19 11:41:57
#20 142.5 Running Basic statistics processor...
#20 142.6   Reference genome:
#20 142.6     Lactobacillus_brantae.fasta, length = 1929842, num fragments = 12, GC % = 47.48
#20 142.6   Contig files: 
#20 142.6     meta_contigs_2
#20 142.6   Calculating N50 and L50...
#20 142.6     meta_contigs_2, N50 = 763, L50 = 1, auN = 763.0, Total length = 763, GC % = 49.80, # N's per 100 kbp =  0.00
#20 142.6   Drawing Nx plot...
#20 142.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/basic_stats/Nx_plot.pdf
#20 142.8   Drawing NGx plot...
#20 142.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/basic_stats/NGx_plot.pdf
#20 142.9   Drawing cumulative plot...
#20 143.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/basic_stats/cumulative_plot.pdf
#20 143.0   Drawing GC content plot...
#20 143.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/basic_stats/GC_content_plot.pdf
#20 143.1   Drawing meta_contigs_2 GC content plot...
#20 143.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 143.2   Drawing Coverage histogram (bin size: 1x)...
#20 143.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/basic_stats/coverage_histogram.pdf
#20 143.3   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 143.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 143.4 Done.
#20 143.4 
#20 143.4 2024-11-19 11:41:58
#20 143.4 Running Contig analyzer...
#20 143.5   meta_contigs_2
#20 143.5   Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 143.5   Aligning contigs to the reference
#20 143.6   Analysis is finished.
#20 143.6   Creating total report...
#20 143.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 143.6   Transposed version of total report...
#20 143.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 143.6   Creating total report...
#20 143.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 143.7   Drawing misassemblies by types plot...
#20 143.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/contigs_reports/misassemblies_plot.pdf
#20 143.8   Drawing misassemblies FRCurve plot...
#20 143.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/contigs_reports/misassemblies_frcurve_plot.pdf
#20 143.9 Done.
#20 143.9 
#20 143.9 2024-11-19 11:41:58
#20 143.9 Running NA-NGA calculation...
#20 143.9   meta_contigs_2, Largest alignment = 402, NA50 = 402, LA50 = 1
#20 143.9   Drawing cumulative plot...
#20 144.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/aligned_stats/cumulative_plot.pdf
#20 144.1   Drawing NAx plot...
#20 144.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/aligned_stats/NAx_plot.pdf
#20 144.2   Drawing NGAx plot...
#20 144.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/aligned_stats/NGAx_plot.pdf
#20 144.3 Done.
#20 144.3 
#20 144.3 2024-11-19 11:41:58
#20 144.3 Running Genome analyzer...
#20 144.4   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 144.4 
#20 144.4   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 144.4   meta_contigs_2
#20 144.6   Analysis is finished.
#20 144.6   Skipping drawing Genome fraction, % histogram... (less than 2 columns histogram makes no sense)
#20 144.6 Done.
#20 144.6 
#20 144.6 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 144.6 
#20 144.6 2024-11-19 11:41:59
#20 144.6 Creating large visual summaries...
#20 144.6 This may take a while: press Ctrl-C to skip this step..
#20 144.6   1 of 2: Creating PDF with all tables and plots...
#20 145.7   2 of 2: Creating Icarus viewers...
#20 145.8 Done
#20 145.8 
#20 145.8 2024-11-19 11:42:00
#20 145.8 RESULTS:
#20 145.8   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/report.txt, report.tsv, and report.tex
#20 145.8   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 145.8   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/report.html
#20 145.8   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/report.pdf
#20 145.8   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_brantae/icarus.html
#20 145.8 
#20 145.8 Starting quast.py for the contigs aligned to Lactobacillus_delbrueckii_subsp._bulgaricus... (logging to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/quast.log)
#20 145.8 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_delbrueckii_subsp._bulgaricus.fasta /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_delbrueckii_subsp._bulgaricus.fasta -R /data/quast_test_output/quast_corrected_input/Lactobacillus_delbrueckii_subsp._bulgaricus.fasta -o /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus --labels "meta_contigs_1, meta_contigs_2"
#20 145.8 
#20 145.8 Started: 2024-11-19 11:42:00
#20 145.8 
#20 145.8 Logging to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/quast.log
#20 145.8 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 145.8 
#20 145.8 CWD: /data
#20 145.8 Main parameters: 
#20 145.8   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 145.8   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 145.8 
#20 145.8 Reference:
#20 145.8   /data/quast_test_output/quast_corrected_input/Lactobacillus_delbrueckii_subsp._bulgaricus.fasta ==> Lactobacillus_delbrueckii_subsp._bulgaricus
#20 145.8 
#20 145.8 Contigs:
#20 145.8   Pre-processing...
#20 145.8   1  /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_delbrueckii_subsp._bulgaricus.fasta ==> meta_contigs_1
#20 145.8   2  /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_delbrueckii_subsp._bulgaricus.fasta ==> meta_contigs_2
#20 145.8 
#20 145.8 2024-11-19 11:42:00
#20 145.8 Running Basic statistics processor...
#20 145.9   Reference genome:
#20 145.9     Lactobacillus_delbrueckii_subsp._bulgaricus.fasta, length = 1832237, num fragments = 1, GC % = 49.76
#20 145.9   Contig files: 
#20 145.9     1  meta_contigs_1
#20 145.9     2  meta_contigs_2
#20 145.9   Calculating N50 and L50...
#20 145.9     1  meta_contigs_1, N50 = 55106, L50 = 1, auN = 51385.4, Total length = 59178, GC % = 50.17, # N's per 100 kbp =  35.49
#20 145.9     2  meta_contigs_2, N50 = 54221, L50 = 1, auN = 50527.6, Total length = 58431, GC % = 50.11, # N's per 100 kbp =  0.00
#20 145.9   Drawing Nx plot...
#20 146.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/Nx_plot.pdf
#20 146.0   Drawing NGx plot...
#20 146.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/NGx_plot.pdf
#20 146.1   Drawing cumulative plot...
#20 146.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/cumulative_plot.pdf
#20 146.3   Drawing GC content plot...
#20 146.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/GC_content_plot.pdf
#20 146.4   Drawing meta_contigs_1 GC content plot...
#20 146.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 146.6   Drawing meta_contigs_2 GC content plot...
#20 146.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 146.7   Drawing Coverage histogram (bin size: 1x)...
#20 146.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/coverage_histogram.pdf
#20 146.9   Drawing meta_contigs_1 coverage histogram (bin size: 1x)...
#20 147.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/meta_contigs_1_coverage_histogram.pdf
#20 147.0   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 147.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 147.1 Done.
#20 147.1 
#20 147.1 2024-11-19 11:42:01
#20 147.1 Running Contig analyzer...
#20 147.2   1  meta_contigs_1
#20 147.2   1  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
#20 147.2   1  Aligning contigs to the reference
#20 147.3   1  Analysis is finished.
#20 147.3   2  meta_contigs_2
#20 147.3   2  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 147.3   2  Aligning contigs to the reference
#20 147.4   2  Analysis is finished.
#20 147.4   Creating total report...
#20 147.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 147.5   Transposed version of total report...
#20 147.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 147.5   Creating total report...
#20 147.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 147.5   Drawing misassemblies by types plot...
