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annotate test-data/test2.log @ 13:675488238c96 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 73d0b20640827d06320405f8d52cead9bf027beb"
author iuc
date Fri, 25 Mar 2022 17:36:59 +0000
parents 875d0f36d66f
children 3061c8b029e5
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875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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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
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3 Version: 5.0.2
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5 System information:
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6 OS: Linux-5.13.0-28-generic-x86_64-with-debian-bullseye-sid (linux_64)
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7 Python version: 3.7.12
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8 CPUs number: 8
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875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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10 Started: 2022-02-06 19:54:35
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875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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12 Logging to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log
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13 NOTICE: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
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15 CWD: /tmp/tmpmqu3v_ze/job_working_directory/000/12/working
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16 Main parameters:
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17 MODE: default, threads: 1, minimum contig length: 500, minimum alignment length: 65, \
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18 ambiguity: all, threshold for extensive misassembly size: 1000
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20 Reference:
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21 /tmp/tmpmqu3v_ze/files/f/2/0/dataset_f20bc8a3-6ab5-43f7-a0a3-42dcc6408039.dat ==> dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039
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23 Contigs:
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24 Pre-processing...
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25 1 /tmp/tmpmqu3v_ze/files/a/e/3/dataset_ae3fd171-9eb4-40d1-a8c8-d896fef3f293.dat ==> contig1
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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26 2 /tmp/tmpmqu3v_ze/files/f/c/b/dataset_fcbec1fc-e7c4-42db-b9e4-7c32ac9882dd.dat ==> contig2
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27
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28 2022-02-06 19:54:39
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29 Running Basic statistics processor...
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30 Reference genome:
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31 dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat, length = 6650, num fragments = 1, GC % = 52.00
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32 Contig files:
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33 1 contig1
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34 2 contig2
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35 Calculating N50 and L50...
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36 1 contig1, N50 = 3980, L50 = 1, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00
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37 2 contig2, N50 = 6650, L50 = 1, Total length = 6650, GC % = 52.00, # N's per 100 kbp = 0.00
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38 Drawing Nx plot...
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39 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/Nx_plot.pdf
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40 Drawing NGx plot...
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41 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/NGx_plot.pdf
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42 Drawing cumulative plot...
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43 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/cumulative_plot.pdf
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44 Drawing GC content plot...
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45 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/GC_content_plot.pdf
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46 Drawing contig1 GC content plot...
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47 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/contig1_GC_content_plot.pdf
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48 Drawing contig2 GC content plot...
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49 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/basic_stats/contig2_GC_content_plot.pdf
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50 Done.
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51
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52 2022-02-06 19:54:40
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53 Running analysis based on unique 101-mers...
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54 Running KMC on reference...
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55 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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56 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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57 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc outputdir/k_mer_stats/tmp \
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58 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
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59 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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60 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \
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61 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc.histo.txt \
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62 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
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63 Analyzing assemblies completeness...
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64 1 contig1
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65 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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66 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \
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67 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
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68 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
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69 -t1 -hp simple outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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70 outputdir/k_mer_stats/tmp/contig1.kmc intersect outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc \
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71 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
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72 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
73 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
74 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig1.kmc.histo.txt >> \
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
75 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
76 2 contig2
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
77 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
78 -t1 -hp -m2 -n128 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/contig2.kmc \
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
79 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
80 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
81 -t1 -hp simple outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
82 outputdir/k_mer_stats/tmp/contig2.kmc intersect outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
83 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
84 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
85 -t1 -hp histogram outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
86 outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a_contig2.kmc.histo.txt >> \
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
87 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
88 Analyzing assemblies correctness...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
89 Downsampling k-mers...
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
90 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/lib/python3.7/site-packages/quast_libs/kmc/kmc_tools \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
91 -t1 -hp filter outputdir/k_mer_stats/tmp/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat.kmc \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
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 \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
93 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
94 1 contig1
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
95 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
96 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
97 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
98 2 contig2
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
99 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
100 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 outputdir/k_mer_stats/tmp/kmc.downsampled.txt \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
101 > outputdir/k_mer_stats/tmp/kmers.coords 2>> outputdir/k_mer_stats/kmc.err
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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102 Creating total report...
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
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
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
104 Done.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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105
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
106 2022-02-06 19:54:41
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
107 Running Contig analyzer...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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108 1 contig1
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
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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...
