/home/sam/software/quast-4.5/quast.py -t 24 /mnt/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta /mnt/owl/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta /mnt/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa /mnt/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa /mnt/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa /mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa /mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa /mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa /mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa Version: 4.5, 15ca3b9 System information: OS: Linux-4.4.0-109-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64) Python version: 2.7.12 CPUs number: 24 Started: 2018-01-16 10:08:35 Logging to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/quast.log CWD: /home/sam/gitrepos/LabDocs/jupyter_nbs/sam Main parameters: Threads: 24, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000 WARNING: Can't draw plots: python-matplotlib is missing or corrupted. Contigs: Pre-processing... 1 /mnt/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta ==> oly_pacbio_.contigs 2 /mnt/owl/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta ==> 20171018_oly_pacbio.contigs 3 /mnt/owl/Athaliana/20171130_oly_pbjelly/jelly.out.fasta ==> jelly.out 4 /mnt/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa ==> Oly_Illumina_Platanus_Assembly_Oly_Out__contig 5 /mnt/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa ==> Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig 6 /mnt/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta ==> 20170918_oly_pacbio_racon1_consensus 7 /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output/scaffolds.reduced.fa ==> Oly_Redundans_Output_scaffolds.reduced 8 /mnt/owl/scaphapoda/Sean/Oly_Redundans_Output_Try_2/scaffolds.reduced.fa ==> Oly_Redundans_Output_Try_2_scaffolds.reduced 9 /mnt/owl/Athaliana/20171005_redundans/scaffolds.reduced.fa ==> 20171005_redundans_scaffolds.reduced 10 /mnt/owl/Athaliana/20171004_redundans/scaffolds.reduced.fa ==> 20171004_redundans_scaffolds.reduced 11 /mnt/owl/Athaliana/20171024_docker_oly_redundans_01/scaffolds.reduced.fa ==> 20171024_docker_oly_redundans_01_scaffolds.reduced 12 /mnt/owl/O_lurida_genome_assemblies_BGI/20161201/cdts-hk.genomics.cn/Ostrea_lurida/Ostrea_lurida.fa ==> Ostrea_lurida 2018-01-16 10:11:11 Running Basic statistics processor... Contig files: 1 oly_pacbio_.contigs 2 20171018_oly_pacbio.contigs 3 jelly.out 4 Oly_Illumina_Platanus_Assembly_Oly_Out__contig 5 Oly_Platanus_Assembly_Kmer-22_Oly_Out__contig 6 20170918_oly_pacbio_racon1_consensus 7 Oly_Redundans_Output_scaffolds.reduced 8 Oly_Redundans_Output_Try_2_scaffolds.reduced 9 20171005_redundans_scaffolds.reduced 10 20171004_redundans_scaffolds.reduced 11 20171024_docker_oly_redundans_01_scaffolds.reduced 12 Ostrea_lurida 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 20171018_oly_pacbio.contigs, N50 = 13157, L50 = 3329, Total length = 132146852, GC % = 36.40, # N's per 100 kbp = 0.00 3 jelly.out, N50 = 12433, L50 = 26241, Total length = 1180563613, GC % = 36.57, # N's per 100 kbp = 6580.58 4 Oly_Illumina_Platanus_Assembly_Oly_Out__contig, N50 = 684, L50 = 2, Total length = 2693, GC % = 46.05, # N's per 100 kbp = 0.00 5 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 6 20170918_oly_pacbio_racon1_consensus, N50 = 13763, L50 = 896, Total length = 33483762, GC % = 36.43, # N's per 100 kbp = 0.00 7 Oly_Redundans_Output_scaffolds.reduced, N50 = 682, L50 = 40, Total length = 85207, GC % = 36.24, # N's per 100 kbp = 17127.70 8 Oly_Redundans_Output_Try_2_scaffolds.reduced, N50 = 4175, L50 = 32022, Total length = 513841258, GC % = 35.90, # N's per 100 kbp = 1019.31 9 20171005_redundans_scaffolds.reduced, N50 = 16565, L50 = 452, Total length = 29292260, GC % = 36.39, # N's per 100 kbp = 918.03 10 20171004_redundans_scaffolds.reduced, N50 = 17679, L50 = 573, Total length = 40561504, GC % = 36.46, # N's per 100 kbp = 695.24 11 20171024_docker_oly_redundans_01_scaffolds.reduced, N50 = 16998, L50 = 1724, Total length = 111139362, GC % = 36.34, # N's per 100 kbp = 626.41 12 Ostrea_lurida, N50 = 4204, L50 = 43989, Total length = 697528655, GC % = 35.83, # N's per 100 kbp = 19149.50 Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2018-01-16 10:14:02 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 1: Creating Icarus viewers... Done 2018-01-16 10:14:56 RESULTS: Text versions of total report are saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/report.html Icarus (contig browser) is saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/icarus.html Log saved to /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/quast_results/results_2018_01_16_10_08_35/quast.log Finished: 2018-01-16 10:14:57 Elapsed time: 0:06:21.404593 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST!