Mercurial > repos > iuc > quast
comparison test-data/test2.log @ 13:74be236ac5fd draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
| author | iuc |
|---|---|
| date | Sun, 06 Feb 2022 21:01:58 +0000 |
| parents | e377f054bcd0 |
| children | 25368452f73b |
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| 12:83b8464a1931 | 13:74be236ac5fd |
|---|---|
| 1 /usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat --features /tmp/tmpfgnwy_vl/files/4/0/6/dataset_406c3bca-dfac-498b-954d-476186610bc9.dat --operons /tmp/tmpfgnwy_vl/files/e/5/8/dataset_e5851e9e-28d2-42f8-9a7a-0d05d0770635.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat --threads 1 | 1 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat --features /tmp/tmpmqu3v_ze/files/2/a/f/dataset_2afd5bcc-2ff5-46bc-83cd-0690bcbd9c67.dat --operons /tmp/tmpmqu3v_ze/files/f/f/a/dataset_ffa07559-8af9-4a08-8719-807dc3575dc8.dat --circos --k-mer-stats --k-mer-size 101 --min-contig 500 --min-alignment 65 --min-identity 95.0 --ambiguity-usage one --ambiguity-score 0.99 --contig-thresholds 0,1000 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.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 18:59:01 | 10 Started: 2022-02-06 19:54:35 |
| 11 | 11 |
| 12 Logging to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log | 12 Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/12/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/000/12/working | 15 CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/12/working |
| 15 Main parameters: | 16 Main parameters: |
| 16 MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \ | 17 MODE: default, threads: 1, 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 Reference: | 20 Reference: |
| 20 /tmp/tmpfgnwy_vl/files/7/5/6/dataset_7567d03a-76ca-49a4-aaa2-334a7b5a8f74.dat ==> dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74 | 21 /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat ==> dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039 |
| 21 | 22 |
| 22 Contigs: | 23 Contigs: |
| 23 Pre-processing... | 24 Pre-processing... |
| 24 1 /tmp/tmpfgnwy_vl/files/2/3/b/dataset_23b499d4-cf8d-47a3-8ba1-906758c987bb.dat ==> contig1 | 25 1 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat ==> contig1 |
| 25 2 /tmp/tmpfgnwy_vl/files/b/3/5/dataset_b3571672-0e6e-4ff5-8e31-b7135a2d1bd6.dat ==> contig2 | 26 2 /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat ==> contig2 |
| 26 | 27 |
| 27 2021-11-07 18:59:01 | 28 2022-02-06 19:54:39 |
| 28 Running Basic statistics processor... | 29 Running Basic statistics processor... |
| 29 Reference genome: | 30 Reference genome: |
| 30 dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat, length = 6650, num fragments = 1, GC % = 52.00 | 31 dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat, length = 6650, num fragments = 1, GC % = 52.00 |
| 31 Contig files: | 32 Contig files: |
| 32 1 contig1 | 33 1 contig1 |
| 33 2 contig2 | 34 2 contig2 |
| 34 Calculating N50 and L50... | 35 Calculating N50 and L50... |
| 35 1 contig1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 | 36 1 contig1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 |
| 36 2 contig2, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 | 37 2 contig2, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 |
| 37 Drawing Nx plot... | 38 Drawing Nx plot... |
| 38 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf | 39 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf |
| 39 Drawing NGx plot... | 40 Drawing NGx plot... |
| 40 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf | 41 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf |
| 41 Drawing cumulative plot... | 42 Drawing cumulative plot... |
| 42 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf | 43 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf |
| 43 Drawing GC content plot... | 44 Drawing GC content plot... |
| 44 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf | 45 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf |
| 45 Drawing contig1 GC content plot... | 46 Drawing contig1 GC content plot... |
| 46 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf | 47 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf |
| 47 Drawing contig2 GC content plot... | 48 Drawing contig2 GC content plot... |
| 48 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf | 49 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf |
| 49 Done. | 50 Done. |
| 50 | 51 |
| 51 2021-11-07 18:59:02 | 52 2022-02-06 19:54:40 |
| 52 Running analysis based on unique 101-mers... | 53 Running analysis based on unique 101-mers... |
| 53 NOTICE: Permission denied accessing /usr/local/lib/python3.7/site-packages/quast_libs/kmc. KMC will be downloaded to home directory /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast | |
| 54 Downloading KMC (file: kmc)... | |
| 55 KMC successfully downloaded! | |
| 56 Downloading KMC (file: kmc_tools)... | |
| 57 KMC successfully downloaded! | |
| 58 Running KMC on reference... | 54 Running KMC on reference... |
| 59 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ | 55 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc \ |
| 60 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat \ | 56 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat \ |
| 61 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp \ | 57 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc outputdir/k_mer_stats/tmp \ |
| 62 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | 58 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err |
| 63 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ | 59 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \ |
| 64 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc.histo.txt \ | 60 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \ |
| 61 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc.histo.txt \ | |
| 65 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | 62 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err |
| 66 Analyzing assemblies completeness... | 63 Analyzing assemblies completeness... |
| 67 1 contig1 | 64 1 contig1 |
| 68 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ | 65 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc \ |
| 69 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ | 66 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ |
| 70 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | 67 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err |
| 71 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ | 68 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \ |
| 72 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \ | 69 -t1 -hp simple outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \ |
| 73 intersect outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc >> \ | 70 outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc \ |
| 71 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 72 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \ | |
| 73 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc \ | |
| 74 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc.histo.txt >> \ | |
| 74 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | 75 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err |
| 75 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ | 76 2 contig2 |
| 76 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig1.kmc.histo.txt \ | 77 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc \ |
| 78 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \ | |
| 79 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 80 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \ | |
| 81 -t1 -hp simple outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \ | |
| 82 outputdir/k_mer_stats/tmp/contig2.kmc intersect outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc \ | |
| 77 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | 83 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err |
| 78 2 contig2 | 84 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \ |
| 79 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \ | 85 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc \ |
| 80 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \ | 86 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc.histo.txt >> \ |
| 81 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 82 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \ | |
| 83 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \ | |
| 84 intersect outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc >> \ | |
| 85 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | 87 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err |
| 86 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \ | |
| 87 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa_contig2.kmc.histo.txt \ | |
| 88 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err | |
| 89 Analyzing assemblies correctness... | 88 Analyzing assemblies correctness... |
| 90 Downsampling k-mers... | 89 Downsampling k-mers... |
| 91 /tmp/tmpfgnwy_vl/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \ | 90 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \ |
| 92 outputdir/k_mer_stats/tmp/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat.kmc outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1_6650.fasta \ | 91 -t1 -hp filter outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \ |
| 93 -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1_6650.filtered.fasta >> outputdir/k_mer_stats/kmc.log \ | 92 outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1_6650.fasta -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1_6650.filtered.fasta \ |
| 94 2>> outputdir/k_mer_stats/kmc.err | 93 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err |
| 95 1 contig1 | 94 1 contig1 |
| 96 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 \ | 95 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \ |
