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comparison test-data/test2.log @ 12:875d0f36d66f 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 21:02:38 +0000
parents 45924fa8d8c5
children 3061c8b029e5
comparison
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11:7594365c546b 12:875d0f36d66f
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!