Mercurial > repos > iuc > quast

annotate test-data/test3.log @ 14:3061c8b029e5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
author iuc
date Fri, 05 Aug 2022 15:21:27 +0000
parents 875d0f36d66f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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1 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-identity 95.0 --min-contig 500 --min-alignment 65 --ambiguity-usage one --ambiguity-score 0.99 --local-mis-size 200 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs --x-for-Nx 90 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat --threads 1
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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3 Version: 5.2.0
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5 System information:
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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6 OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64)
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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7 Python version: 3.9.13
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8 CPUs number: 8
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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10 Started: 2022-07-07 16:55:02
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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12 Logging to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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13 WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
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14
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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15 CWD: /tmp/tmphjbhe4x0/job_working_directory/000/15/working
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16 Main parameters:
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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17 MODE: default, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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18 min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000
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20 Contigs:
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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21 Pre-processing...
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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22 1 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat ==> contigs1_fna
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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23 2 /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat ==> contigs2_fna
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25 2022-07-07 16:55:11
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26 Running Basic statistics processor...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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27 Contig files:
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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28 1 contigs1_fna
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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29 2 contigs2_fna
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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30 Calculating N50 and L50...
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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31 1 contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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32 2 contigs2_fna, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00
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33 Drawing Nx plot...
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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34 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf
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35 Drawing cumulative plot...
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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36 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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37 Drawing GC content plot...
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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38 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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39 Drawing contigs1_fna GC content plot...
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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40 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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41 Drawing contigs2_fna GC content plot...
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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42 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf
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43 Done.
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45 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
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46
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47 2022-07-07 16:55:13
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48 Creating large visual summaries...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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49 This may take a while: press Ctrl-C to skip this step..
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50 1 of 2: Creating PDF with all tables and plots...
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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51 2 of 2: Creating Icarus viewers...
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52 Done
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54 2022-07-07 16:55:14
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55 RESULTS:
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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56 Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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57 Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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58 HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.html
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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59 PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.pdf
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
iuc
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60 Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/icarus.html
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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61 Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log
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62
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63 Finished: 2022-07-07 16:55:14
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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64 Elapsed time: 0:00:11.737584
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65 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0
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67 Thank you for using QUAST!