/usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/EGG-INFO/scripts/quast.py --test Version: 4.6.3 System information: OS: Linux-4.13.0-43-generic-x86_64-with-Ubuntu-16.04-xenial (linux_64) Python version: 2.7.12 CPUs number: 8 Started: 2018-06-11 18:12:07 Logging to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/quast.log NOTICE: Maximum number of threads is set to 2 (use --threads option to set it manually) CWD: /home/birch/BIRCH/local/install/quast-4.6.3 Main parameters: Threads: 2, minimum contig length: 500, ambiguity: one, threshold for extensive misassembly size: 1000 WARNING: Can't draw plots: python-matplotlib is missing or corrupted. Reference: test_data/reference.fasta.gz ==> reference Contigs: Pre-processing... 1 test_data/contigs_1.fasta ==> contigs_1 2 test_data/contigs_2.fasta ==> contigs_2 2018-06-11 18:12:07 Running Basic statistics processor... Reference genome: reference.fasta, length = 10000, num fragments = 1, GC % = 52.07 Contig files: 1 contigs_1 2 contigs_2 Calculating N50 and L50... 1 contigs_1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 2 contigs_2, N50 = 3360, L50 = 1, Total length = 5460, GC % = 52.44, # N's per 100 kbp = 0.00 Done. 2018-06-11 18:12:07 Running Contig analyzer... NOTICE: Previous try of E-MEM compilation was unsuccessful! For forced retrying, please remove /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/make.emem.failed and restart QUAST. Currently, QUAST will use Nucmer which is absolutely fine, albeit slower. 1 contigs_1 2 contigs_2 2 Logging to files /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/contigs_report_contigs_2.stdout and contigs_report_contigs_2.stderr... 1 Logging to files /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/contigs_report_contigs_1.stdout and contigs_report_contigs_1.stderr... 2 Aligning contigs to the reference 1 Aligning contigs to the reference 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/nucmer \ -c 65 -l 65 --maxmatch -p quast_test_output/contigs_reports/nucmer_output/contigs_2 \ quast_test_output/quast_corrected_input/reference.fasta quast_test_output/quast_corrected_input/contigs_2.fasta \ >> quast_test_output/contigs_reports/contigs_report_contigs_2.stdout 2>> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/nucmer \ -c 65 -l 65 --maxmatch -p quast_test_output/contigs_reports/nucmer_output/contigs_1 \ quast_test_output/quast_corrected_input/reference.fasta quast_test_output/quast_corrected_input/contigs_1.fasta \ >> quast_test_output/contigs_reports/contigs_report_contigs_1.stdout 2>> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/delta-filter \ -i 95.0 -l 0 quast_test_output/contigs_reports/nucmer_output/contigs_1.delta \ > quast_test_output/contigs_reports/nucmer_output/contigs_1.fdelta 2> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/delta-filter \ -i 95.0 -l 0 quast_test_output/contigs_reports/nucmer_output/contigs_2.delta \ > quast_test_output/contigs_reports/nucmer_output/contigs_2.fdelta 2> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/mummerplot \ --html --layout -p quast_test_output/contigs_reports/nucmer_output/contigs_1 \ quast_test_output/contigs_reports/nucmer_output/contigs_1.delta > quast_test_output/contigs_reports/contigs_report_contigs_1.stdout \ 2> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/mummerplot \ --html --layout -p quast_test_output/contigs_reports/nucmer_output/contigs_2 \ quast_test_output/contigs_reports/nucmer_output/contigs_2.delta > quast_test_output/contigs_reports/contigs_report_contigs_2.stdout \ 2> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/gnuplot/src/gnuplot \ quast_test_output/contigs_reports/nucmer_output/contigs_2.gp > /dev/null 2> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/gnuplot/src/gnuplot \ quast_test_output/contigs_reports/nucmer_output/contigs_1.gp > /dev/null 2> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr 2 MUMmer plot saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/contigs_2_mummerplot.html 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/show-coords \ quast_test_output/contigs_reports/nucmer_output/contigs_2.delta > quast_test_output/contigs_reports/nucmer_output/contigs_2.coords_tmp \ 2> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr 1 MUMmer plot saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/contigs_1_mummerplot.html 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/show-coords \ quast_test_output/contigs_reports/nucmer_output/contigs_1.delta > quast_test_output/contigs_reports/nucmer_output/contigs_1.coords_tmp \ 2> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/show-snps \ -S -T -H quast_test_output/contigs_reports/nucmer_output/contigs_2.delta < quast_test_output/contigs_reports/nucmer_output/contigs_2.coords.headless \ > quast_test_output/contigs_reports/nucmer_output/contigs_2.all_snps 2> quast_test_output/contigs_reports/contigs_report_contigs_2.stderr 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/MUMmer/show-snps \ -S -T -H quast_test_output/contigs_reports/nucmer_output/contigs_1.delta < quast_test_output/contigs_reports/nucmer_output/contigs_1.coords.headless \ > quast_test_output/contigs_reports/nucmer_output/contigs_1.all_snps 2> quast_test_output/contigs_reports/contigs_report_contigs_1.stderr 1 Analysis is finished. Gzipping /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/nucmer_output/contigs_1.all_snps to reduce disk space usage... saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/nucmer_output/contigs_1.all_snps.gz 2 Analysis is finished. Gzipping /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/nucmer_output/contigs_2.all_snps to reduce disk space usage... saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/nucmer_output/contigs_2.all_snps.gz Creating total report... saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex Transposed version of total report... saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex Creating total report... saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex Done. 2018-06-11 18:12:08 Running NA-NGA calculation... 