#20 147.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/contigs_reports/misassemblies_plot.pdf
#20 147.6   Drawing misassemblies FRCurve plot...
#20 147.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/contigs_reports/misassemblies_frcurve_plot.pdf
#20 147.7 Done.
#20 147.7 
#20 147.7 2024-11-19 11:42:02
#20 147.7 Running NA-NGA calculation...
#20 147.8   1  meta_contigs_1, Largest alignment = 15991, NA50 = 10840, LA50 = 3
#20 147.8   2  meta_contigs_2, Largest alignment = 12715, NA50 = 10840, LA50 = 3
#20 147.8   Drawing cumulative plot...
#20 147.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/aligned_stats/cumulative_plot.pdf
#20 147.9   Drawing NAx plot...
#20 148.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/aligned_stats/NAx_plot.pdf
#20 148.1   Drawing NGAx plot...
#20 148.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/aligned_stats/NGAx_plot.pdf
#20 148.2 Done.
#20 148.2 
#20 148.2 2024-11-19 11:42:02
#20 148.2 Running Genome analyzer...
#20 148.3   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 148.3 
#20 148.3   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 148.3   1  meta_contigs_1
#20 148.5   1  Analysis is finished.
#20 148.5   2  meta_contigs_2
#20 148.6   2  Analysis is finished.
#20 148.6   Drawing Genome fraction, % histogram...
#20 148.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/genome_stats/genome_fraction_histogram.pdf
#20 148.7 Done.
#20 148.7 
#20 148.7 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 148.7 
#20 148.7 2024-11-19 11:42:03
#20 148.7 Creating large visual summaries...
#20 148.7 This may take a while: press Ctrl-C to skip this step..
#20 148.7   1 of 2: Creating PDF with all tables and plots...
#20 150.3   2 of 2: Creating Icarus viewers...
#20 150.3 Done
#20 150.3 
#20 150.3 2024-11-19 11:42:04
#20 150.3 RESULTS:
#20 150.3   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/report.txt, report.tsv, and report.tex
#20 150.3   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 150.3   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/report.html
#20 150.3   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/report.pdf
#20 150.3   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_delbrueckii_subsp._bulgaricus/icarus.html
#20 150.3 
#20 150.3 Starting quast.py for the contigs aligned to Lactobacillus_modestisalitolerans... (logging to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/quast.log)
#20 150.3 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_modestisalitolerans.fasta /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_modestisalitolerans.fasta -R /data/quast_test_output/quast_corrected_input/Lactobacillus_modestisalitolerans.fasta -o /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans --labels "meta_contigs_1, meta_contigs_2"
#20 150.3 
#20 150.3 Started: 2024-11-19 11:42:04
#20 150.3 
#20 150.3 Logging to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/quast.log
#20 150.3 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 150.3 
#20 150.3 CWD: /data
#20 150.3 Main parameters: 
#20 150.3   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 150.3   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 150.3 
#20 150.3 Reference:
#20 150.3   /data/quast_test_output/quast_corrected_input/Lactobacillus_modestisalitolerans.fasta ==> Lactobacillus_modestisalitolerans
#20 150.3 
#20 150.3 Contigs:
#20 150.3   Pre-processing...
#20 150.3   1  /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_modestisalitolerans.fasta ==> meta_contigs_1
#20 150.3   2  /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_modestisalitolerans.fasta ==> meta_contigs_2
#20 150.3 
#20 150.3 2024-11-19 11:42:04
#20 150.3 Running Basic statistics processor...
#20 150.5   Reference genome:
#20 150.5     Lactobacillus_modestisalitolerans.fasta, length = 2749234, num fragments = 37, GC % = 48.63
#20 150.5 WARNING:   Reference genome is fragmented. You may consider rerunning QUAST using --fragmented option. QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from # misassemblies).
#20 150.5   Contig files: 
#20 150.5     1  meta_contigs_1
#20 150.5     2  meta_contigs_2
#20 150.5   Calculating N50 and L50...
#20 150.5     1  meta_contigs_1, N50 = 1152, L50 = 1, auN = 1152.0, Total length = 1152, GC % = 50.88, # N's per 100 kbp =  1736.11
#20 150.5     2  meta_contigs_2, N50 = 763, L50 = 1, auN = 763.0, Total length = 763, GC % = 49.80, # N's per 100 kbp =  0.00
#20 150.5   Drawing Nx plot...
#20 150.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/Nx_plot.pdf
#20 150.6   Drawing NGx plot...
#20 150.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/NGx_plot.pdf
#20 150.7   Drawing cumulative plot...
#20 150.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/cumulative_plot.pdf
#20 150.8   Drawing GC content plot...
#20 150.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/GC_content_plot.pdf
#20 150.9   Drawing meta_contigs_1 GC content plot...
#20 151.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 151.0   Drawing meta_contigs_2 GC content plot...
#20 151.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 151.1   Drawing Coverage histogram (bin size: 1x)...
#20 151.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/coverage_histogram.pdf
#20 151.3   Drawing meta_contigs_1 coverage histogram (bin size: 1x)...
#20 151.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/meta_contigs_1_coverage_histogram.pdf
#20 151.4   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 151.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 151.5 Done.
#20 151.5 
#20 151.5 2024-11-19 11:42:06
#20 151.5 Running Contig analyzer...
#20 151.7   1  meta_contigs_1
#20 151.7   1  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
#20 151.7   1  Aligning contigs to the reference
#20 151.8   1  Analysis is finished.
#20 151.8   2  meta_contigs_2
#20 151.8   2  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 151.8   2  Aligning contigs to the reference
#20 151.9   2  Analysis is finished.
#20 151.9   Creating total report...
#20 151.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 151.9   Transposed version of total report...
#20 151.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 151.9   Creating total report...
#20 151.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 151.9   Drawing misassemblies by types plot...
#20 152.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/contigs_reports/misassemblies_plot.pdf
#20 152.0   Drawing misassemblies FRCurve plot...
#20 152.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/contigs_reports/misassemblies_frcurve_plot.pdf
#20 152.1 Done.
#20 152.1 
#20 152.1 2024-11-19 11:42:06
#20 152.1 Running NA-NGA calculation...
#20 152.1   1  meta_contigs_1, Largest alignment = 285, NA50 = None, LA50 = None
#20 152.1   2  meta_contigs_2, Largest alignment = 402, NA50 = 402, LA50 = 1
#20 152.2   Drawing cumulative plot...
#20 152.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/aligned_stats/cumulative_plot.pdf
#20 152.3   Drawing NAx plot...
#20 152.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/aligned_stats/NAx_plot.pdf
#20 152.4   Drawing NGAx plot...
#20 152.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/aligned_stats/NGAx_plot.pdf
#20 152.5 Done.
#20 152.5 
#20 152.5 2024-11-19 11:42:07
#20 152.5 Running Genome analyzer...
#20 152.7   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 152.7 
#20 152.7   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 152.7   1  meta_contigs_1
#20 152.9   1  Analysis is finished.
#20 152.9   2  meta_contigs_2
#20 153.2   2  Analysis is finished.
#20 153.2   Drawing Genome fraction, % histogram...
#20 153.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/genome_stats/genome_fraction_histogram.pdf
#20 153.3 Done.
#20 153.3 
#20 153.3 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 153.3 
#20 153.3 2024-11-19 11:42:07
#20 153.3 Creating large visual summaries...
