/Library/Python/2.7/site-packages/quast-4.6.1-py2.7.egg/EGG-INFO/scripts/quast.py -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 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 -t 4 -m 1000 Version: 4.6.1 System information: OS: Darwin-17.3.0-x86_64-i386-64bit (macosx) Python version: 2.7.10 CPUs number: 4 Started: 2017-12-17 19:57:30 Logging to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/quast.log NOTICE: Output directory already exists. Existing Nucmer alignments can be used CWD: /Users/Mike_Lee/working_genomics_de_novo_temp Main parameters: Threads: 4, minimum contig length: 1000, ambiguity: one, threshold for extensive misassembly size: 1000 Reference: 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 2017-12-17 19:57:32 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 = 8492975, 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 /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/Nx_plot.pdf Drawing NGx plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/NGx_plot.pdf Drawing cumulative plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/cumulative_plot.pdf Drawing GC content plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/GC_content_plot.pdf Drawing spades_default GC content plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/spades_default_GC_content_plot.pdf Drawing spades_kmers_careful GC content plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/spades_kmers_careful_GC_content_plot.pdf Drawing megahit_default GC content plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/megahit_default_GC_content_plot.pdf Drawing megahit_min_count_3 GC content plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/megahit_min_count_3_GC_content_plot.pdf Drawing Coverage histogram (bin size: 1x)... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/coverage_histogram.pdf Drawing spades_default coverage histogram (bin size: 1x)... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/spades_default_coverage_histogram.pdf Drawing spades_kmers_careful coverage histogram (bin size: 1x)... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/basic_stats/spades_kmers_careful_coverage_histogram.pdf Done. 2017-12-17 19:57:41 Running Contig analyzer... NOTICE: Previous try of E-MEM compilation was unsuccessful! For forced retrying, please remove /Library/Python/2.7/site-packages/quast-4.6.1-py2.7.egg/quast_libs/MUMmer/make.emem.failed and restart QUAST. Currently, QUAST will use Nucmer which is absolutely fine, albeit slower. 2 spades_kmers_careful 1 spades_default 3 megahit_default 4 megahit_min_count_3 3 Logging to files /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/contigs_report_megahit_default.stdout and contigs_report_megahit_default.stderr... 2 Logging to files /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/contigs_report_spades_kmers_careful.stdout and contigs_report_spades_kmers_careful.stderr... 1 Logging to files /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/contigs_report_spades_default.stdout and contigs_report_spades_default.stderr... 4 Logging to files /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/contigs_report_megahit_min_count_3.stdout and contigs_report_megahit_min_count_3.stderr... 2 Using existing alignments... 1 Using existing alignments... 3 Using existing alignments... 4 Using existing alignments... 1 Analysis is finished. 3 Analysis is finished. 4 Analysis is finished. 2 Analysis is finished. Creating total report... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Drawing misassemblies by types plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/misassemblies_plot.pdf Drawing misassemblies FRCurve plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/contigs_reports/misassemblies_frcurve_plot.pdf Done. 2017-12-17 19:57:52 Running NA-NGA calculation... 1 spades_default, Largest alignment = 445563, NA50 = 143914, NGA50 = 143431, LA50 = 17, LGA50 = 18 2 spades_kmers_careful, Largest alignment = 505920, 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 /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/aligned_stats/cumulative_plot.pdf Drawing NAx plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/aligned_stats/NAx_plot.pdf Drawing NGAx plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/aligned_stats/NGAx_plot.pdf Done. 2017-12-17 19:57:54 Running Genome analyzer... Loaded 7705 genes NOTICE: No file with operons provided. Use the -O option if you want to specify it. 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 genes cumulative plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/genome_stats/genes_cumulative_plot.pdf Drawing genes FRCurve plot... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/genome_stats/genes_frcurve_plot.pdf Drawing # complete genes histogram... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/genome_stats/complete_genes_histogram.pdf Drawing Genome fraction, % histogram... saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/genome_stats/genome_fraction_histogram.pdf Done. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2017-12-17 19:58:07 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 2017-12-17 19:58:10 RESULTS: Text versions of total report are saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/report.html PDF version (tables and plots) is saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/report.pdf Icarus (contig browser) is saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/icarus.html Log saved to /Users/Mike_Lee/working_genomics_de_novo_temp/quast_B_cep_out/quast.log Finished: 2017-12-17 19:58:10 Elapsed time: 0:00:39.867763 NOTICEs: 4; WARNINGs: 0; non-fatal ERRORs: 0 Thank you for using QUAST!