/nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/quast -o quast_B_cep_out -R reference_genome/BCep_ref.fna -G reference_genome/BCep_ref.gff -l spades_default, spades_kmers_careful, megahit_default, megahit_min_count_3 -t 4 -m 1000 spades_default_assembly/contigs.fasta spades_kmers_set_careful_assembly/contigs.fasta megahit_default_assembly/final.contigs.fa megahit_min_count_3_assembly/final.contigs.fa Version: 5.0.2 System information: OS: Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-redhat-7.9-Maipo (linux_64) Python version: 3.6.10 CPUs number: 144 Started: 2021-12-11 14:37:34 Logging to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/quast.log CWD: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir Main parameters: MODE: default, threads: 4, minimum contig length: 1000, minimum alignment length: 65, \ ambiguity: one, threshold for extensive misassembly size: 1000 Reference: /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/reference_genome/BCep_ref.fna ==> BCep_ref Contigs: Pre-processing... 1 spades_default_assembly/contigs.fasta ==> spades_default 2 spades_kmers_set_careful_assembly/contigs.fasta ==> spades_kmers_careful 3 megahit_default_assembly/final.contigs.fa ==> megahit_default 4 megahit_min_count_3_assembly/final.contigs.fa ==> megahit_min_count_3 2021-12-11 14:37:43 Running Basic statistics processor... Reference genome: BCep_ref.fna, length = 8605945, num fragments = 4, GC % = 66.61 Contig files: 1 spades_default 2 spades_kmers_careful 3 megahit_default 4 megahit_min_count_3 Calculating N50 and L50... 1 spades_default, N50 = 151907, L50 = 16, Total length = 8447218, GC % = 66.67, # N's per 100 kbp = 0.00 2 spades_kmers_careful, N50 = 217699, L50 = 12, Total length = 8472540, GC % = 66.67, # N's per 100 kbp = 0.00 3 megahit_default, N50 = 144335, L50 = 19, Total length = 8492269, GC % = 66.66, # N's per 100 kbp = 0.00 4 megahit_min_count_3, N50 = 131456, L50 = 20, Total length = 8493797, GC % = 66.66, # N's per 100 kbp = 0.00 Drawing Nx plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/Nx_plot.pdf Drawing NGx plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/NGx_plot.pdf Drawing cumulative plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/GC_content_plot.pdf Drawing spades_default GC content plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/spades_default_GC_content_plot.pdf Drawing spades_kmers_careful GC content plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/spades_kmers_careful_GC_content_plot.pdf Drawing megahit_default GC content plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/megahit_default_GC_content_plot.pdf Drawing megahit_min_count_3 GC content plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/megahit_min_count_3_GC_content_plot.pdf Drawing Coverage histogram (bin size: 1x)... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/coverage_histogram.pdf Drawing spades_default coverage histogram (bin size: 1x)... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/spades_default_coverage_histogram.pdf Drawing spades_kmers_careful coverage histogram (bin size: 1x)... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/basic_stats/spades_kmers_careful_coverage_histogram.pdf Done. 2021-12-11 14:37:50 Running Contig analyzer... 1 spades_default 2 spades_kmers_careful 3 megahit_default 4 megahit_min_count_3 1 Logging to files /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/contigs_report_spades_default.stdout and contigs_report_spades_default.stderr... 2 Logging to files /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/contigs_report_spades_kmers_careful.stdout and contigs_report_spades_kmers_careful.stderr... 3 Logging to files /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/contigs_report_megahit_default.stdout and contigs_report_megahit_default.stderr... 4 Logging to files /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/contigs_report_megahit_min_count_3.stdout and contigs_report_megahit_min_count_3.stderr... 