#20 153.3 This may take a while: press Ctrl-C to skip this step..
#20 153.3   1 of 2: Creating PDF with all tables and plots...
#20 154.8   2 of 2: Creating Icarus viewers...
#20 154.9 Done
#20 154.9 
#20 154.9 2024-11-19 11:42:09
#20 154.9 RESULTS:
#20 154.9   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/report.txt, report.tsv, and report.tex
#20 154.9   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 154.9   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/report.html
#20 154.9   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/report.pdf
#20 154.9   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_modestisalitolerans/icarus.html
#20 154.9 
#20 154.9 Starting quast.py for the contigs aligned to Lactobacillus_pentosus... (logging to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/quast.log)
#20 154.9 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_pentosus.fasta /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_pentosus.fasta -R /data/quast_test_output/quast_corrected_input/Lactobacillus_pentosus.fasta -o /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus --labels "meta_contigs_1, meta_contigs_2"
#20 154.9 
#20 154.9 Started: 2024-11-19 11:42:09
#20 154.9 
#20 154.9 Logging to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/quast.log
#20 154.9 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 154.9 
#20 154.9 CWD: /data
#20 154.9 Main parameters: 
#20 154.9   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 154.9   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 154.9 
#20 154.9 Reference:
#20 154.9   /data/quast_test_output/quast_corrected_input/Lactobacillus_pentosus.fasta ==> Lactobacillus_pentosus
#20 154.9 
#20 154.9 Contigs:
#20 154.9   Pre-processing...
#20 154.9   1  /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_pentosus.fasta ==> meta_contigs_1
#20 154.9   2  /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_pentosus.fasta ==> meta_contigs_2
#20 154.9 
#20 154.9 2024-11-19 11:42:09
#20 154.9 Running Basic statistics processor...
#20 155.1   Reference genome:
#20 155.1     Lactobacillus_pentosus.fasta, length = 3702061, num fragments = 4, GC % = 46.19
#20 155.1   Contig files: 
#20 155.1     1  meta_contigs_1
#20 155.1     2  meta_contigs_2
#20 155.1   Calculating N50 and L50...
#20 155.1     1  meta_contigs_1, N50 = 48458, L50 = 1, auN = 46697.7, Total length = 50324, GC % = 45.77, # N's per 100 kbp =  39.74
#20 155.1     2  meta_contigs_2, N50 = 49658, L50 = 1, auN = 48245.0, Total length = 51135, GC % = 45.73, # N's per 100 kbp =  0.00
#20 155.1   Drawing Nx plot...
#20 155.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/Nx_plot.pdf
#20 155.2   Drawing NGx plot...
#20 155.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/NGx_plot.pdf
#20 155.3   Drawing cumulative plot...
#20 155.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/cumulative_plot.pdf
#20 155.4   Drawing GC content plot...
#20 155.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/GC_content_plot.pdf
#20 155.5   Drawing meta_contigs_1 GC content plot...
#20 155.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 155.7   Drawing meta_contigs_2 GC content plot...
#20 155.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 155.8   Drawing Coverage histogram (bin size: 1x)...
#20 155.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/coverage_histogram.pdf
#20 155.9   Drawing meta_contigs_1 coverage histogram (bin size: 1x)...
#20 156.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/meta_contigs_1_coverage_histogram.pdf
#20 156.0   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 156.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 156.1 Done.
#20 156.1 
#20 156.1 2024-11-19 11:42:10
#20 156.1 Running Contig analyzer...
#20 156.3   1  meta_contigs_1
#20 156.3   1  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
#20 156.3   1  Aligning contigs to the reference
#20 156.4   1  Analysis is finished.
#20 156.4   2  meta_contigs_2
#20 156.4   2  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 156.4   2  Aligning contigs to the reference
#20 156.6   2  Analysis is finished.
#20 156.6   Creating total report...
#20 156.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 156.7   Transposed version of total report...
#20 156.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 156.7   Creating total report...
#20 156.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 156.7   Drawing misassemblies by types plot...
#20 156.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/contigs_reports/misassemblies_plot.pdf
#20 156.8   Drawing misassemblies FRCurve plot...
#20 157.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/contigs_reports/misassemblies_frcurve_plot.pdf
#20 157.0 Done.
#20 157.0 
#20 157.0 2024-11-19 11:42:11
#20 157.0 Running NA-NGA calculation...
#20 157.0   1  meta_contigs_1, Largest alignment = 812, NA50 = None, LA50 = None
#20 157.0   2  meta_contigs_2, Largest alignment = 812, NA50 = None, LA50 = None
#20 157.0   Drawing cumulative plot...
#20 157.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/aligned_stats/cumulative_plot.pdf
#20 157.1   Drawing NAx plot...
#20 157.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/aligned_stats/NAx_plot.pdf
#20 157.3   Drawing NGAx plot...
#20 157.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/aligned_stats/NGAx_plot.pdf
#20 157.4 Done.
#20 157.4 
#20 157.4 2024-11-19 11:42:12
#20 157.4 Running Genome analyzer...
#20 157.6   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 157.6 
#20 157.6   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 157.6   1  meta_contigs_1
#20 157.9   1  Analysis is finished.
#20 157.9   2  meta_contigs_2
#20 158.3   2  Analysis is finished.
#20 158.3   Drawing Genome fraction, % histogram...
#20 158.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/genome_stats/genome_fraction_histogram.pdf
#20 158.3 Done.
#20 158.3 
#20 158.3 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 158.4 
#20 158.4 2024-11-19 11:42:13
#20 158.4 Creating large visual summaries...
#20 158.4 This may take a while: press Ctrl-C to skip this step..
#20 158.4   1 of 2: Creating PDF with all tables and plots...
#20 159.9   2 of 2: Creating Icarus viewers...
#20 159.9 Done
#20 159.9 
#20 159.9 2024-11-19 11:42:14
#20 159.9 RESULTS:
#20 159.9   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/report.txt, report.tsv, and report.tex
#20 159.9   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 160.0   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/report.html
#20 160.0   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/report.pdf
#20 160.0   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_pentosus/icarus.html
#20 160.0 
#20 160.0 Starting quast.py for the contigs aligned to Lactobacillus_psittaci... (logging to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/quast.log)
#20 160.0 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_psittaci.fasta /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_psittaci.fasta -R /data/quast_test_output/quast_corrected_input/Lactobacillus_psittaci.fasta -o /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci --labels "meta_contigs_1, meta_contigs_2"
#20 160.0 
#20 160.0 Started: 2024-11-19 11:42:14
#20 160.0 
#20 160.0 Logging to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/quast.log
#20 160.0 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 160.0 
#20 160.0 CWD: /data
#20 160.0 Main parameters: 
#20 160.0   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 160.0   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 160.0 
#20 160.0 Reference:
#20 160.0   /data/quast_test_output/quast_corrected_input/Lactobacillus_psittaci.fasta ==> Lactobacillus_psittaci
#20 160.0 
#20 160.0 Contigs:
#20 160.0   Pre-processing...
#20 160.0   1  /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_psittaci.fasta ==> meta_contigs_1
#20 160.0   2  /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_psittaci.fasta ==> meta_contigs_2
#20 160.0 
#20 160.0 2024-11-19 11:42:14
#20 160.0 Running Basic statistics processor...
