/Applications/bioinfo/quast-4.5/quast.py -t 8 -o /Volumes/Serine/wd/18-03-05/quast/ /Volumes/Serine/wd/18-03-05/mkfasta/duck4-10k.1.fasta.gz /Volumes/Serine/wd/18-03-05/mkfasta/duck4-10k.2.fasta.gz /Volumes/Serine/wd/18-03-05/mkfasta/duck4.1.fasta.gz /Volumes/Serine/wd/18-03-05/mkfasta/duck4.2.fasta.gz Version: 4.5 System information: OS: Darwin-14.5.0-x86_64-i386-64bit (macosx) Python version: 2.7.12 CPUs number: 8 Started: 2018-03-05 09:01:14 Logging to /Volumes/Serine/wd/18-03-05/quast/quast.log NOTICE: Output directory already exists. Existing Nucmer alignments can be used CWD: /Users/sr320/git-repos/nb-2018/P_generosa Main parameters: Threads: 8, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... 1 /Volumes/Serine/wd/18-03-05/mkfasta/duck4-10k.1.fasta.gz ==> duck4-10k.1 2 /Volumes/Serine/wd/18-03-05/mkfasta/duck4-10k.2.fasta.gz ==> duck4-10k.2 3 /Volumes/Serine/wd/18-03-05/mkfasta/duck4.1.fasta.gz ==> duck4.1 4 /Volumes/Serine/wd/18-03-05/mkfasta/duck4.2.fasta.gz ==> duck4.2 2018-03-05 09:08:32 Running Basic statistics processor... Contig files: 1 duck4-10k.1 2 duck4-10k.2 3 duck4.1 4 duck4.2 Calculating N50 and L50... 1 duck4-10k.1, N50 = 1607401, L50 = 216, Total length = 1397407710, GC % = 33.75, # N's per 100 kbp = 14275.16 2 duck4-10k.2, N50 = 1615007, L50 = 216, Total length = 1396117256, GC % = 33.75, # N's per 100 kbp = 14288.10 3 duck4.1, N50 = 177022, L50 = 834, Total length = 2205550088, GC % = 33.92, # N's per 100 kbp = 9137.01 4 duck4.2, N50 = 172688, L50 = 837, Total length = 2204281463, GC % = 33.91, # N's per 100 kbp = 9142.12 Drawing Nx plot... saved to /Volumes/Serine/wd/18-03-05/quast/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /Volumes/Serine/wd/18-03-05/quast/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /Volumes/Serine/wd/18-03-05/quast/basic_stats/GC_content_plot.pdf Drawing duck4-10k.1 GC content plot... saved to /Volumes/Serine/wd/18-03-05/quast/basic_stats/duck4-10k.1_GC_content_plot.pdf Drawing duck4-10k.2 GC content plot... saved to /Volumes/Serine/wd/18-03-05/quast/basic_stats/duck4-10k.2_GC_content_plot.pdf Drawing duck4.1 GC content plot... saved to /Volumes/Serine/wd/18-03-05/quast/basic_stats/duck4.1_GC_content_plot.pdf Drawing duck4.2 GC content plot... saved to /Volumes/Serine/wd/18-03-05/quast/basic_stats/duck4.2_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2018-03-05 09:16:19 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 2: Creating Icarus viewers... 2 of 2: Creating PDF with all tables and plots... Done 2018-03-05 09:18:36 RESULTS: Text versions of total report are saved to /Volumes/Serine/wd/18-03-05/quast/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /Volumes/Serine/wd/18-03-05/quast/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /Volumes/Serine/wd/18-03-05/quast/report.html PDF version (tables and plots) is saved to /Volumes/Serine/wd/18-03-05/quast/report.pdf Icarus (contig browser) is saved to /Volumes/Serine/wd/18-03-05/quast/icarus.html Log saved to /Volumes/Serine/wd/18-03-05/quast/quast.log Finished: 2018-03-05 09:18:36 Elapsed time: 0:17:22.042675 NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!