1 Aligning contigs to the reference 2 Aligning contigs to the reference 3 Aligning contigs to the reference 4 Aligning contigs to the reference 1 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/minimap2 \ -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \ --min-occ 200 -g 2500 --score-N 2 --cs -t 1 quast_B_cep_out/quast_corrected_input/BCep_ref.fna \ quast_B_cep_out/quast_corrected_input/spades_default.fasta > quast_B_cep_out/contigs_reports/minimap_output/spades_default.coords_tmp \ 2>> quast_B_cep_out/contigs_reports/contigs_report_spades_default.stderr 3 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/minimap2 \ -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \ --min-occ 200 -g 2500 --score-N 2 --cs -t 1 quast_B_cep_out/quast_corrected_input/BCep_ref.fna \ quast_B_cep_out/quast_corrected_input/megahit_default.fa > quast_B_cep_out/contigs_reports/minimap_output/megahit_default.coords_tmp \ 2>> quast_B_cep_out/contigs_reports/contigs_report_megahit_default.stderr 2 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/minimap2 \ -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \ --min-occ 200 -g 2500 --score-N 2 --cs -t 1 quast_B_cep_out/quast_corrected_input/BCep_ref.fna \ quast_B_cep_out/quast_corrected_input/spades_kmers_careful.fasta > quast_B_cep_out/contigs_reports/minimap_output/spades_kmers_careful.coords_tmp \ 2>> quast_B_cep_out/contigs_reports/contigs_report_spades_kmers_careful.stderr 4 /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/conda/anaconda3/envs/de_novo_example/bin/minimap2 \ -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \ --min-occ 200 -g 2500 --score-N 2 --cs -t 1 quast_B_cep_out/quast_corrected_input/BCep_ref.fna \ quast_B_cep_out/quast_corrected_input/megahit_min_count_3.fa > quast_B_cep_out/contigs_reports/minimap_output/megahit_min_count_3.coords_tmp \ 2>> quast_B_cep_out/contigs_reports/contigs_report_megahit_min_count_3.stderr 3 Analysis is finished. 1 Analysis is finished. 4 Analysis is finished. 2 Analysis is finished. Creating total report... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Drawing misassemblies by types plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/contigs_reports/misassemblies_frcurve_plot.pdf Done. 2021-12-11 14:37:55 Running NA-NGA calculation... 1 spades_default, Largest alignment = 455950, NA50 = 143914, NGA50 = 143431, LA50 = 17, LGA50 = 18 2 spades_kmers_careful, Largest alignment = 505898, NA50 = 198969, NGA50 = 198969, LA50 = 13, LGA50 = 13 3 megahit_default, Largest alignment = 350746, NA50 = 144083, NGA50 = 144083, LA50 = 20, LGA50 = 20 4 megahit_min_count_3, Largest alignment = 350746, NA50 = 125159, NGA50 = 125159, LA50 = 21, LGA50 = 21 Drawing cumulative plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/aligned_stats/cumulative_plot.pdf Drawing NAx plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/aligned_stats/NAx_plot.pdf Drawing NGAx plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/aligned_stats/NGAx_plot.pdf Done. 2021-12-11 14:37:56 Running Genome analyzer... NOTICE: No file with operons were provided. Use the -O option if you want to specify it. Loaded 7705 genomic features of type "gene" 1 spades_default 2 spades_kmers_careful 3 megahit_default 4 megahit_min_count_3 1 Analysis is finished. 2 Analysis is finished. 3 Analysis is finished. 4 Analysis is finished. Drawing genomic features cumulative plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/genome_stats/features_cumulative_plot.pdf Drawing genomic features FRCurve plot... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/genome_stats/features_frcurve_plot.pdf Drawing # complete genomic features histogram... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/genome_stats/complete_features_histogram.pdf Drawing Genome fraction, % histogram... saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/genome_stats/genome_fraction_histogram.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 2021-12-11 14:38:01 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 2021-12-11 14:38:04 RESULTS: Text versions of total report are saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) is saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/report.html PDF version (tables and plots) is saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/report.pdf Icarus (contig browser) is saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/icarus.html Log is saved to /nfs/cds-peta/exports/biol_micro_cds_gr_sunagawa/scratch/qingli/genomics_de_novo_temp/working_dir/quast_B_cep_out/quast.log Finished: 2021-12-11 14:38:04 Elapsed time: 0:00:29.756256 NOTICEs: 2; WARNINGs: 1; non-fatal ERRORs: 0 Thank you for using QUAST!