#20 160.0   Reference genome:
#20 160.0     Lactobacillus_psittaci.fasta, length = 1542852, num fragments = 23, GC % = 35.66
#20 160.0   Contig files: 
#20 160.0     1  meta_contigs_1
#20 160.0     2  meta_contigs_2
#20 160.0   Calculating N50 and L50...
#20 160.0     1  meta_contigs_1, N50 = 27969, L50 = 1, auN = 27969.0, Total length = 27969, GC % = 40.15, # N's per 100 kbp =  7.15
#20 160.0     2  meta_contigs_2, N50 = 763, L50 = 1, auN = 763.0, Total length = 763, GC % = 49.80, # N's per 100 kbp =  0.00
#20 160.0   Drawing Nx plot...
#20 160.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/Nx_plot.pdf
#20 160.2   Drawing NGx plot...
#20 160.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/NGx_plot.pdf
#20 160.3   Drawing cumulative plot...
#20 160.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/cumulative_plot.pdf
#20 160.5   Drawing GC content plot...
#20 160.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/GC_content_plot.pdf
#20 160.6   Drawing meta_contigs_1 GC content plot...
#20 160.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 160.7   Drawing meta_contigs_2 GC content plot...
#20 160.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 160.9   Drawing Coverage histogram (bin size: 1x)...
#20 161.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/coverage_histogram.pdf
#20 161.6   Drawing meta_contigs_1 coverage histogram (bin size: 1x)...
#20 161.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/meta_contigs_1_coverage_histogram.pdf
#20 161.7   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 161.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 161.8 Done.
#20 161.8 
#20 161.8 2024-11-19 11:42:16
#20 161.8 Running Contig analyzer...
#20 161.9   1  meta_contigs_1
#20 161.9   1  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
#20 161.9   1  Aligning contigs to the reference
#20 162.0   1  Analysis is finished.
#20 162.0   2  meta_contigs_2
#20 162.0   2  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 162.0   2  Aligning contigs to the reference
#20 162.0   2  Analysis is finished.
#20 162.0   Creating total report...
#20 162.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 162.0   Transposed version of total report...
#20 162.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 162.1   Creating total report...
#20 162.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 162.1   Drawing misassemblies by types plot...
#20 162.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/contigs_reports/misassemblies_plot.pdf
#20 162.1   Drawing misassemblies FRCurve plot...
#20 162.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/contigs_reports/misassemblies_frcurve_plot.pdf
#20 162.3 Done.
#20 162.3 
#20 162.3 2024-11-19 11:42:16
#20 162.3 Running NA-NGA calculation...
#20 162.3   1  meta_contigs_1, Largest alignment = 394, NA50 = None, LA50 = None
#20 162.3   2  meta_contigs_2, Largest alignment = 397, NA50 = 397, LA50 = 1
#20 162.3   Drawing cumulative plot...
#20 162.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/aligned_stats/cumulative_plot.pdf
#20 162.4   Drawing NAx plot...
#20 162.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/aligned_stats/NAx_plot.pdf
#20 162.6   Drawing NGAx plot...
#20 162.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/aligned_stats/NGAx_plot.pdf
#20 162.7 Done.
#20 162.7 
#20 162.7 2024-11-19 11:42:17
#20 162.7 Running Genome analyzer...
#20 162.8   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 162.8 
#20 162.8   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 162.8   1  meta_contigs_1
#20 162.9   1  Analysis is finished.
#20 162.9   2  meta_contigs_2
#20 163.0   2  Analysis is finished.
#20 163.0   Drawing Genome fraction, % histogram...
#20 163.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/genome_stats/genome_fraction_histogram.pdf
#20 163.1 Done.
#20 163.1 
#20 163.1 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 163.2 
#20 163.2 2024-11-19 11:42:17
#20 163.2 Creating large visual summaries...
#20 163.2 This may take a while: press Ctrl-C to skip this step..
#20 163.2   1 of 2: Creating PDF with all tables and plots...
#20 164.8   2 of 2: Creating Icarus viewers...
#20 164.9 Done
#20 164.9 
#20 164.9 2024-11-19 11:42:19
#20 164.9 RESULTS:
#20 164.9   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/report.txt, report.tsv, and report.tex
#20 164.9   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 164.9   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/report.html
#20 164.9   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/report.pdf
#20 164.9   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_psittaci/icarus.html
#20 164.9 
#20 164.9 Starting quast.py for the contigs aligned to Lactobacillus_reuteri... (logging to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/quast.log)
#20 164.9 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_reuteri.fasta /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_reuteri.fasta -R /data/quast_test_output/quast_corrected_input/Lactobacillus_reuteri.fasta -o /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri --labels "meta_contigs_1, meta_contigs_2"
#20 164.9 
#20 164.9 Started: 2024-11-19 11:42:19
#20 164.9 
#20 164.9 Logging to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/quast.log
#20 164.9 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 164.9 
#20 164.9 CWD: /data
#20 164.9 Main parameters: 
#20 164.9   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 164.9   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 164.9 
#20 164.9 Reference:
#20 164.9   /data/quast_test_output/quast_corrected_input/Lactobacillus_reuteri.fasta ==> Lactobacillus_reuteri
#20 164.9 
#20 164.9 Contigs:
#20 164.9   Pre-processing...
#20 164.9   1  /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_reuteri.fasta ==> meta_contigs_1
#20 164.9   2  /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_reuteri.fasta ==> meta_contigs_2
#20 164.9 
#20 164.9 2024-11-19 11:42:19
#20 164.9 Running Basic statistics processor...
#20 165.0   Reference genome:
#20 165.0     Lactobacillus_reuteri.fasta, length = 2031507, num fragments = 1, GC % = 39.02
#20 165.0   Contig files: 
#20 165.0     1  meta_contigs_1
#20 165.0     2  meta_contigs_2
#20 165.0   Calculating N50 and L50...
#20 165.0     1  meta_contigs_1, N50 = 17535, L50 = 2, auN = 19706.4, Total length = 61785, GC % = 41.24, # N's per 100 kbp =  21.04
#20 165.0     2  meta_contigs_2, N50 = 27260, L50 = 1, auN = 22002.0, Total length = 45633, GC % = 40.60, # N's per 100 kbp =  0.00
#20 165.0   Drawing Nx plot...
#20 165.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/Nx_plot.pdf
#20 165.1   Drawing NGx plot...
#20 165.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/NGx_plot.pdf
#20 165.2   Drawing cumulative plot...
#20 165.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/cumulative_plot.pdf
#20 165.4   Drawing GC content plot...
#20 165.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/GC_content_plot.pdf
#20 165.5   Drawing meta_contigs_1 GC content plot...
#20 165.7     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 165.7   Drawing meta_contigs_2 GC content plot...
#20 165.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 165.8   Drawing Coverage histogram (bin size: 1x)...
#20 165.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/coverage_histogram.pdf
#20 165.9   Drawing meta_contigs_1 coverage histogram (bin size: 1x)...
#20 166.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/meta_contigs_1_coverage_histogram.pdf
#20 166.1   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 166.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 166.2 Done.
#20 166.2 
#20 166.2 2024-11-19 11:42:20
#20 166.2 Running Contig analyzer...
#20 166.3   1  meta_contigs_1
#20 166.3   1  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
#20 166.3   1  Aligning contigs to the reference
#20 166.4   1  Analysis is finished.
