/usr/local/bioinformatics/quast-4.5/quast.py -t 24 /home/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta /home/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa /home/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa /home/owl/scaphapoda/Sean/Oly_Redundans_Output/contigs.fa /home/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/contigs.fa /home/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta Version: 4.5, 15ca3b9 System information: OS: Linux-4.4.0-96-generic-x86_64-with-debian-8.9 (linux_64) Python version: 2.7.13 CPUs number: 24 Started: 2017-10-03 15:35:29 Logging to /home/data/quast_results/results_2017_10_03_15_35_28/quast.log CWD: /home/data Main parameters: Threads: 24, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... 1 /home/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta ==> oly_pacbio_.contigs 2 /home/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa ==> Oly_Illumina_Platanus_Assembly_Oly_Out__contig 3 /home/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa ==> Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig 4 /home/owl/scaphapoda/Sean/Oly_Redundans_Output/contigs.fa ==> Oly_Redundans_Output_contigs 5 /home/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/contigs.fa ==> Oly_Redundans_Output_Try_2_contigs 6 /home/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta ==> 20170918_oly_pacbio_racon1_consensus 2017-10-03 15:38:40 Running Basic statistics processor... Contig files: 1 oly_pacbio_.contigs 2 Oly_Illumina_Platanus_Assembly_Oly_Out__contig 3 Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig 4 Oly_Redundans_Output_contigs 5 Oly_Redundans_Output_Try_2_contigs 6 20170918_oly_pacbio_racon1_consensus Calculating N50 and L50... 1 oly_pacbio_.contigs, N50 = 14117, L50 = 1230, Total length = 46288879, GC % = 36.45, # N's per 100 kbp = 0.00 2 Oly_Illumina_Platanus_Assembly_Oly_Out__contig, N50 = 684, L50 = 2, Total length = 2693, GC % = 46.05, # N's per 100 kbp = 0.00 3 Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig, N50 = 1245, L50 = 97869, Total length = 417951161, GC % = 35.70, # N's per 100 kbp = 0.00 4 Oly_Redundans_Output_contigs, N50 = 677, L50 = 44, Total length = 85212, GC % = 36.38, # N's per 100 kbp = 16826.27 5 Oly_Redundans_Output_Try_2_contigs, N50 = 1245, L50 = 97869, Total length = 417951161, GC % = 35.70, # N's per 100 kbp = 0.00 6 20170918_oly_pacbio_racon1_consensus, N50 = 13763, L50 = 896, Total length = 33483762, GC % = 36.43, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/GC_content_plot.pdf Drawing oly_pacbio_.contigs GC content plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/oly_pacbio_.contigs_GC_content_plot.pdf Drawing Oly_Illumina_Platanus_Assembly_Oly_Out__contig GC content plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/Oly_Illumina_Platanus_Assembly_Oly_Out__contig_GC_content_plot.pdf Drawing Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig GC content plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig_GC_content_plot.pdf Drawing Oly_Redundans_Output_contigs GC content plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/Oly_Redundans_Output_contigs_GC_content_plot.pdf Drawing Oly_Redundans_Output_Try_2_contigs GC content plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/Oly_Redundans_Output_Try_2_contigs_GC_content_plot.pdf Drawing 20170918_oly_pacbio_racon1_consensus GC content plot... saved to /home/data/quast_results/results_2017_10_03_15_35_28/basic_stats/20170918_oly_pacbio_racon1_consensus_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2017-10-03 15:39:54 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 2017-10-03 15:40:21 RESULTS: Text versions of total report are saved to /home/data/quast_results/results_2017_10_03_15_35_28/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/data/quast_results/results_2017_10_03_15_35_28/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /home/data/quast_results/results_2017_10_03_15_35_28/report.html PDF version (tables and plots) is saved to /home/data/quast_results/results_2017_10_03_15_35_28/report.pdf Icarus (contig browser) is saved to /home/data/quast_results/results_2017_10_03_15_35_28/icarus.html Log saved to /home/data/quast_results/results_2017_10_03_15_35_28/quast.log Finished: 2017-10-03 15:40:21 Elapsed time: 0:04:52.740676 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!