/usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/EGG-INFO/scripts/quast.py --output-dir quast_results_simple --threads 6 --split-scaffolds --labels MaSuRCA,canu-erate-0.085,canu-erate-0.150 --eukaryote --large --k-mer-stats --gene-finding --conserved-genes-finding --est-ref-size 818000000 --no-icarus --no-snps masurca.final.genome.scf.fasta Deimos.pacbio.canu.contigs.erate0.085.fasta Deimos.pacbio.canu.contigs.erate0.150.fasta Version: 5.0.2 System information: OS: Linux-4.15.0-47-generic-x86_64-with-Ubuntu-18.04-bionic (linux_64) Python version: 2.7.15 CPUs number: 8 Started: 2019-05-02 17:12:22 Logging to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/quast.log CWD: /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast Main parameters: MODE: large, threads: 6, eukaryotic: true, split scaffolds: true, minimum contig length: 3000, \ minimum alignment length: 500, ambiguity: one, threshold for extensive misassembly size: 7000 Contigs: Pre-processing... 1 masurca.final.genome.scf.fasta ==> MaSuRCA 1 breaking scaffolds into contigs: 1 15828 scaffolds (MaSuRCA) were broken into 15901 contigs (MaSuRCA_broken) 2 Deimos.pacbio.canu.contigs.erate0.085.fasta ==> canu-erate-0.085 2 breaking scaffolds into contigs: 2 WARNING: nothing was broken, skipping 'canu-erate-0.085 broken' from further analysis 3 Deimos.pacbio.canu.contigs.erate0.150.fasta ==> canu-erate-0.150 3 breaking scaffolds into contigs: 3 WARNING: nothing was broken, skipping 'canu-erate-0.150 broken' from further analysis 2019-05-02 17:21:40 Running Basic statistics processor... Estimated reference length = 818000000 Contig files: 1 MaSuRCA 2 MaSuRCA_broken 3 canu-erate-0.085 4 canu-erate-0.150 Calculating N50 and L50... 1 MaSuRCA, N50 = 67531, L50 = 2729, Total length = 727692787, GC % = 34.17, # N's per 100 kbp = 1.00 2 MaSuRCA_broken, N50 = 67255, L50 = 2746, Total length = 727685487, GC % = 34.17, # N's per 100 kbp = 0.00 3 canu-erate-0.085, N50 = 27740, L50 = 5068, Total length = 529765198, GC % = 34.05, # N's per 100 kbp = 0.00 4 canu-erate-0.150, N50 = 29034, L50 = 4592, Total length = 495546873, GC % = 33.86, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/Nx_plot.pdf Drawing NGx plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/NGx_plot.pdf Drawing cumulative plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/GC_content_plot.pdf Drawing MaSuRCA GC content plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/MaSuRCA_GC_content_plot.pdf Drawing MaSuRCA_broken GC content plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/MaSuRCA_broken_GC_content_plot.pdf Drawing canu-erate-0.085 GC content plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/canu-erate-0.085_GC_content_plot.pdf Drawing canu-erate-0.150 GC content plot... saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/basic_stats/canu-erate-0.150_GC_content_plot.pdf Done. 2019-05-02 17:25:09 Running GeneMark-ES... 1 MaSuRCA 2 MaSuRCA_broken 1 perl -I /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/lib \ /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/linux_64/gmes_petap.pl \ --ES --cores 1 --sequence quast_results_simple/quast_corrected_input/MaSuRCA.fasta \ --out quast_results_simple/predicted_genes/tmpMaSuRCA > quast_results_simple/predicted_genes/MaSuRCA_genemark.stderr \ 2> quast_results_simple/predicted_genes/MaSuRCA_genemark.stderr 2 perl -I /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/lib \ /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/linux_64/gmes_petap.pl \ --ES --cores 1 --sequence quast_results_simple/quast_corrected_input/MaSuRCA_broken.fasta \ --out quast_results_simple/predicted_genes/tmpMaSuRCA_broken > quast_results_simple/predicted_genes/MaSuRCA_broken_genemark.stderr \ 2> quast_results_simple/predicted_genes/MaSuRCA_broken_genemark.stderr 3 canu-erate-0.085 3 perl -I /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/lib \ /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/linux_64/gmes_petap.pl \ --ES --cores 1 --sequence quast_results_simple/quast_corrected_input/canu_erate_0_085.fasta \ --out quast_results_simple/predicted_genes/tmpcanu_erate_0_085 > quast_results_simple/predicted_genes/canu-erate-0-085_genemark.stderr \ 2> quast_results_simple/predicted_genes/canu-erate-0-085_genemark.stderr 4 canu-erate-0.150 4 perl -I /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/lib \ /usr/local/lib/python2.7/dist-packages/quast-5.0.2-py2.7.egg/quast_libs/genemark-es/linux_64/gmes_petap.pl \ --ES --cores 1 --sequence quast_results_simple/quast_corrected_input/canu_erate_0_150.fasta \ --out quast_results_simple/predicted_genes/tmpcanu_erate_0_150 > quast_results_simple/predicted_genes/canu-erate-0-150_genemark.stderr \ 2> quast_results_simple/predicted_genes/canu-erate-0-150_genemark.stderr 4 Genes = 107071 unique, 777387 total 4 Predicted genes (GFF): /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/predicted_genes/canu-erate-0-150_genemark_genes.gff.gz 3 Genes = 114356 unique, 841573 total 3 Predicted genes (GFF): /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/predicted_genes/canu-erate-0-085_genemark_genes.gff.gz 2 Genes = 134059 unique, 1085337 total 2 Predicted genes (GFF): /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/predicted_genes/MaSuRCA_broken_genemark_genes.gff.gz 1 Genes = 133689 unique, 1084337 total 1 Predicted genes (GFF): /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/predicted_genes/MaSuRCA_genemark_genes.gff.gz Done. 2019-05-03 21:38:37 Running BUSCO... Logs and results will be saved under /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/busco_stats... Done. 2019-05-04 01:03:23 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 1: Creating PDF with all tables and plots... Done 2019-05-04 01:03:26 RESULTS: Text versions of total report are saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/report.html PDF version (tables and plots) is saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/report.pdf Log is saved to /mnt/space_158.42.124.151/internal_projects/180730_pedseral_thc/03-quast/quast_results_simple/quast.log Finished: 2019-05-04 01:03:28 Elapsed time: 1 day, 7:51:05.784196 NOTICEs: 0; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!