| 97 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \ | 96 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ |
| 98 2>> outputdir/k_mer_stats/kmc.err | 97 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err |
| 99 2 contig2 | 98 2 contig2 |
| 100 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 \ | 99 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \ |
| 101 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \ | 100 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ |
| 102 2>> outputdir/k_mer_stats/kmc.err | 101 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err |
| 103 Creating total report... | 102 Creating total report... |
| 104 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex | 103 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex |
| 105 Done. | 104 Done. |
| 106 | 105 |
| 107 2021-11-07 18:59:04 | 106 2022-02-06 19:54:41 |
| 108 Running Contig analyzer... | 107 Running Contig analyzer... |
| 109 1 contig1 | 108 1 contig1 |
| 110 1 Logging to files /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... | 109 1 Logging to files /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... |
| 111 1 Aligning contigs to the reference | 110 1 Aligning contigs to the reference |
| 112 1 /usr/local/bin/minimap2 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 \ | 111 1 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \ |
| 113 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat \ | 112 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \ |
| 113 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat \ | |
| 114 outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \ | 114 outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \ |
| 115 2>> outputdir/contigs_reports/contigs_report_contig1.stderr | 115 2>> outputdir/contigs_reports/contigs_report_contig1.stderr |
| 116 1 Analysis is finished. | 116 1 Analysis is finished. |
| 117 | 117 |
| 118 2 contig2 | 118 2 contig2 |
| 119 2 Logging to files /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... | 119 2 Logging to files /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... |
| 120 2 Aligning contigs to the reference | 120 2 Aligning contigs to the reference |
| 121 2 /usr/local/bin/minimap2 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 \ | 121 2 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \ |
| 122 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_7567d03a_76ca_49a4_aaa2_334a7b5a8f74.dat \ | 122 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \ |
| 123 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat \ | |
| 123 outputdir/quast_corrected_input/contig2 > outputdir/contigs_reports/minimap_output/contig2.coords_tmp \ | 124 outputdir/quast_corrected_input/contig2 > outputdir/contigs_reports/minimap_output/contig2.coords_tmp \ |
| 124 2>> outputdir/contigs_reports/contigs_report_contig2.stderr | 125 2>> outputdir/contigs_reports/contigs_report_contig2.stderr |
| 125 2 Analysis is finished. | 126 2 Analysis is finished. |
| 126 | 127 |
| 127 Creating total report... | 128 Creating total report... |
| 128 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex | 129 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex |
| 129 Transposed version of total report... | 130 Transposed version of total report... |
| 130 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex | 131 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex |
| 131 Creating total report... | 132 Creating total report... |
| 132 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex | 133 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex |
| 133 Drawing misassemblies by types plot... | 134 Drawing misassemblies by types plot... |
| 134 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf | 135 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf |
| 135 Drawing misassemblies FRCurve plot... | 136 Drawing misassemblies FRCurve plot... |
| 136 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf | 137 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf |
| 137 Done. | 138 Done. |
| 138 | 139 |
| 139 2021-11-07 18:59:04 | 140 2022-02-06 19:54:41 |
| 140 Running NA-NGA calculation... | 141 Running NA-NGA calculation... |
| 141 1 contig1, Largest alignment = 2030, NA50 = 1610, NGA50 = 1610, LA50 = 2, LGA50 = 2 | 142 1 contig1, Largest alignment = 2030, NA50 = 1610, NGA50 = 1610, LA50 = 2, LGA50 = 2 |
| 142 2 contig2, Largest alignment = 6650, NA50 = 6650, NGA50 = 6650, LA50 = 1, LGA50 = 1 | 143 2 contig2, Largest alignment = 6650, NA50 = 6650, NGA50 = 6650, LA50 = 1, LGA50 = 1 |
| 143 Drawing cumulative plot... | 144 Drawing cumulative plot... |
| 144 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf | 145 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf |
| 145 Drawing NAx plot... | 146 Drawing NAx plot... |
| 146 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf | 147 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf |
| 147 Drawing NGAx plot... | 148 Drawing NGAx plot... |
| 148 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf | 149 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf |
