Mercurial > repos > iuc > quast
comparison test-data/test2.log @ 9:45924fa8d8c5 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
| author | iuc |
|---|---|
| date | Mon, 08 Nov 2021 09:03:00 +0000 |
| parents | |
| children | 875d0f36d66f |
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| 8:ebb0dcdb621a | 9:45924fa8d8c5 |
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| 1 /usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat --features /tmp/tmpfgnwy_vl/files/4/0/6/dataset_406c3bca-dfac-498b-954d-476186610bc9.dat --operons /tmp/tmpfgnwy_vl/files/e/5/8/dataset_e5851e9e-28d2-42f8-9a7a-0d05d0770635.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat --threads 1 | |
| 2 | |
| 3 Version: 5.0.2 | |
| 4 | |
| 5 System information: | |
| 6 OS: Linux-5.11.0-37-generic-x86_64-with-debian-10.9 (linux_64) | |
| 7 Python version: 3.7.12 | |
| 8 CPUs number: 8 | |
| 9 | |
| 10 Started: 2021-11-07 18:59:01 | |
| 11 | |
| 12 Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log | |
| 13 | |
| 14 CWD: /tmp/tmpfgnwy_vl/job_working_directory/000/12/working | |
| 15 Main parameters: | |
| 16 MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \ | |
| 17 ambiguity: one, threshold for extensive misassembly size: 1000 | |
| 18 | |
| 19 Reference: | |
| 20 /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat ==> dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74 | |
| 21 | |
| 22 Contigs: | |
| 23 Pre-processing... | |
| 24 1 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat ==> contig1 | |
| 25 2 /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat ==> contig2 | |
| 26 | |
| 27 2021-11-07 18:59:01 | |
| 28 Running Basic statistics processor... | |
| 29 Reference genome: | |
| 30 dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat, length = 6650, num fragments = 1, GC % = 52.00 | |
| 31 Contig files: | |
| 32 1 contig1 | |
| 33 2 contig2 | |
| 34 Calculating N50 and L50... | |
| 35 1 contig1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 | |
| 36 2 contig2, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 | |
| 37 Drawing Nx plot... | |
| 38 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf | |
| 39 Drawing NGx plot... | |
| 40 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf | |
| 41 Drawing cumulative plot... | |
| 42 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf | |
| 43 Drawing GC content plot... | |
| 44 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf | |
| 45 Drawing contig1 GC content plot... | |
| 46 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf | |
| 47 Drawing contig2 GC content plot... | |
| 48 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf | |
| 49 Done. | |
| 50 | |
| 51 2021-11-07 18:59:02 | |
| 52 Running analysis based on unique 101-mers... | |
| 53 NOTICE: Permission denied accessing /usr/local/lib/python3.7/site-packages/quast_libs/kmc. KMC will be downloaded to home directory /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast | |
| 54 Downloading KMC (file: kmc)... | |
| 55 KMC successfully downloaded! | |
| 56 Downloading KMC (file: kmc_tools)... | |
| 57 KMC successfully downloaded! | |
| 58 Running KMC on reference... | |
| 59 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ | |
| 60 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat \ | |
| 61 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp \ | |
| 62 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 63 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ | |
| 64 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc.histo.txt \ | |
| 65 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 66 Analyzing assemblies completeness... | |
| 67 1 contig1 | |
| 68 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ | |
| 69 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ | |
| 70 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 71 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ | |
| 72 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \ | |
| 73 intersect outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc >> \ | |
| 74 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 75 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ | |
| 76 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc.histo.txt \ | |
| 77 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 78 2 contig2 | |
| 79 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ | |
| 80 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \ | |
| 81 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 82 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ | |
| 83 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \ | |
| 84 intersect outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc >> \ | |
| 85 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 86 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ | |
| 87 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc.histo.txt \ | |
| 88 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 89 Analyzing assemblies correctness... | |
| 90 Downsampling k-mers... | |
| 91 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \ | |
| 92 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1_6650.fasta \ | |
| 93 -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1_6650.filtered.fasta >> outputdir/k_mer_stats/kmc.log \ | |