#20 166.4   2  meta_contigs_2
#20 166.4   2  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 166.4   2  Aligning contigs to the reference
#20 166.5   2  Analysis is finished.
#20 166.5   Creating total report...
#20 166.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 166.6   Transposed version of total report...
#20 166.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 166.6   Creating total report...
#20 166.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 166.6   Drawing misassemblies by types plot...
#20 166.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/contigs_reports/misassemblies_plot.pdf
#20 166.8   Drawing misassemblies FRCurve plot...
#20 166.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/contigs_reports/misassemblies_frcurve_plot.pdf
#20 166.9 Done.
#20 166.9 
#20 166.9 2024-11-19 11:42:21
#20 166.9 Running NA-NGA calculation...
#20 166.9   1  meta_contigs_1, Largest alignment = 25049, NA50 = 7531, LA50 = 2
#20 166.9   2  meta_contigs_2, Largest alignment = 25049, NA50 = 25049, LA50 = 1
#20 166.9   Drawing cumulative plot...
#20 167.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/aligned_stats/cumulative_plot.pdf
#20 167.1   Drawing NAx plot...
#20 167.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/aligned_stats/NAx_plot.pdf
#20 167.2   Drawing NGAx plot...
#20 167.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/aligned_stats/NGAx_plot.pdf
#20 167.3 Done.
#20 167.3 
#20 167.3 2024-11-19 11:42:21
#20 167.3 Running Genome analyzer...
#20 167.4   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 167.4 
#20 167.4   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 167.4   1  meta_contigs_1
#20 167.6   1  Analysis is finished.
#20 167.6   2  meta_contigs_2
#20 167.8   2  Analysis is finished.
#20 167.8   Drawing Genome fraction, % histogram...
#20 167.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/genome_stats/genome_fraction_histogram.pdf
#20 167.8 Done.
#20 167.8 
#20 167.8 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 167.9 
#20 167.9 2024-11-19 11:42:22
#20 167.9 Creating large visual summaries...
#20 167.9 This may take a while: press Ctrl-C to skip this step..
#20 167.9   1 of 2: Creating PDF with all tables and plots...
#20 169.3   2 of 2: Creating Icarus viewers...
#20 169.3 Done
#20 169.3 
#20 169.3 2024-11-19 11:42:23
#20 169.3 RESULTS:
#20 169.3   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/report.txt, report.tsv, and report.tex
#20 169.3   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 169.3   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/report.html
#20 169.3   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/report.pdf
#20 169.3   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri/icarus.html
#20 169.3 
#20 169.3 Starting quast.py for the contigs aligned to Lactobacillus_reuteri_TD1... (logging to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/quast.log)
#20 169.3 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_reuteri_TD1.fasta /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_reuteri_TD1.fasta -R /data/quast_test_output/quast_corrected_input/Lactobacillus_reuteri_TD1.fasta -o /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1 --labels "meta_contigs_1, meta_contigs_2"
#20 169.3 
#20 169.3 Started: 2024-11-19 11:42:23
#20 169.3 
#20 169.3 Logging to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/quast.log
#20 169.3 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 169.3 
#20 169.3 CWD: /data
#20 169.3 Main parameters: 
#20 169.3   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 169.3   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 169.3 
#20 169.3 Reference:
#20 169.3   /data/quast_test_output/quast_corrected_input/Lactobacillus_reuteri_TD1.fasta ==> Lactobacillus_reuteri_TD1
#20 169.3 
#20 169.3 Contigs:
#20 169.3   Pre-processing...
#20 169.3   1  /data/quast_test_output/quast_corrected_input/meta_contigs_1_to_Lactobacillus_reuteri_TD1.fasta ==> meta_contigs_1
#20 169.3   2  /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Lactobacillus_reuteri_TD1.fasta ==> meta_contigs_2
#20 169.3 
#20 169.3 2024-11-19 11:42:23
#20 169.3 Running Basic statistics processor...
#20 169.4   Reference genome:
#20 169.4     Lactobacillus_reuteri_TD1.fasta, length = 2145445, num fragments = 1, GC % = 38.78
#20 169.4   Contig files: 
#20 169.4     1  meta_contigs_1
#20 169.4     2  meta_contigs_2
#20 169.4   Calculating N50 and L50...
#20 169.4     1  meta_contigs_1, N50 = 17535, L50 = 2, auN = 18007.5, Total length = 69110, GC % = 40.75, # N's per 100 kbp =  18.81
#20 169.4     2  meta_contigs_2, N50 = 16099, L50 = 2, auN = 18447.2, Total length = 62961, GC % = 40.75, # N's per 100 kbp =  0.00
#20 169.4   Drawing Nx plot...
#20 169.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/Nx_plot.pdf
#20 169.5   Drawing NGx plot...
#20 169.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/NGx_plot.pdf
#20 169.6   Drawing cumulative plot...
#20 169.8     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/cumulative_plot.pdf
#20 169.8   Drawing GC content plot...
#20 169.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/GC_content_plot.pdf
#20 169.9   Drawing meta_contigs_1 GC content plot...
#20 170.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 170.0   Drawing meta_contigs_2 GC content plot...
#20 170.1     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 170.1   Drawing Coverage histogram (bin size: 4x)...
#20 170.3     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/coverage_histogram.pdf
#20 170.3   Drawing meta_contigs_1 coverage histogram (bin size: 4x)...
#20 170.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/meta_contigs_1_coverage_histogram.pdf
#20 170.4   Drawing meta_contigs_2 coverage histogram (bin size: 4x)...
#20 170.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 170.5 Done.
#20 170.5 
#20 170.5 2024-11-19 11:42:25
#20 170.5 Running Contig analyzer...
#20 170.6   1  meta_contigs_1
#20 170.6   1  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/contigs_reports/contigs_report_meta_contigs_1.stdout and contigs_report_meta_contigs_1.stderr...
#20 170.6   1  Aligning contigs to the reference
#20 170.8   1  Analysis is finished.
#20 170.8   2  meta_contigs_2
#20 170.8   2  Logging to files /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 170.8   2  Aligning contigs to the reference
#20 170.9   2  Analysis is finished.
#20 170.9   Creating total report...
#20 170.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 170.9   Transposed version of total report...
#20 170.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 170.9   Creating total report...
#20 170.9     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 170.9   Drawing misassemblies by types plot...
#20 171.0     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/contigs_reports/misassemblies_plot.pdf
#20 171.0   Drawing misassemblies FRCurve plot...
#20 171.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/contigs_reports/misassemblies_frcurve_plot.pdf
#20 171.2 Done.
#20 171.2 
#20 171.2 2024-11-19 11:42:25
#20 171.2 Running NA-NGA calculation...
#20 171.2   1  meta_contigs_1, Largest alignment = 25033, NA50 = 10380, LA50 = 2
#20 171.2   2  meta_contigs_2, Largest alignment = 25033, NA50 = 10380, LA50 = 2
#20 171.2   Drawing cumulative plot...
#20 171.4     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/aligned_stats/cumulative_plot.pdf
#20 171.4   Drawing NAx plot...
#20 171.5     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/aligned_stats/NAx_plot.pdf
#20 171.5   Drawing NGAx plot...
#20 171.6     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/aligned_stats/NGAx_plot.pdf
#20 171.6 Done.