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
110 1 Aligning contigs to the reference
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
111 1 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
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112 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
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diff changeset
113 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat \
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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114 outputdir/quast_corrected_input/contig1 > outputdir/contigs_reports/minimap_output/contig1.coords_tmp \
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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115 2>> outputdir/contigs_reports/contigs_report_contig1.stderr
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
116 1 Analysis is finished.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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117
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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118 2 contig2
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
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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...
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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120 2 Aligning contigs to the reference
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
121 2 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/minimap2 \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
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122 -c -x asm5 -B5 -O4,16 --no-long-join -r 85 -N 50 -s 65 -z 200 --mask-level 0.9 \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
123 --min-occ 200 -g 2500 --score-N 2 --cs -t 1 outputdir/quast_corrected_input/dataset_f20bc8a3_6ab5_43f7_a0a3_42dcc6408039.dat \
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
124 outputdir/quast_corrected_input/contig2 > outputdir/contigs_reports/minimap_output/contig2.coords_tmp \
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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125 2>> outputdir/contigs_reports/contigs_report_contig2.stderr
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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126 2 Analysis is finished.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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127
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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diff changeset
128 Creating total report...
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
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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
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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130 Transposed version of total report...
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
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
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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132 Creating total report...
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
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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
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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134 Drawing misassemblies by types plot...
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
135 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_plot.pdf
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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136 Drawing misassemblies FRCurve plot...
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
137 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/contigs_reports/misassemblies_frcurve_plot.pdf
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
diff changeset
138 Done.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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139
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
parents: 9
diff changeset
140 2022-02-06 19:54:41
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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141 Running NA-NGA calculation...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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142 1 contig1, Largest alignment = 2030, NA50 = 1610, NGA50 = 1610, LA50 = 2, LGA50 = 2
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
parents:
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143 2 contig2, Largest alignment = 6650, NA50 = 6650, NGA50 = 6650, LA50 = 1, LGA50 = 1
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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144 Drawing cumulative plot...
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145 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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146 Drawing NAx plot...
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147 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/NAx_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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148 Drawing NGAx plot...
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149 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/aligned_stats/NGAx_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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150 Done.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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151
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152 2022-02-06 19:54:42
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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153 Running Genome analyzer...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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154 Loaded 14 genomic features of type "ANY"
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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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.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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156 WARNING: Incorrect format of operon's file! GFF, NCBI and the plain TXT format accepted. See manual.
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157 WARNING: /tmp/tmpmqu3v_ze/files/f/f/a/dataset_ffa07559-8af9-4a08-8719-807dc3575dc8.dat was skipped
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158 WARNING: No genomic features of type "operon" were loaded.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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159 1 contig1
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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160 1 Analysis is finished.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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161 2 contig2
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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162 2 Analysis is finished.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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163 Drawing genomic features cumulative plot...
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164 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_cumulative_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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165 Drawing genomic features FRCurve plot...
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166 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/features_frcurve_plot.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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167 Drawing # complete genomic features histogram...
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168 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/complete_features_histogram.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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169 Drawing Genome fraction, % histogram...
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875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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170 saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/genome_stats/genome_fraction_histogram.pdf
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45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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171 Done.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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172
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173 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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174
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175 2022-02-06 19:54:42
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176 Creating large visual summaries...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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177 This may take a while: press Ctrl-C to skip this step..
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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178 1 of 3: Creating Icarus viewers...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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179 2 of 3: Creating Circos plot...
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180 /home/laptop/miniconda3/envs/mulled-v1-77a890c6a67835ab995adc5c8cf65f55886a6cbedc27599b62f1d6a231bcca56/bin/circos \
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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181 -conf outputdir/circos/circos.conf > outputdir/circos/circos.log 2> outputdir/circos/circos.err
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182 3 of 3: Creating PDF with all tables and plots...
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183 Done
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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184
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185 2022-02-06 19:54:46
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186 RESULTS:
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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
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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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
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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189 HTML version (interactive tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.html
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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190 PDF version (tables and plots) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/report.pdf
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
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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)
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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192 Icarus (contig browser) is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/icarus.html
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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193 Log is saved to /tmp/tmpmqu3v_ze/job_working_directory/000/12/working/outputdir/quast.log
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194
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195 Finished: 2022-02-06 19:54:46
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
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196 Elapsed time: 0:00:11.313989
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197 NOTICEs: 3; WARNINGs: 3; non-fatal ERRORs: 0
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198
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199 Thank you for using QUAST!