| 94 2>> outputdir/k_mer_stats/kmc.err | |
| 95 1 contig1 | |
| 96 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 \ | |
| 97 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \ | |
| 98 2>> outputdir/k_mer_stats/kmc.err | |
| 99 2 contig2 | |
| 100 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 \ | |
| 101 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \ | |
| 102 2>> outputdir/k_mer_stats/kmc.err | |
| 103 Creating total report... | |
| 104 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex | |
| 105 Done. | |
| 106 | |
| 107 2021-11-07 18:59:04 | |
| 108 Running Contig analyzer... | |
| 109 1 contig1 | |
| 110 1 Logging to files /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... | |
| 111 1 Aligning contigs to the reference | |
| 112 1 /usr/local/bin/minimap2 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 \ | |
| 113 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat \ | |
| 114 outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \ | |
| 115 2>> outputdir/contigs_reports/contigs_report_contig1.stderr | |
| 116 1 Analysis is finished. | |
| 117 | |
| 118 2 contig2 | |
| 119 2 Logging to files /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... | |
| 120 2 Aligning contigs to the reference | |
| 121 2 /usr/local/bin/minimap2 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 \ | |
| 122 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat \ | |
| 123 outputdir/quast_corrected_input/contig2 > outputdir/contigs_reports/minimap_output/contig2.coords_tmp \ | |
| 124 2>> outputdir/contigs_reports/contigs_report_contig2.stderr | |
| 125 2 Analysis is finished. | |
| 126 | |
| 127 Creating total report... | |
| 128 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex | |
| 129 Transposed version of total report... | |
| 130 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex | |
| 131 Creating total report... | |
| 132 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex | |
| 133 Drawing misassemblies by types plot... | |
| 134 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf | |
| 135 Drawing misassemblies FRCurve plot... | |
| 136 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf | |
| 137 Done. | |
| 138 | |
| 139 2021-11-07 18:59:04 | |
| 140 Running NA-NGA calculation... | |
| 141 1 contig1, Largest alignment = 2030, NA50 = 1610, NGA50 = 1610, LA50 = 2, LGA50 = 2 | |
| 142 2 contig2, Largest alignment = 6650, NA50 = 6650, NGA50 = 6650, LA50 = 1, LGA50 = 1 | |
| 143 Drawing cumulative plot... | |
| 144 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf | |
| 145 Drawing NAx plot... | |
| 146 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf | |
| 147 Drawing NGAx plot... | |
| 148 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf | |
| 149 Done. | |
| 150 | |
| 151 2021-11-07 18:59:05 | |
| 152 Running Genome analyzer... | |
| 153 Loaded 14 genomic features of type "ANY" | |
| 154 NOTICE: Reference name in file with genomic features of type "ANY" (NC_000913.3) does not match the name in the reference file (NC_000913.3_1_6650). QUAST will ignore this issue and count as if they match. | |
| 155 WARNING: Incorrect format of operon's file! GFF, NCBI and the plain TXT format accepted. See manual. | |
| 156 WARNING: /tmp/tmpfgnwy_vl/files/e/5/8/dataset_e5851e9e-28d2-42f8-9a7a-0d05d0770635.dat was skipped | |
| 157 WARNING: No genomic features of type "operon" were loaded. | |
| 158 1 contig1 | |
| 159 1 Analysis is finished. | |
| 160 2 contig2 | |
| 161 2 Analysis is finished. | |
| 162 Drawing genomic features cumulative plot... | |
| 163 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf | |
| 164 Drawing genomic features FRCurve plot... | |
| 165 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf | |
| 166 Drawing # complete genomic features histogram... | |
| 167 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf | |
| 168 Drawing Genome fraction, % histogram... | |
| 169 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf | |
| 170 Done. | |
| 171 | |
| 172 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. | |
| 173 | |
| 174 2021-11-07 18:59:05 | |
| 175 Creating large visual summaries... | |
| 176 This may take a while: press Ctrl-C to skip this step.. | |
| 177 1 of 3: Creating Icarus viewers... | |
| 178 2 of 3: Creating Circos plot... | |
| 179 /usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \ | |
| 180 2> outputdir/circos/circos.err | |
| 181 3 of 3: Creating PDF with all tables and plots... | |
| 182 Done | |
| 183 | |
| 184 2021-11-07 18:59:15 | |
| 185 RESULTS: | |
| 186 Text versions of total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex | |
| 187 Text versions of transposed total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex | |
| 188 HTML version (interactive tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.html | |
| 189 PDF version (tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.pdf | |
| 190 Circos plot is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf) | |
| 191 Icarus (contig browser) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/icarus.html | |
| 192 Log is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log | |
| 193 | |
| 194 Finished: 2021-11-07 18:59:15 | |
| 195 Elapsed time: 0:00:13.941680 | |
| 196 NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0 | |
| 197 | |
| 198 Thank you for using QUAST! |