/home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast.py test_data/contigs_1.fasta test_data/contigs_2.fasta -R test_data/reference.fasta.gz -G test_data/genes.txt -O test_data/operons.txt -1 test_data/reads1.fastq.gz -2 test_data/reads2.fastq.gz -o quast_test_output Version: 4.6.3 System information: OS: Linux-2.6.32-696.28.1.el6.x86_64-x86_64-with-redhat-6.9-Santiago (linux_64) Python version: 2.7.13 CPUs number: 64 Started: 2018-06-19 14:04:05 Logging to /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/quast.log NOTICE: Output directory already exists. Existing Nucmer alignments can be used NOTICE: Maximum number of threads is set to 16 (use --threads option to set it manually) CWD: /home/psgendb/BIRCHDEV/pkg/quast-4.6.3 Main parameters: Threads: 16, 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... WARNING: Skipping contigs_2 because it doesn't contain contigs >= 500 bp. 1 test_data/contigs_1.fasta ==> contigs_1 2018-06-19 14:04:05 Running Reads analyzer... Logging to files /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/structural_variations/sv_calling.log and /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/structural_variations/sv_calling.err... Pre-processing reads... Running BWA... /home/psgendb/BIRCHDEV/python/lib64/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/bwa/bwa \ index -p reference /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/quast_corrected_input/reference.fasta \ >> /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/structural_variations/sv_calling.log \ 2>> /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/structural_variations/sv_calling.err The tool returned non-zero. See ../sv_calling.err for stderr. /home/psgendb/BIRCHDEV/python/lib64/python2.7/dist-packages/quast-4.6.3-py2.7.egg/quast_libs/bwa/bwa \ mem -t 16 reference /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/test_data/reads1.fastq.gz \ /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/test_data/reads2.fastq.gz > reference.sam 2>> \ /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/structural_variations/sv_calling.err The tool returned non-zero. See ../sv_calling.err for stderr. Done. ERROR! Failed running BWA for the reference. See /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/structural_variations/sv_calling.log for information. Failed searching structural variations. Done. 2018-06-19 14:04:05 Running Basic statistics processor... Reference genome: reference.fasta, length = 10000, num fragments = 1, GC % = 52.07 Contig files: contigs_1 Calculating N50 and L50... contigs_1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 Done. 2018-06-19 14:04:05 Running Contig analyzer... NOTICE: Previous try of E-MEM compilation was unsuccessful! For forced retrying, please remove /home/psgendb/BIRCHDEV/python/lib64/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. contigs_1 Logging to files /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/contigs_reports/contigs_report_contigs_1.stdout and contigs_report_contigs_1.stderr... Aligning contigs to the reference /home/psgendb/BIRCHDEV/python/lib64/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 The tool returned non-zero. See quast_test_output/contigs_reports/contigs_report_contigs_1.stderr for stderr. ERROR! Failed aligning contigs contigs_1 to the reference (non-zero exit code). Run with the --debug flag to see additional information. Failed aligning the contigs for all the assemblies. Only basic stats are going to be evaluated. NOTICE: Genes are not predicted by default. Use --gene-finding option to enable it. 2018-06-19 14:04:05 Creating large visual summaries... This may take a while: press Ctrl-C to skip this step.. 1 of 1: Creating Icarus viewers... Done 2018-06-19 14:04:05 RESULTS: Text versions of total report are saved to /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/report.txt, report.tsv, and report.tex Text versions of transposed total report are saved to /home/psgendb/BIRCHDEV/pkg/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/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/report.html Icarus (contig browser) is saved to /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/icarus.html Log saved to /home/psgendb/BIRCHDEV/pkg/quast-4.6.3/quast_test_output/quast.log Finished: 2018-06-19 14:04:05 Elapsed time: 0:00:00.569419 NOTICEs: 4; WARNINGs: 1; non-fatal ERRORs: 2 Thank you for using QUAST!