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author greg
date Tue, 14 Mar 2023 15:21:14 +0000
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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
2
3 Version: 5.2.0
4
5 System information:
6 OS: Linux-5.13.0-51-generic-x86_64-with-glibc2.31 (linux_64)
7 Python version: 3.9.13
8 CPUs number: 8
9
10 Started: 2022-07-07 16:53:46
11
12 Logging to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/quast.log
13 WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
14
15 CWD: /tmp/tmphjbhe4x0/job_working_directory/000/12/working
16 Main parameters:
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
19
20 Reference:
21 /tmp/tmphjbhe4x0/files/a/d/a/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat ==> dataset_adad470c-d758-46ef-afd5-390f178fb362
22
23 Contigs:
24 Pre-processing...
25 1 /tmp/tmphjbhe4x0/files/d/f/0/dataset_df0f2e39-68eb-4a15-949f-d6678854d50e.dat ==> contig1
26 2 /tmp/tmphjbhe4x0/files/3/4/7/dataset_34703c25-26f5-4dc0-9211-fc1217c11724.dat ==> contig2
27
28 2022-07-07 16:53:55
29 Running Basic statistics processor...
30 Reference genome:
31 dataset_adad470c-d758-46ef-afd5-390f178fb362.dat, length = 6650, num fragments = 1, GC % = 52.00
32 Contig files:
33 1 contig1
34 2 contig2
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
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...
39 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf
40 Drawing NGx plot...
41 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf
42 Drawing cumulative plot...
43 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf
44 Drawing GC content plot...
45 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf
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
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
50 Done.
51
52 2022-07-07 16:53:58
53 Running analysis based on unique 101-mers...
54 Running KMC on reference...
55 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \
56 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat \
57 outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc outputdir/k_mer_stats/tmp \
58 >> 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 \
60 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
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
63 Analyzing assemblies completeness...
64 1 contig1
65 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc \
66 -t1 -hp -m2 -n128 -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
68 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
69 -t1 -hp simple outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
70 outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \
71 >> 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 \
73 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc \
74 outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd_contig1.kmc.histo.txt >> \
75 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
76 2 contig2
77 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/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-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/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
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...
89 Downsampling k-mers...
90 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/lib/python3.9/site-packages/quast_libs/kmc/kmc_tools \
91 -t1 -hp filter outputdir/k_mer_stats/tmp/dataset_adad470c-d758-46ef-afd5-390f178fb362.dat.kmc \
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 \
93 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
94 1 contig1
95 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
96 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \
97 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err
98 2 contig2
99 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
100 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \
101 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err
102 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
104 Done.
105
106 2022-07-07 16:54:01
107 Running Contig analyzer...
108 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...
110 1 Aligning contigs to the reference
111 1 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
112 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \
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 2>> outputdir/contigs_reports/contigs_report_contig1.stderr
116 1 Analysis is finished.
117
118 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 Aligning contigs to the reference
121 2 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/minimap2 \
122 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s 65 -z 200 --mask-level \
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 \
125 2>> outputdir/contigs_reports/contigs_report_contig2.stderr
126 2 Analysis is finished.
127
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
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
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
134 Drawing misassemblies by types plot...
135 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf
136 Drawing misassemblies FRCurve plot...
137 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf
138 Done.
139
140 2022-07-07 16:54:01
141 Running NA-NGA calculation...
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
144 Drawing cumulative plot...
145 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf
146 Drawing NAx plot...
147 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf
148 Drawing NGAx plot...
149 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf
150 Done.
151
152 2022-07-07 16:54:02
153 Running Genome analyzer...
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.
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
158 WARNING: No genomic features of type "operon" were loaded.
159 1 contig1
160 1 Analysis is finished.
161 2 contig2
162 2 Analysis is finished.
163 Drawing genomic features cumulative plot...
164 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf
165 Drawing genomic features FRCurve plot...
166 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf
167 Drawing # complete genomic features histogram...
168 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf
169 Drawing Genome fraction, % histogram...
170 saved to /tmp/tmphjbhe4x0/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf
171 Done.
172
173 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
174
175 2022-07-07 16:54:04
176 Creating large visual summaries...
177 This may take a while: press Ctrl-C to skip this step..
178 1 of 3: Creating PDF with all tables and plots...
179 2 of 3: Creating Icarus viewers...
180 3 of 3: Creating Circos plot...
181 /home/laptop/miniconda3/envs/mulled-v1-92b15e9954bc988dbc8d54298d41c8a76a5ff384441fcf564162dec5c1c0faf0/bin/circos \
182 -conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err
183 Done
184
185 2022-07-07 16:54:16
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
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
189 HTML version (interactive tables and plots) is saved to /tmp/tmphjbhe4x0/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
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)
192 Icarus (contig browser) is saved to /tmp/tmphjbhe4x0/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
194
195 Finished: 2022-07-07 16:54:16
196 Elapsed time: 0:00:30.044753
197 NOTICEs: 2; WARNINGs: 4; non-fatal ERRORs: 0
198
199 Thank you for using QUAST!