#20 171.6 
#20 171.6 2024-11-19 11:42:26
#20 171.6 Running Genome analyzer...
#20 171.7   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 171.7 
#20 171.7   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 171.7   1  meta_contigs_1
#20 171.9   1  Analysis is finished.
#20 171.9   2  meta_contigs_2
#20 172.1   2  Analysis is finished.
#20 172.1   Drawing Genome fraction, % histogram...
#20 172.2     saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/genome_stats/genome_fraction_histogram.pdf
#20 172.2 Done.
#20 172.2 
#20 172.2 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 172.2 
#20 172.2 2024-11-19 11:42:26
#20 172.2 Creating large visual summaries...
#20 172.2 This may take a while: press Ctrl-C to skip this step..
#20 172.2   1 of 2: Creating PDF with all tables and plots...
#20 173.8   2 of 2: Creating Icarus viewers...
#20 173.9 Done
#20 173.9 
#20 173.9 2024-11-19 11:42:28
#20 173.9 RESULTS:
#20 173.9   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/report.txt, report.tsv, and report.tex
#20 173.9   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 173.9   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/report.html
#20 173.9   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/report.pdf
#20 173.9   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Lactobacillus_reuteri_TD1/icarus.html
#20 173.9 
#20 173.9 Starting quast.py for the contigs aligned to Streptococcus_agalactiae_SS1219... (logging to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/quast.log)
#20 173.9 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Streptococcus_agalactiae_SS1219.fasta -R /data/quast_test_output/quast_corrected_input/Streptococcus_agalactiae_SS1219.fasta -o /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219 --labels meta_contigs_2
#20 173.9 
#20 173.9 Started: 2024-11-19 11:42:28
#20 173.9 
#20 173.9 Logging to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/quast.log
#20 173.9 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 173.9 
#20 173.9 CWD: /data
#20 173.9 Main parameters: 
#20 173.9   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 173.9   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 173.9 
#20 173.9 Reference:
#20 173.9   /data/quast_test_output/quast_corrected_input/Streptococcus_agalactiae_SS1219.fasta ==> Streptococcus_agalactiae_SS1219
#20 173.9 
#20 173.9 Contigs:
#20 173.9   Pre-processing...
#20 173.9   /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Streptococcus_agalactiae_SS1219.fasta ==> meta_contigs_2
#20 173.9 
#20 173.9 2024-11-19 11:42:28
#20 173.9 Running Basic statistics processor...
#20 174.0   Reference genome:
#20 174.0     Streptococcus_agalactiae_SS1219.fasta, length = 1801666, num fragments = 70, GC % = 35.29
#20 174.0 WARNING:   Reference genome is fragmented. You may consider rerunning QUAST using --fragmented option. QUAST will try to detect misassemblies caused by the fragmentation and mark them fake (will be excluded from # misassemblies).
#20 174.0   Contig files: 
#20 174.0     meta_contigs_2
#20 174.0   Calculating N50 and L50...
#20 174.0     meta_contigs_2, N50 = 763, L50 = 1, auN = 763.0, Total length = 763, GC % = 49.80, # N's per 100 kbp =  0.00
#20 174.0   Drawing Nx plot...
#20 174.1     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/basic_stats/Nx_plot.pdf
#20 174.1   Drawing NGx plot...
#20 174.2     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/basic_stats/NGx_plot.pdf
#20 174.2   Drawing cumulative plot...
#20 174.3     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/basic_stats/cumulative_plot.pdf
#20 174.3   Drawing GC content plot...
#20 174.5     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/basic_stats/GC_content_plot.pdf
#20 174.5   Drawing meta_contigs_2 GC content plot...
#20 174.6     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 174.6   Drawing Coverage histogram (bin size: 1x)...
#20 174.8     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/basic_stats/coverage_histogram.pdf
#20 174.8   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 174.9     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 174.9 Done.
#20 174.9 
#20 174.9 2024-11-19 11:42:29
#20 174.9 Running Contig analyzer...
#20 175.0   meta_contigs_2
#20 175.0   Logging to files /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 175.0   Aligning contigs to the reference
#20 175.1   Analysis is finished.
#20 175.1   Creating total report...
#20 175.1     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 175.1   Transposed version of total report...
#20 175.1     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 175.1   Creating total report...
#20 175.1     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 175.1   Drawing misassemblies by types plot...
#20 175.2     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/contigs_reports/misassemblies_plot.pdf
#20 175.2   Drawing misassemblies FRCurve plot...
#20 175.3     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/contigs_reports/misassemblies_frcurve_plot.pdf
#20 175.3 Done.
#20 175.3 
#20 175.3 2024-11-19 11:42:29
#20 175.3 Running NA-NGA calculation...
#20 175.3   meta_contigs_2, Largest alignment = 150, NA50 = None, LA50 = None
#20 175.3   Drawing cumulative plot...
#20 175.4     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/aligned_stats/cumulative_plot.pdf
#20 175.4   Drawing NAx plot...
#20 175.5     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/aligned_stats/NAx_plot.pdf
#20 175.5   Drawing NGAx plot...
#20 175.6     saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/aligned_stats/NGAx_plot.pdf
#20 175.6 Done.
#20 175.6 
#20 175.6 2024-11-19 11:42:30
#20 175.6 Running Genome analyzer...
#20 175.7   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 175.7 
#20 175.7   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 175.7   meta_contigs_2
#20 175.8   Analysis is finished.
#20 175.8   Skipping drawing Genome fraction, % histogram... (less than 2 columns histogram makes no sense)
#20 175.8 Done.
#20 175.8 
#20 175.8 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 175.9 
#20 175.9 2024-11-19 11:42:30
#20 175.9 Creating large visual summaries...
#20 175.9 This may take a while: press Ctrl-C to skip this step..
#20 175.9   1 of 2: Creating PDF with all tables and plots...
#20 176.9   2 of 2: Creating Icarus viewers...
#20 176.9 Done
#20 176.9 
#20 176.9 2024-11-19 11:42:31
#20 176.9 RESULTS:
#20 176.9   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/report.txt, report.tsv, and report.tex
#20 176.9   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 176.9   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/report.html
#20 176.9   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/report.pdf
#20 176.9   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Streptococcus_agalactiae_SS1219/icarus.html
#20 176.9 
#20 176.9 Starting quast.py for the contigs aligned to Streptococcus_pneumoniae... (logging to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/quast.log)
#20 176.9 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Streptococcus_pneumoniae.fasta -R /data/quast_test_output/quast_corrected_input/Streptococcus_pneumoniae.fasta -o /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae --labels meta_contigs_2
#20 176.9 
#20 176.9 Started: 2024-11-19 11:42:31
#20 176.9 
#20 176.9 Logging to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/quast.log
#20 176.9 NOTICE: Maximum number of threads is set to 1 (use --threads option to set it manually)
#20 176.9 
#20 176.9 CWD: /data
#20 176.9 Main parameters: 
#20 176.9   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 176.9   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 176.9 
#20 176.9 Reference:
#20 176.9   /data/quast_test_output/quast_corrected_input/Streptococcus_pneumoniae.fasta ==> Streptococcus_pneumoniae
#20 176.9 
#20 176.9 Contigs:
#20 176.9   Pre-processing...
#20 177.0   /data/quast_test_output/quast_corrected_input/meta_contigs_2_to_Streptococcus_pneumoniae.fasta ==> meta_contigs_2
#20 177.0 
#20 177.0 2024-11-19 11:42:31
#20 177.0 Running Basic statistics processor...
#20 177.1   Reference genome:
#20 177.1     Streptococcus_pneumoniae.fasta, length = 2096290, num fragments = 1, GC % = 39.67
#20 177.1   Contig files: 
#20 177.1     meta_contigs_2
#20 177.1   Calculating N50 and L50...
#20 177.1     meta_contigs_2, N50 = 763, L50 = 1, auN = 763.0, Total length = 763, GC % = 49.80, # N's per 100 kbp =  0.00
#20 177.1   Drawing Nx plot...
#20 177.2     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/basic_stats/Nx_plot.pdf
#20 177.2   Drawing NGx plot...
#20 177.3     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/basic_stats/NGx_plot.pdf
#20 177.3   Drawing cumulative plot...
#20 177.5     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/basic_stats/cumulative_plot.pdf
#20 177.5   Drawing GC content plot...
#20 177.6     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/basic_stats/GC_content_plot.pdf
#20 177.6   Drawing meta_contigs_2 GC content plot...
#20 177.7     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 177.7   Drawing Coverage histogram (bin size: 1x)...
#20 177.8     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/basic_stats/coverage_histogram.pdf
#20 177.8   Drawing meta_contigs_2 coverage histogram (bin size: 1x)...
#20 178.0     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/basic_stats/meta_contigs_2_coverage_histogram.pdf
#20 178.0 Done.
#20 178.0 
#20 178.0 2024-11-19 11:42:32
#20 178.0 Running Contig analyzer...
#20 178.1   meta_contigs_2
#20 178.1   Logging to files /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/contigs_reports/contigs_report_meta_contigs_2.stdout and contigs_report_meta_contigs_2.stderr...
#20 178.1   Aligning contigs to the reference
#20 178.2   Analysis is finished.
#20 178.2   Creating total report...
#20 178.2     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
#20 178.2   Transposed version of total report...
#20 178.2     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
#20 178.2   Creating total report...
#20 178.2     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
#20 178.2   Drawing misassemblies by types plot...
#20 178.3     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/contigs_reports/misassemblies_plot.pdf
#20 178.3   Drawing misassemblies FRCurve plot...
#20 178.4     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/contigs_reports/misassemblies_frcurve_plot.pdf
#20 178.4 Done.
#20 178.4 
#20 178.4 2024-11-19 11:42:33
#20 178.4 Running NA-NGA calculation...
#20 178.4   meta_contigs_2, Largest alignment = 150, NA50 = None, LA50 = None
#20 178.4   Drawing cumulative plot...
#20 178.6     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/aligned_stats/cumulative_plot.pdf
#20 178.6   Drawing NAx plot...
#20 178.7     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/aligned_stats/NAx_plot.pdf
#20 178.7   Drawing NGAx plot...
#20 178.8     saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/aligned_stats/NGAx_plot.pdf
#20 178.8 Done.
#20 178.8 
#20 178.8 2024-11-19 11:42:33
#20 178.8 Running Genome analyzer...
#20 178.9   NOTICE: No file with genomic features were provided. Use the --features option if you want to specify it.
#20 178.9 
#20 178.9   NOTICE: No file with operons were provided. Use the -O option if you want to specify it.
#20 178.9   meta_contigs_2
#20 179.2   Analysis is finished.
#20 179.2   Skipping drawing Genome fraction, % histogram... (less than 2 columns histogram makes no sense)
#20 179.2 Done.
#20 179.2 
#20 179.2 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 179.2 
#20 179.2 2024-11-19 11:42:33
#20 179.2 Creating large visual summaries...
#20 179.2 This may take a while: press Ctrl-C to skip this step..
#20 179.2   1 of 2: Creating PDF with all tables and plots...
#20 180.2   2 of 2: Creating Icarus viewers...
#20 180.3 Done
#20 180.3 
#20 180.3 2024-11-19 11:42:34
#20 180.3 RESULTS:
#20 180.3   Text versions of total report are saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/report.txt, report.tsv, and report.tex
#20 180.3   Text versions of transposed total report are saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 180.3   HTML version (interactive tables and plots) is saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/report.html
#20 180.3   PDF version (tables and plots) is saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/report.pdf
#20 180.3   Icarus (contig browser) is saved to /data/quast_test_output/runs_per_reference/Streptococcus_pneumoniae/icarus.html
#20 180.3 
#20 180.3 Starting quast.py for the contigs not aligned anywhere... (logging to /data/quast_test_output/not_aligned/quast.log)
#20 180.3 /quast-5.3.0/quast.py --min-identity 90.0 --colors #E31A1C,#1F78B4 --ls solid,solid --no-check-meta --contig-thresholds 1000,5000,10000,25000,50000 -t 1 /data/quast_test_output/quast_corrected_input/meta_contigs_1_not_aligned_anywhere.fasta /data/quast_test_output/quast_corrected_input/meta_contigs_2_not_aligned_anywhere.fasta -o /data/quast_test_output/not_aligned --labels "meta_contigs_1, meta_contigs_2"
#20 180.3 
#20 180.3 Started: 2024-11-19 11:42:34
#20 180.3 
#20 180.3 Logging to /data/quast_test_output/not_aligned/quast.log
#20 180.3 
#20 180.3 CWD: /data
#20 180.3 Main parameters: 
#20 180.3   MODE: meta, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 90.0, \
#20 180.3   ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000
#20 180.3 
#20 180.3 Contigs:
#20 180.3   Pre-processing...
#20 180.3   1  /data/quast_test_output/quast_corrected_input/meta_contigs_1_not_aligned_anywhere.fasta ==> meta_contigs_1
#20 180.3   2  /data/quast_test_output/quast_corrected_input/meta_contigs_2_not_aligned_anywhere.fasta ==> meta_contigs_2
#20 180.3 
#20 180.3 2024-11-19 11:42:34
#20 180.3 Running Basic statistics processor...
#20 180.3   Contig files: 
#20 180.3     1  meta_contigs_1
#20 180.3     2  meta_contigs_2
#20 180.3   Calculating N50 and L50...
#20 180.3     1  meta_contigs_1, N50 = 1610, L50 = 1, auN = 1409.0, Total length = 2730, GC % = 51.94, # N's per 100 kbp =  0.00
#20 180.3     2  meta_contigs_2, N50 = 885, L50 = 1, auN = 885.0, Total length = 885, GC % = 0.00, # N's per 100 kbp =  0.00
#20 180.3   Drawing Nx plot...
#20 180.4     saved to /data/quast_test_output/not_aligned/basic_stats/Nx_plot.pdf
#20 180.4   Drawing cumulative plot...
#20 180.5     saved to /data/quast_test_output/not_aligned/basic_stats/cumulative_plot.pdf
#20 180.5   Drawing GC content plot...
#20 180.7     saved to /data/quast_test_output/not_aligned/basic_stats/GC_content_plot.pdf
#20 180.7   Drawing meta_contigs_1 GC content plot...
#20 180.8     saved to /data/quast_test_output/not_aligned/basic_stats/meta_contigs_1_GC_content_plot.pdf
#20 180.8   Drawing meta_contigs_2 GC content plot...
