Mercurial > repos > iuc > quast
comparison test-data/test3.log @ 12:875d0f36d66f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
| author | iuc |
|---|---|
| date | Sun, 06 Feb 2022 21:02:38 +0000 |
| parents | 45924fa8d8c5 |
| children | 3061c8b029e5 |
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| 11:7594365c546b | 12:875d0f36d66f |
|---|---|
| 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! |