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comparison test-data/test3.log @ 13:74be236ac5fd draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
author iuc
date Sun, 06 Feb 2022 21:01:58 +0000
parents e377f054bcd0
children 25368452f73b
comparison
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12:83b8464a1931 13:74be236ac5fd
1 /usr/local/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs /tmp/tmpfgnwy_vl/files/7/8/2/dataset_78284ced-4f1f-4eb6-a4e0-97cb937c125a.dat /tmp/tmpfgnwy_vl/files/6/b/d/dataset_6bd1949d-014f-47ff-8b78-b609c6a19455.dat --threads 1 1 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contigs1_fna,contigs2_fna -o outputdir --eukaryote --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000,500 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --skip-unaligned-mis-contigs /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat --threads 1
2 2
3 Version: 5.0.2 3 Version: 5.0.2
4 4
5 System information: 5 System information:
6 OS: Linux-5.11.0-37-generic-x86_64-with-debian-10.9 (linux_64) 6 OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64)
7 Python version: 3.7.12 7 Python version: 3.7.12
8 CPUs number: 8 8 CPUs number: 8
9 9
10 Started: 2021-11-07 18:59:34 10 Started: 2022-02-06 19:55:07
11 11
12 Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/quast.log 12 Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log
13 NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
13 14
14 CWD: /tmp/tmpfgnwy_vl/job_working_directory/000/15/working 15 CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/15/working
15 Main parameters: 16 Main parameters:
16 MODE: default, threads: 1, eukaryotic: true, minimum contig length: 500, minimum alignment length: 65, \ 17 MODE: default, threads: 1, eukaryotic: true, minimum contig length: 500, minimum alignment length: 65, \
17 ambiguity: one, threshold for extensive misassembly size: 1000 18 ambiguity: all, threshold for extensive misassembly size: 1000
18 19
19 Contigs: 20 Contigs:
20 Pre-processing... 21 Pre-processing...
21 1 /tmp/tmpfgnwy_vl/files/7/8/2/dataset_78284ced-4f1f-4eb6-a4e0-97cb937c125a.dat ==> contigs1_fna 22 1 /tmp/tmpmqu3v_ze/files/c/a/f/dataset_cafcd90b-16e7-46aa-8617-cdefd1766b23.dat ==> contigs1_fna
22 2 /tmp/tmpfgnwy_vl/files/6/b/d/dataset_6bd1949d-014f-47ff-8b78-b609c6a19455.dat ==> contigs2_fna 23 2 /tmp/tmpmqu3v_ze/files/6/4/e/dataset_64ec6db4-a92f-4ec5-b641-96e96830b6b5.dat ==> contigs2_fna
23 24
24 2021-11-07 18:59:34 25 2022-02-06 19:55:10
25 Running Basic statistics processor... 26 Running Basic statistics processor...
26 Contig files: 27 Contig files:
27 1 contigs1_fna 28 1 contigs1_fna
28 2 contigs2_fna 29 2 contigs2_fna
29 Calculating N50 and L50... 30 Calculating N50 and L50...
30 1 contigs1_fna, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 31 1 contigs1_fna, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00
31 2 contigs2_fna, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 32 2 contigs2_fna, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00
32 Drawing Nx plot... 33 Drawing Nx plot...
33 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf 34 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/Nx_plot.pdf
34 Drawing cumulative plot... 35 Drawing cumulative plot...
35 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf 36 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/cumulative_plot.pdf
36 Drawing GC content plot... 37 Drawing GC content plot...
37 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf 38 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/GC_content_plot.pdf
38 Drawing contigs1_fna GC content plot... 39 Drawing contigs1_fna GC content plot...
39 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf 40 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf
40 Drawing contigs2_fna GC content plot... 41 Drawing contigs2_fna GC content plot...
41 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf 42 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/basic_stats/contigs2_fna_GC_content_plot.pdf
42 Done. 43 Done.
43 44
44 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. 45 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
45 46
46 2021-11-07 18:59:35 47 2022-02-06 19:55:11
47 Creating large visual summaries... 48 Creating large visual summaries...
48 This may take a while: press Ctrl-C to skip this step.. 49 This may take a while: press Ctrl-C to skip this step..
49 1 of 2: Creating Icarus viewers... 50 1 of 2: Creating Icarus viewers...
50 2 of 2: Creating PDF with all tables and plots... 51 2 of 2: Creating PDF with all tables and plots...
51 Done 52 Done
52 53
53 2021-11-07 18:59:36 54 2022-02-06 19:55:12
54 RESULTS: 55 RESULTS:
55 Text versions of total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex 56 Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.txt, report.tsv, and report.tex
56 Text versions of transposed total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex 57 Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
57 HTML version (interactive tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.html 58 HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.html
58 PDF version (tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/report.pdf 59 PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/report.pdf
59 Icarus (contig browser) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/icarus.html 60 Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/icarus.html
60 Log is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/15/working/outputdir/quast.log 61 Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/15/working/outputdir/quast.log
61 62
62 Finished: 2021-11-07 18:59:36 63 Finished: 2022-02-06 19:55:12
63 Elapsed time: 0:00:02.245904 64 Elapsed time: 0:00:04.673393
64 NOTICEs: 1; WARNINGs: 0; non-fatal ERRORs: 0 65 NOTICEs: 2; WARNINGs: 0; non-fatal ERRORs: 0
65 66
66 Thank you for using QUAST! 67 Thank you for using QUAST!