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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 contig1,contig2 -o outputdir -r /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat --features /tmp/tmphjbhe4x0/files/3/1/a/dataset_31a7a886-1c84-4423-8fc9-cdfda1537f40.dat --operons /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat --circos --k-mer-stats --k-mer-size 101 --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 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat --threads 1 1 /usr/local/bin/quast --labels contig1,contig2 -o outputdir -r /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat --features /tmp/tmplvd_uy2v/files/a/3/1/dataset_a314adcb-6b74-48ce-9b09-e2eba7a43bd1.dat --operons /tmp/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat --circos --k-mer-stats --k-mer-size 101 --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 --extensive-mis-size 1000 --scaffold-gap-max-size 1000 --unaligned-part-size 500 --x-for-Nx 90 /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.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 16:53:46 10 Started: 2024-11-12 11:21:53
11 11
12 Logging to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log 12 Logging to /tmp/tmplvd_uy2v/job_working_directory/000/12/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/000/12/working 15 CWD: /tmp/tmplvd_uy2v/job_working_directory/000/12/working
16 Main parameters: 16 Main parameters:
17 MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \ 17 MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
18 ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000 18 ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000
19 19
20 Reference: 20 Reference:
21 /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat ==> dataset_adad470c-d758-46ef-afd5-390f178fb362 21 /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39
22 22
23 Contigs: 23 Contigs:
24 Pre-processing... 24 Pre-processing...
25 1 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat ==> contig1 25 1 /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat ==> contig1
26 2 /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat ==> contig2 26 2 /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat ==> contig2
27 27
28 2022-07-07 16:53:55 28 2024-11-12 11:21:54
29 Running Basic statistics processor... 29 Running Basic statistics processor...
30 Reference genome: 30 Reference genome:
31 dataset_adad470c-d758-46ef-afd5-390f178fb362.dat, length = 6650, num fragments = 1, GC % = 52.00 31 dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat, length = 6650, num fragments = 1, GC % = 52.00
32 Contig files: 32 Contig files:
33 1 contig1 33 1 contig1
34 2 contig2 34 2 contig2
35 Calculating N50 and L50... 35 Calculating N50 and L50...
36 1 contig1, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00 36 1 contig1, N50 = 3980, L50 = 1, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00
37 2 contig2, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00 37 2 contig2, N50 = 6650, L50 = 1, auN = 6650.0, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00
38 Drawing Nx plot... 38 Drawing Nx plot...
39 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf 39 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf
40 Drawing NGx plot... 40 Drawing NGx plot...
41 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf 41 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf
42 Drawing cumulative plot... 42 Drawing cumulative plot...
43 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf 43 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf
44 Drawing GC content plot... 44 Drawing GC content plot...
45 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf 45 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf
46 Drawing contig1 GC content plot... 46 Drawing contig1 GC content plot...
47 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf 47 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf
48 Drawing contig2 GC content plot... 48 Drawing contig2 GC content plot...
49 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf 49 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf
50 Done. 50 Done.
51 51
52 2022-07-07 16:53:58 52 2024-11-12 11:21:54
53 Running analysis based on unique 101-mers... 53 Running analysis based on unique 101-mers...
54 NOTICE: Permission denied accessing /usr/local/lib/python3.12/site-packages/quast_libs/kmc. KMC will be downloaded to home directory /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast
55 Downloading KMC (file: kmc)...
56 KMC successfully downloaded!
57 Downloading KMC (file: kmc_tools)...
58 KMC successfully downloaded!
54 Running KMC on reference... 59 Running KMC on reference...
55 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ 60 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
56 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \ 61 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
57 outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc outputdir/k_mer_stats/tmp \ 62 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp \
58 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 63 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
59 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ 64 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
60 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ 65 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc.histo.txt \
61 outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc.histo.txt \
62 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 66 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
63 Analyzing assemblies completeness... 67 Analyzing assemblies completeness...
64 1 contig1 68 1 contig1
65 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ 69 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
66 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \ 70 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \
67 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 71 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
68 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ 72 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
69 -t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ 73 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \
70 outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \ 74 intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc >> \
75 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
76 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
77 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc.histo.txt \
71 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 78 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
72 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ 79 2 contig2
73 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \ 80 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
74 outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc.histo.txt >> \ 81 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \
82 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
83 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
84 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \
85 intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc >> \
75 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 86 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
76 2 contig2 87 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
77 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \ 88 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc.histo.txt \
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-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
81 -t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
82 outputdir/k_mer_stats/tmp/contig2.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \
83 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 89 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
84 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
85 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc \
86 outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig2.kmc.histo.txt >> \
87 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
88 Analyzing assemblies correctness... 90 Analyzing assemblies correctness...
89 Downsampling k-mers... 91 Downsampling k-mers...
90 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \ 92 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \
91 -t1 -hp filter outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \ 93 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.fasta \
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 -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.filtered.fasta >> outputdir/k_mer_stats/kmc.log \
93 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err 95 2>> outputdir/k_mer_stats/kmc.err
94 1 contig1 96 1 contig1
95 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ 97 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 \
96 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ 98 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \
97 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err 99 2>> outputdir/k_mer_stats/kmc.err
98 2 contig2 100 2 contig2
99 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ 101 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 \
100 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \ 102 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \
101 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err 103 2>> outputdir/k_mer_stats/kmc.err
102 Creating total report... 104 Creating total report...
103 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex 105 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/k_mer_stats/kmers_report.txt, kmers_report.tsv, and kmers_report.tex
104 Done. 106 Done.
105 107
106 2022-07-07 16:54:01 108 2024-11-12 11:21:55
107 Running Contig analyzer... 109 Running Contig analyzer...
108 1 contig1 110 1 contig1
109 1 Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr... 111 1 Logging to files /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig1.stdout and contigs_report_contig1.stderr...
