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comparison test-data/test3.log @ 18:c791615bcc55 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 5b2225491719b922003c69f0394bfc3eb238b360
author iuc
date Sat, 04 Oct 2025 15:48:40 +0000
parents 2f0ede3447fb
children
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17:2f0ede3447fb 18:c791615bcc55
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 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/tmpq9nvn3a2/files/9/1/e/dataset_91ea48a6-22ee-45b1-9f7f-206c94f14ba8.dat --threads 1 --no-krona
2 2
3 Version: 5.3.0 3 Version: 5.3.0
4 4
5 System information: 5 System information:
6 OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64) 6 OS: Linux-6.8.0-83-generic-x86_64-with-glibc2.36 (linux_64)
7 Python version: 3.12.3 7 Python version: 3.12.3
8 CPUs number: 12 8 CPUs number: 8
9 9
10 Started: 2024-11-12 11:22:10 10 Started: 2025-09-26 14:27:05
11 11
12 Logging to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log 12 Logging to /tmp/tmpq9nvn3a2/job_working_directory/000/8/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/tmplvd_uy2v/job_working_directory/000/14/working 15 CWD: /tmp/tmpq9nvn3a2/job_working_directory/000/8/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 /tmp/tmplvd_uy2v/files/9/3/d/dataset_93dcca11-36ea-4b55-9eac-980009de363e.dat ==> contigs1_fna 22 /tmp/tmpq9nvn3a2/files/9/1/e/dataset_91ea48a6-22ee-45b1-9f7f-206c94f14ba8.dat ==> contigs1_fna
23 23
24 2024-11-12 11:22:11 24 2025-09-26 14:27:06
25 Running Basic statistics processor... 25 Running Basic statistics processor...
26 Contig files: 26 Contig files:
27 contigs1_fna 27 contigs1_fna
28 Calculating N50 and L50... 28 Calculating N50 and L50...
29 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
30 Drawing Nx plot... 30 Drawing Nx plot...
31 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/Nx_plot.pdf 31 saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/basic_stats/Nx_plot.pdf
32 Drawing cumulative plot... 32 Drawing cumulative plot...
33 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/cumulative_plot.pdf 33 saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/basic_stats/cumulative_plot.pdf
34 Drawing GC content plot... 34 Drawing GC content plot...
35 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/GC_content_plot.pdf 35 saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/basic_stats/GC_content_plot.pdf
36 Drawing contigs1_fna GC content plot... 36 Drawing contigs1_fna GC content plot...
37 saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf 37 saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/basic_stats/contigs1_fna_GC_content_plot.pdf
38 Done. 38 Done.
39 39
40 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.
41 41
42 2024-11-12 11:22:11 42 2025-09-26 14:27:06
43 Creating large visual summaries... 43 Creating large visual summaries...
44 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..
45 1 of 2: Creating PDF with all tables and plots... 45 1 of 2: Creating PDF with all tables and plots...
46 2 of 2: Creating Icarus viewers... 46 2 of 2: Creating Icarus viewers...
47 Done 47 Done
48 48
49 2024-11-12 11:22:11 49 2025-09-26 14:27:07
50 RESULTS: 50 RESULTS:
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 51 Text versions of total report are saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/report.txt, report.tsv, and 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 52 Text versions of transposed total report are saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
53 HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.html 53 HTML version (interactive tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/report.html
54 PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/report.pdf 54 PDF version (tables and plots) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/report.pdf
55 Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/icarus.html 55 Icarus (contig browser) is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/icarus.html
56 Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/14/working/outputdir/quast.log 56 Log is saved to /tmp/tmpq9nvn3a2/job_working_directory/000/8/working/outputdir/quast.log
57 57
58 Finished: 2024-11-12 11:22:11 58 Finished: 2025-09-26 14:27:07
59 Elapsed time: 0:00:01.104288 59 Elapsed time: 0:00:01.640426
60 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0 60 NOTICEs: 1; WARNINGs: 1; non-fatal ERRORs: 0
61 61
62 Thank you for using QUAST! 62 Thank you for using QUAST!