/home/sam/programs/quast-5.0.2/quast.py --threads=20 --min-contig=100 --labels=Olurida_v090,canu_sb_01,canu_sjw_01,platanus_sb_01,platanus_sb_02,racon_sjw_01 /home/sam/data/O_lurida/genomes/Olur_v090.SPolished.asm.wengan.fasta /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/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 Version: 5.0.2 System information: OS: Linux-4.4.0-210-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64) Python version: 2.7.12 CPUs number: 24 Started: 2021-05-21 07:46:13 Logging to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/quast.log CWD: /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons Main parameters: MODE: default, threads: 20, minimum contig length: 100, minimum alignment length: 65, \ ambiguity: one, threshold for extensive misassembly size: 1000 Contigs: Pre-processing... 1 /home/sam/data/O_lurida/genomes/Olur_v090.SPolished.asm.wengan.fasta ==> Olurida_v090 2 /mnt/owl/scaphapoda/Sean/Oly_Canu_Output/oly_pacbio_.contigs.fasta ==> canu_sb_01 3 /mnt/owl/Athaliana/20171018_oly_pacbio_canu/20171018_oly_pacbio.contigs.fasta ==> canu_sjw_01 4 /mnt/owl/scaphapoda/Sean/Oly_Illumina_Platanus_Assembly/Oly_Out__contig.fa ==> platanus_sb_01 5 /mnt/owl/scaphapoda/Sean/Oly_Platanus_Assembly_Kmer-22/Oly_Out__contig.fa ==> platanus_sb_02 6 /mnt/owl/Athaliana/201709_oly_pacbio_assembly_minimap_asm_racon/20170918_oly_pacbio_racon1_consensus.fasta ==> racon_sjw_01 2021-05-21 07:54:39 Running Basic statistics processor... Contig files: 1 Olurida_v090 2 canu_sb_01 3 canu_sjw_01 4 platanus_sb_01 5 platanus_sb_02 6 racon_sjw_01 Calculating N50 and L50... 1 Olurida_v090, N50 = 9729, L50 = 6029, Total length = 177359031, GC % = 36.06, # N's per 100 kbp = 0.00 2 canu_sb_01, N50 = 14117, L50 = 1230, Total length = 46288879, GC % = 36.45, # N's per 100 kbp = 0.00 3 canu_sjw_01, N50 = 13157, L50 = 3329, Total length = 132146852, GC % = 36.40, # N's per 100 kbp = 0.00 4 platanus_sb_01, N50 = 132, L50 = 24682, Total length = 8249461, GC % = 35.24, # N's per 100 kbp = 0.00 5 platanus_sb_02, N50 = 288, L50 = 740214, Total length = 1108644927, GC % = 36.17, # N's per 100 kbp = 0.00 6 racon_sjw_01, N50 = 13763, L50 = 896, Total length = 33496662, GC % = 36.43, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/Nx_plot.pdf Drawing cumulative plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/GC_content_plot.pdf Drawing Olurida_v090 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/Olurida_v090_GC_content_plot.pdf Drawing canu_sb_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/canu_sb_01_GC_content_plot.pdf Drawing canu_sjw_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/canu_sjw_01_GC_content_plot.pdf Drawing platanus_sb_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/platanus_sb_01_GC_content_plot.pdf Drawing platanus_sb_02 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/platanus_sb_02_GC_content_plot.pdf Drawing racon_sjw_01 GC content plot... saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/basic_stats/racon_sjw_01_GC_content_plot.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2021-05-21 07:57:04 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 2021-05-21 07:58:26 RESULTS: Text versions of total report are saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/report.html PDF version (tables and plots) is saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/report.pdf Icarus (contig browser) is saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/icarus.html Log is saved to /home/sam/analyses/20210521_olur_quast_non-scaffold_assembly-comparisons/quast_results/results_2021_05_21_07_46_10/quast.log Finished: 2021-05-21 07:58:27 Elapsed time: 0:12:13.233214 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!