1 contigs_1, Largest alignment = 2030, NA50 = 1950, NGA50 = 1610, LA50 = 2, LGA50 = 3 2 contigs_2, Largest alignment = 2100, NA50 = 1471, NGA50 = 700, LA50 = 2, LGA50 = 4 Done. 2018-06-11 18:12:08 Running Genome analyzer... Loaded 10 genes Loaded 2 operons 1 contigs_1 2 contigs_2 2 Analysis is finished. 1 Analysis is finished. Done. 2018-06-11 18:12:08 Running GlimmerHMM... 1 contigs_1 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/glimmerhmm \ quast_test_output/predicted_genes/tmp/tmpgOTTLW/0.fasta -d /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/trained/arabidopsis \ -g -o quast_test_output/predicted_genes/tmp/tmpgOTTLW/0.gff >> quast_test_output/predicted_genes/contigs_1_glimmer.stderr \ 2>> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/glimmerhmm \ quast_test_output/predicted_genes/tmp/tmpgOTTLW/1.fasta -d /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/trained/arabidopsis \ -g -o quast_test_output/predicted_genes/tmp/tmpgOTTLW/1.gff >> quast_test_output/predicted_genes/contigs_1_glimmer.stderr \ 2>> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 1 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/glimmerhmm \ quast_test_output/predicted_genes/tmp/tmpgOTTLW/2.fasta -d /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/trained/arabidopsis \ -g -o quast_test_output/predicted_genes/tmp/tmpgOTTLW/2.gff >> quast_test_output/predicted_genes/contigs_1_glimmer.stderr \ 2>> quast_test_output/predicted_genes/contigs_1_glimmer.stderr 1 Genes = 7 unique, 7 total 1 Predicted genes (GFF): /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/predicted_genes/contigs_1_glimmer_genes.gff.gz 2 contigs_2 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/glimmerhmm \ quast_test_output/predicted_genes/tmp/tmpvbk3En/0.fasta -d /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/trained/arabidopsis \ -g -o quast_test_output/predicted_genes/tmp/tmpvbk3En/0.gff >> quast_test_output/predicted_genes/contigs_2_glimmer.stderr \ 2>> quast_test_output/predicted_genes/contigs_2_glimmer.stderr 2 /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/glimmerhmm \ quast_test_output/predicted_genes/tmp/tmpvbk3En/1.fasta -d /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/glimmer/trained/arabidopsis \ -g -o quast_test_output/predicted_genes/tmp/tmpvbk3En/1.gff >> quast_test_output/predicted_genes/contigs_2_glimmer.stderr \ 2>> quast_test_output/predicted_genes/contigs_2_glimmer.stderr 2 Genes = 6 unique, 6 total 2 Predicted genes (GFF): /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/predicted_genes/contigs_2_glimmer_genes.gff.gz Done. 2018-06-11 18:12:08 Running GeneMarkS... 1 contigs_1 2 contigs_2 2 perl /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/genemark/linux_64/gmsn.pl \ --name contigs_2 --clean --out quast_test_output/predicted_genes/tmp/tmp92rT1M \ quast_test_output/quast_corrected_input/contigs_2.fasta > quast_test_output/predicted_genes/contigs_2_genemark.stderr \ 2> quast_test_output/predicted_genes/contigs_2_genemark.stderr 1 perl /usr/local/lib/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/genemark/linux_64/gmsn.pl \ --name contigs_1 --clean --out quast_test_output/predicted_genes/tmp/tmpE_kZQw \ quast_test_output/quast_corrected_input/contigs_1.fasta > quast_test_output/predicted_genes/contigs_1_genemark.stderr \ 2> quast_test_output/predicted_genes/contigs_1_genemark.stderr The tool returned non-zero. See quast_test_output/predicted_genes/contigs_2_genemark.stderr for stderr. The tool returned non-zero. See quast_test_output/predicted_genes/contigs_1_genemark.stderr for stderr. WARNING: License period for GeneMark has ended! To update license, please visit http://exon.gatech.edu/GeneMark/license_download.cgi page and fill in the form. You should choose GeneMarkS tool and your operating system (note that GeneMark is free for non-commercial use). Download the license key and replace your ~/.gm_key with the updated version. After that you can restart QUAST. 2018-06-11 18:12:08 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 1: Creating Icarus viewers... Done 2018-06-11 18:12:08 RESULTS: Text versions of total report are saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/transposed_report.txt, transposed_report.tsv, and transposed_report.tex HTML version (interactive tables and plots) saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/report.html Icarus (contig browser) is saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/icarus.html Log saved to /home/birch/BIRCH/local/install/quast-4.6.3/quast_test_output/quast.log Finished: 2018-06-11 18:12:08 Elapsed time: 0:00:01.506260 NOTICEs: 2; WARNINGs: 2; non-fatal ERRORs: 0 Thank you for using QUAST! TEST PASSED with WARNINGS!