110 1 Aligning contigs to the reference 112 1 Aligning contigs to the reference
111 1 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ 113 1 /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \
112 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \ 114 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
113 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \
114 outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \ 115 outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \
115 2>> outputdir/contigs_reports/contigs_report_contig1.stderr 116 2>> outputdir/contigs_reports/contigs_report_contig1.stderr
116 1 Analysis is finished. 117 1 Analysis is finished.
117 118
118 2 contig2 119 2 contig2
119 2 Logging to files /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/contigs_report_contig2.stdout and contigs_report_contig2.stderr... 120 2 Logging to files /tmp/tmplvd_uy2v/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 121 2 Aligning contigs to the reference
121 2 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \ 122 2 /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \
122 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \ 123 65 -z 200 --mask-level 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
123 0.9 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \
124 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 \
125 2>> outputdir/contigs_reports/contigs_report_contig2.stderr 125 2>> outputdir/contigs_reports/contigs_report_contig2.stderr
126 2 Analysis is finished. 126 2 Analysis is finished.
127 127
128 Creating total report... 128 Creating total report...
129 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex 129 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_report.txt, misassemblies_report.tsv, and misassemblies_report.tex
130 Transposed version of total report... 130 Transposed version of total report...
131 saved to /tmp/tmphjbhe4x0/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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/transposed_report_misassemblies.txt, transposed_report_misassemblies.tsv, and transposed_report_misassemblies.tex
132 Creating total report... 132 Creating total report...
133 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex 133 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/unaligned_report.txt, unaligned_report.tsv, and unaligned_report.tex
134 Drawing misassemblies by types plot... 134 Drawing misassemblies by types plot...
135 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf 135 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf
136 Drawing misassemblies FRCurve plot... 136 Drawing misassemblies FRCurve plot...
137 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf 137 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf
138 Done. 138 Done.
139 139
140 2022-07-07 16:54:01 140 2024-11-12 11:21:55
141 Running NA-NGA calculation... 141 Running NA-NGA calculation...
142 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
143 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
144 Drawing cumulative plot... 144 Drawing cumulative plot...
145 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf 145 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf
146 Drawing NAx plot... 146 Drawing NAx plot...
147 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf 147 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf
148 Drawing NGAx plot... 148 Drawing NGAx plot...
149 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf 149 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf
150 Done. 150 Done.
151 151
152 2022-07-07 16:54:02 152 2024-11-12 11:21:56
153 Running Genome analyzer... 153 Running Genome analyzer...
154 Loaded 14 genomic features of type "ANY" 154 Loaded 14 genomic features of type "ANY"
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 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.
156 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.
157 WARNING: /tmp/tmphjbhe4x0/files/2/9/8/dataset_29831cd9-b20d-4b69-af42-19aa1c84bbbb.dat was skipped 157 WARNING: /tmp/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat was skipped
158 WARNING: No genomic features of type "operon" were loaded. 158 WARNING: No genomic features of type "operon" were loaded.
159 1 contig1 159 1 contig1
160 1 Analysis is finished. 160 1 Analysis is finished.
161 2 contig2 161 2 contig2
162 2 Analysis is finished. 162 2 Analysis is finished.
163 Drawing genomic features cumulative plot... 163 Drawing genomic features cumulative plot...
164 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf 164 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf
165 Drawing genomic features FRCurve plot... 165 Drawing genomic features FRCurve plot...
166 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf 166 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf
167 Drawing # complete genomic features histogram... 167 Drawing # complete genomic features histogram...
168 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf 168 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf
169 Drawing Genome fraction, % histogram... 169 Drawing Genome fraction, % histogram...
170 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf 170 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf
171 Done. 171 Done.
172 172
173 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.
174 174
175 2022-07-07 16:54:04 175 2024-11-12 11:21:56
176 Creating large visual summaries... 176 Creating large visual summaries...
177 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..
178 1 of 3: Creating PDF with all tables and plots... 178 1 of 3: Creating PDF with all tables and plots...
179 2 of 3: Creating Icarus viewers... 179 2 of 3: Creating Icarus viewers...
180 3 of 3: Creating Circos plot... 180 3 of 3: Creating Circos plot...
181 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/circos \ 181 /usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \
182 -conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err 182 2> outputdir/circos/circos.err
183 Done 183 Done
184 184
185 2022-07-07 16:54:16 185 2024-11-12 11:22:00
186 RESULTS: 186 RESULTS:
187 Text versions of total report are saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex 187 Text versions of total report are saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.txt, report.tsv, and report.tex
188 Text versions of transposed total report are saved to /tmp/tmphjbhe4x0/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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/transposed_report.txt, transposed_report.tsv, and transposed_report.tex
189 HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.html 189 HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.html
190 PDF version (tables and plots) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/report.pdf 190 PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.pdf
191 Circos plot is saved to /tmp/tmphjbhe4x0/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/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/circos/circos.png (legend is in legend.txt, configuration file is in circos.conf)
192 Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/icarus.html 192 Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/icarus.html
193 Log is saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log 193 Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log
194 194
195 Finished: 2022-07-07 16:54:16 195 Finished: 2024-11-12 11:22:00
196 Elapsed time: 0:00:30.044753 196 Elapsed time: 0:00:07.048981
197 NOTICEs: 2; WARNINGs: 4; non-fatal ERRORs: 0 197 NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0
198 198
199 Thank you for using QUAST! 199 Thank you for using QUAST!