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comparison test-data/test3.log @ 16:a3b35edea53a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
author iuc
date Tue, 12 Nov 2024 12:46:19 +0000
parents 3061c8b029e5
children
comparison
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15:72472698a2df 16:a3b35edea53a
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 1 /usr/local/bin/quast --labels contigs1_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/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat --threads 1
2 2
3 Version: 5.2.0 3 Version: 5.3.0
4 4
5 System information: 5 System information:
6 OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64) 6 OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64)
7 Python version: 3.9.13 7 Python version: 3.12.3
8 CPUs number: 8 8 CPUs number: 12
9 9
10 Started: 2022-07-07 16:55:02 10 Started: 2024-11-12 11:22:10
11 11
12 Logging to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log 12 Logging to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log
13 WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified 13 WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
14 14
15 CWD: /tmp/tmphjbhe4x0/job_working_directory/000/15/working 15 CWD: /tmp/tmplvd_uy2v/job_working_directory/000/14/working
16 Main parameters: 16 Main parameters:
17 MODE: default, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \ 17 MODE: default, threads: 1, eukaryotic: true, min contig length: 500, min alignment length: 65, \
18 min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 18 min alignment IDY: 95.0, ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000
19 19
20 Contigs: 20 Contigs:
21 Pre-processing... 21 Pre-processing...
22 1 /tmp/tmphjbhe4x0/files/0/2/b/dataset_02bce539-33f0-4693-bfe9-a92ebf1615f8.dat ==> contigs1_fna 22 /tmp/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat ==> contigs1_fna
23 2 /tmp/tmphjbhe4x0/files/6/0/2/dataset_60253425-26a2-4019-bae6-07285864be68.dat ==> contigs2_fna
24 23
25 2022-07-07 16:55:11 24 2024-11-12 11:22:11
26 Running Basic statistics processor... 25 Running Basic statistics processor...
27 Contig files: 26 Contig files:
28 1 contigs1_fna 27 contigs1_fna
29 2 contigs2_fna
30 Calculating N50 and L50... 28 Calculating N50 and L50...
31 1 contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 29 contigs1_fna, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00
32 2 contigs2_fna, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00
33 Drawing Nx plot... 30 Drawing Nx plot...
34 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf 31 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/Nx_plot.pdf
35 Drawing cumulative plot... 32 Drawing cumulative plot...
36 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf 33 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/cumulative_plot.pdf
37 Drawing GC content plot... 34 Drawing GC content plot...
38 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf 35 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/GC_content_plot.pdf
39 Drawing contigs1_fna GC content plot... 36 Drawing contigs1_fna GC content plot...
40 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf 37 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf
41 Drawing contigs2_fna GC content plot...
42 saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf
43 Done. 38 Done.
44 39
45 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 40 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
46 41
47 2022-07-07 16:55:13 42 2024-11-12 11:22:11
48 Creating large visual summaries... 43 Creating large visual summaries...
49 This may take a while: press Ctrl-C to skip this step.. 44 This may take a while: press Ctrl-C to skip this step..
50 1 of 2: Creating PDF with all tables and plots... 45 1 of 2: Creating PDF with all tables and plots...
51 2 of 2: Creating Icarus viewers... 46 2 of 2: Creating Icarus viewers...
52 Done 47 Done
53 48
54 2022-07-07 16:55:14 49 2024-11-12 11:22:11
55 RESULTS: 50 RESULTS:
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 51 Text versions of total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.txt, report.tsv, and report.tex
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 52 Text versions of transposed total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
58 HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.html 53 HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.html
59 PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/report.pdf 54 PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.pdf
60 Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/icarus.html 55 Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/icarus.html
61 Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/15/working/outputdir/quast.log 56 Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log
62 57
63 Finished: 2022-07-07 16:55:14 58 Finished: 2024-11-12 11:22:11
64 Elapsed time: 0:00:11.737584 59 Elapsed time: 0:00:01.104288
65 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 60 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0
66 61
67 Thank you for using QUAST! 62 Thank you for using QUAST!