#20 180.9     saved to /data/quast_test_output/not_aligned/basic_stats/meta_contigs_2_GC_content_plot.pdf
#20 180.9 Done.
#20 180.9 
#20 180.9 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
#20 181.0 
#20 181.0 2024-11-19 11:42:35
#20 181.0 Creating large visual summaries...
#20 181.0 This may take a while: press Ctrl-C to skip this step..
#20 181.0   1 of 2: Creating PDF with all tables and plots...
#20 181.5   2 of 2: Creating Icarus viewers...
#20 181.5 Done
#20 181.5 
#20 181.5 2024-11-19 11:42:36
#20 181.5 RESULTS:
#20 181.5   Text versions of total report are saved to /data/quast_test_output/not_aligned/report.txt, report.tsv, and report.tex
#20 181.5   Text versions of transposed total report are saved to /data/quast_test_output/not_aligned/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
#20 181.5   HTML version (interactive tables and plots) is saved to /data/quast_test_output/not_aligned/report.html
#20 181.5   PDF version (tables and plots) is saved to /data/quast_test_output/not_aligned/report.pdf
#20 181.5   Icarus (contig browser) is saved to /data/quast_test_output/not_aligned/icarus.html
#20 181.5 
#20 181.5 2024-11-19 11:42:36
#20 181.5 Summarizing results...
#20 181.5   Drawing # contigs metaQUAST summary plot...
#20 181.7     saved to /data/quast_test_output/summary/PDF/num_contigs.pdf
#20 181.7   Drawing Largest contig metaQUAST summary plot...
#20 181.8     saved to /data/quast_test_output/summary/PDF/Largest_contig.pdf
#20 181.8   Drawing Total length metaQUAST summary plot...
#20 182.0     saved to /data/quast_test_output/summary/PDF/Total_length.pdf
#20 182.0   Drawing Largest alignment metaQUAST summary plot...
#20 182.1     saved to /data/quast_test_output/summary/PDF/Largest_alignment.pdf
#20 182.2   Drawing Total aligned length metaQUAST summary plot...
#20 182.3     saved to /data/quast_test_output/summary/PDF/Total_aligned_length.pdf
#20 182.3   Drawing Total length (>= 1000 bp) metaQUAST summary plot...
#20 182.5     saved to /data/quast_test_output/summary/PDF/Total_length_(ge_1000_bp).pdf
#20 182.5   Drawing Total length (>= 10000 bp) metaQUAST summary plot...
#20 182.6     saved to /data/quast_test_output/summary/PDF/Total_length_(ge_10000_bp).pdf
#20 182.6   Drawing Total length (>= 50000 bp) metaQUAST summary plot...
#20 182.8     saved to /data/quast_test_output/summary/PDF/Total_length_(ge_50000_bp).pdf
#20 182.8   Drawing # misassemblies metaQUAST summary plot...
#20 183.0     saved to /data/quast_test_output/summary/PDF/num_misassemblies.pdf
#20 183.0   Drawing metaQUAST summary misassemblies plot for meta_contigs_1...
#20 183.1     saved to /data/quast_test_output/summary/PDF/meta_contigs_1_misassemblies.pdf
#20 183.1   Drawing metaQUAST summary misassemblies plot for meta_contigs_2...
#20 183.3     saved to /data/quast_test_output/summary/PDF/meta_contigs_2_misassemblies.pdf
#20 183.3   Drawing Misassembled contigs length metaQUAST summary plot...
#20 183.4     saved to /data/quast_test_output/summary/PDF/Misassembled_contigs_length.pdf
#20 183.4   Drawing # mismatches per 100 kbp metaQUAST summary plot...
#20 183.6     saved to /data/quast_test_output/summary/PDF/num_mismatches_per_100_kbp.pdf
#20 183.6   Drawing # indels per 100 kbp metaQUAST summary plot...
#20 183.8     saved to /data/quast_test_output/summary/PDF/num_indels_per_100_kbp.pdf
#20 183.8   Drawing # N's per 100 kbp metaQUAST summary plot...
#20 183.9     saved to /data/quast_test_output/summary/PDF/num_Ns_per_100_kbp.pdf
#20 183.9   Drawing Genome fraction (%) metaQUAST summary plot...
#20 184.1     saved to /data/quast_test_output/summary/PDF/Genome_fraction.pdf
#20 184.1   Drawing Duplication ratio metaQUAST summary plot...
#20 184.2     saved to /data/quast_test_output/summary/PDF/Duplication_ratio.pdf
#20 184.2   Drawing NGA50 metaQUAST summary plot...
#20 184.4     saved to /data/quast_test_output/summary/PDF/NGA50.pdf
#20 184.4   Drawing LGA50 metaQUAST summary plot...
#20 184.6     saved to /data/quast_test_output/summary/PDF/LGA50.pdf
#20 184.6 
#20 184.6   Text versions of reports and plots for each metric (for all references and assemblies) are saved to /data/quast_test_output/summary/
#20 184.6   Icarus (contig browser) is saved to /data/quast_test_output/icarus.html
#20 184.6   Drawing interactive Krona plots...
#20 184.7   Krona chart for meta_contigs_1 is saved to /data/quast_test_output/krona_charts/meta_contigs_1_taxonomy_chart.html
#20 184.7   Krona chart for meta_contigs_2 is saved to /data/quast_test_output/krona_charts/meta_contigs_2_taxonomy_chart.html
#20 184.7   Summary Krona chart is saved to /data/quast_test_output/krona_charts/summary_taxonomy_chart.html
#20 184.7   Extended version of HTML-report (for all references and assemblies) is saved to /data/quast_test_output/report.html
#20 184.7 
#20 184.7 MetaQUAST finished.
#20 184.7   Log is saved to /data/quast_test_output/metaquast.log
#20 184.7 
#20 184.7 Finished: 2024-11-19 11:42:39
#20 184.7 Elapsed time: 0:03:04.583047
#20 184.7 Total NOTICEs: 23; WARNINGs: 1; non-fatal ERRORs: 0
#20 184.7 
#20 184.7 Thank you for using QUAST!
#20 184.7 
#20 184.7 TEST PASSED with WARNINGS!
#20 DONE 184.9s

#21 [test 4/4] RUN tail -n5 ./quast_test_sv_output/quast.log &&    tail -n5 ./quast_test_lg_output/quast.log &&    tail -n5 ./quast_test_output/metaquast.log
#21 0.068 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0
#21 0.068 
#21 0.068 Thank you for using QUAST!
#21 0.068 
#21 0.068 TEST PASSED!
#21 0.069 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0
#21 0.069 
#21 0.069 Thank you for using QUAST!
#21 0.069 
#21 0.069 TEST PASSED!
#21 0.070 Total NOTICEs: 23; WARNINGs: 1; non-fatal ERRORs: 0
#21 0.070 
#21 0.070 Thank you for using QUAST!
#21 0.070 
#21 0.070 TEST PASSED with WARNINGS!
#21 DONE 0.1s

[erinyoung]

I have no changes to recommend. Thank you for putting this together!

[erinyoung]

Thank you for putting this together.

I have deployed the image built from this dockerfile to dockerhub and quay. You can check the status of the deploy at https://github.com/StaPH-B/docker-builds/actions/runs/11923462162.