| 149 Done. | 150 Done. |
| 150 | 151 |
| 151 2021-11-07 18:59:05 | 152 2022-02-06 19:54:42 |
| 152 Running Genome analyzer... | 153 Running Genome analyzer... |
| 153 Loaded 14 genomic features of type "ANY" | 154 Loaded 14 genomic features of type "ANY" |
| 154 NOTICE: Reference name in file with genomic features of type "ANY" (NC_000913.3) does not match the name in the reference file (NC_000913.3_1_6650). QUAST will ignore this issue and count as if they match. | 155 NOTICE: Reference name in file with genomic features of type "ANY" (NC_000913.3) does not match the name in the reference file (NC_000913.3_1_6650). QUAST will ignore this issue and count as if they match. |
| 155 WARNING: Incorrect format of operon's file! GFF, NCBI and the plain TXT format accepted. See manual. | 156 WARNING: Incorrect format of operon's file! GFF, NCBI and the plain TXT format accepted. See manual. |
| 156 WARNING: /tmp/tmpfgnwy_vl/files/e/5/8/dataset_e5851e9e-28d2-42f8-9a7a-0d05d0770635.dat was skipped | 157 WARNING: /tmp/tmpmqu3v_ze/files/f/f/a/dataset_ffa07559-8af9-4a08-8719-807dc3575dc8.dat was skipped |
| 157 WARNING: No genomic features of type "operon" were loaded. | 158 WARNING: No genomic features of type "operon" were loaded. |
| 158 1 contig1 | 159 1 contig1 |
| 159 1 Analysis is finished. | 160 1 Analysis is finished. |
| 160 2 contig2 | 161 2 contig2 |
| 161 2 Analysis is finished. | 162 2 Analysis is finished. |
| 162 Drawing genomic features cumulative plot... | 163 Drawing genomic features cumulative plot... |
| 163 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf | 164 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf |
| 164 Drawing genomic features FRCurve plot... | 165 Drawing genomic features FRCurve plot... |
| 165 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf | 166 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf |
| 166 Drawing # complete genomic features histogram... | 167 Drawing # complete genomic features histogram... |
| 167 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf | 168 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf |
| 168 Drawing Genome fraction, % histogram... | 169 Drawing Genome fraction, % histogram... |
| 169 saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf | 170 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf |
| 170 Done. | 171 Done. |
| 171 | 172 |
| 172 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. | 173 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it. |
| 173 | 174 |
| 174 2021-11-07 18:59:05 | 175 2022-02-06 19:54:42 |
| 175 Creating large visual summaries... | 176 Creating large visual summaries... |
| 176 This may take a while: press Ctrl-C to skip this step.. | 177 This may take a while: press Ctrl-C to skip this step.. |
| 177 1 of 3: Creating Icarus viewers... | 178 1 of 3: Creating Icarus viewers... |
| 178 2 of 3: Creating Circos plot... | 179 2 of 3: Creating Circos plot... |
| 179 /usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \ | 180 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/circos \ |
| 180 2> outputdir/circos/circos.err | 181 -conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err |
| 181 3 of 3: Creating PDF with all tables and plots... | 182 3 of 3: Creating PDF with all tables and plots... |
| 182 Done | 183 Done |
| 183 | 184 |
| 184 2021-11-07 18:59:15 | 185 2022-02-06 19:54:46 |
| 185 RESULTS: | 186 RESULTS: |
| 186 Text versions of total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex | 187 Text versions of total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex |
| 187 Text versions of transposed total report are saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex | 188 Text versions of transposed total report are saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex |
| 188 HTML version (interactive tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.html | 189 HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.html |
| 189 PDF version (tables and plots) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/report.pdf | 190 PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.pdf |
| 190 Circos plot is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf) | 191 Circos plot is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf) |
| 191 Icarus (contig browser) is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/icarus.html | 192 Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/icarus.html |
| 192 Log is saved to /tmp/tmpfgnwy_vl/job_working_directory/000/12/working/outputdir/quast.log | 193 Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log |
| 193 | 194 |
| 194 Finished: 2021-11-07 18:59:15 | 195 Finished: 2022-02-06 19:54:46 |
| 195 Elapsed time: 0:00:13.941680 | 196 Elapsed time: 0:00:11.313989 |
| 196 NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0 | 197 NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0 |
| 197 | 198 |
| 198 Thank you for using QUAST! | 199 Thank you for using QUAST! |