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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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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
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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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3 Version: 5.3.0
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5 System information:
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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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6 OS: Linux-6.8.0-107047-tuxedo-x86_64-with-glibc2.36 (linux_64)
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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7 Python version: 3.12.3
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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8 CPUs number: 12
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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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10 Started: 2024-11-12 11:21:53
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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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12 Logging to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log
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13 WARNING: --ambiguity-usage was set to 'all' because not default --ambiguity-score was specified
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15 CWD: /tmp/tmplvd_uy2v/job_working_directory/000/12/working
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16 Main parameters:
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3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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17 MODE: default, threads: 1, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0, \
3061c8b029e5 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit b4d6989e1e185120ce470df5c2b0d93330d5e124
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18 ambiguity: all, min local misassembly length: 200, min extensive misassembly length: 1000
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20 Reference:
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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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21 /tmp/tmplvd_uy2v/files/e/1/3/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat ==> dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39
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23 Contigs:
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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24 Pre-processing...
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25 1 /tmp/tmplvd_uy2v/files/3/8/d/dataset_38d5fa8c-0b60-486f-b06b-e24a07671ffe.dat ==> contig1
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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26 2 /tmp/tmplvd_uy2v/files/e/5/9/dataset_e59d5fa8-3ded-458c-9a91-73dd5f99e1cf.dat ==> contig2
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28 2024-11-12 11:21:54
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29 Running Basic statistics processor...
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30 Reference genome:
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31 dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.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, auN = 2934.0, Total length = 6710, GC % = 51.28, # N's per 100 kbp = 0.00
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37 2 contig2, N50 = 6650, L50 = 1, auN = 6650.0, 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/tmplvd_uy2v/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/tmplvd_uy2v/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/tmplvd_uy2v/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/tmplvd_uy2v/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/tmplvd_uy2v/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/tmplvd_uy2v/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 2024-11-12 11:21:54
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53 Running analysis based on unique 101-mers...
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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
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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55 Downloading KMC (file: kmc)...
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56 KMC successfully downloaded!
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57 Downloading KMC (file: kmc_tools)...
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58 KMC successfully downloaded!
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59 Running KMC on reference...
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60 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
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61 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat \
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62 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp \
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63 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
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64 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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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 \
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66 >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
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67 Analyzing assemblies completeness...
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68 1 contig1
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69 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
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70 -k101 -fm -cx1 -ci1 outputdir/quast_corrected_input/contig1 outputdir/k_mer_stats/tmp/contig1.kmc \
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71 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
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72 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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73 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig1.kmc \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
74 intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig1.kmc >> \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
75 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
76 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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diff changeset
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 \
12
875d0f36d66f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"
iuc
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diff changeset
78 >> 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
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79 2 contig2
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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diff changeset
80 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc -t1 -hp -m2 -n128 \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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diff changeset
81 -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
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diff changeset
82 outputdir/k_mer_stats/tmp >> outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
83 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp simple \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
84 outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6f-a98ad32b0f39.dat.kmc outputdir/k_mer_stats/tmp/contig2.kmc \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
85 intersect outputdir/k_mer_stats/tmp/dataset_e13fd81e-aca0-4d05-9a6_contig2.kmc >> \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
86 outputdir/k_mer_stats/kmc.log 2>> outputdir/k_mer_stats/kmc.err
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
87 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp histogram \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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 \
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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89 >> 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
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diff changeset
90 Analyzing assemblies correctness...
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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91 Downsampling k-mers...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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92 /tmp/tmplvd_uy2v/job_working_directory/000/12/home/.quast/kmc/kmc_tools -t1 -hp filter \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
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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 \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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94 -ci1 -fa outputdir/k_mer_stats/tmp/kmers_NC_000913.3_1-6650.filtered.fasta >> outputdir/k_mer_stats/kmc.log \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
parents: 14
diff changeset
95 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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diff changeset
96 1 contig1
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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diff changeset
97 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig1 \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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98 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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99 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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100 2 contig2
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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101 /usr/local/bin/minimap2 -cx sr -s202 --frag=no -t 1 outputdir/quast_corrected_input/contig2 \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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102 outputdir/k_mer_stats/tmp/kmc.downsampled.txt > outputdir/k_mer_stats/tmp/kmers.coords \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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103 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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104 Creating total report...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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106 Done.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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107
16
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108 2024-11-12 11:21:55
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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109 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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110 1 contig1
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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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...
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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112 1 Aligning contigs to the reference
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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113 1 /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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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 \
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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115 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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116 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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117 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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118
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
iuc
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119 2 contig2
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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...
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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121 2 Aligning contigs to the reference
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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122 2 /usr/local/bin/minimap2 -c -x asm10 -B5 -O4,16 --no-long-join -r 200 -N 50 -s \
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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 \
9
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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"
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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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128 Creating total report...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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
9
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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130 Transposed version of total report...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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
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...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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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
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...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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135 saved to /tmp/tmplvd_uy2v/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...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
iuc
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137 saved to /tmp/tmplvd_uy2v/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
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138 Done.
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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139
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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140 2024-11-12 11:21:55
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
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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...
16
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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145 saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/aligned_stats/cumulative_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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146 Drawing NAx plot...
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147 saved to /tmp/tmplvd_uy2v/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/tmplvd_uy2v/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 2024-11-12 11:21:56
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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"
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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.
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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/tmplvd_uy2v/files/c/2/a/dataset_c2a3099a-44dc-4abf-88ec-691e4984bd83.dat was skipped
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158 WARNING: No genomic features of type "operon" were loaded.
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159 1 contig1
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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/tmplvd_uy2v/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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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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166 saved to /tmp/tmplvd_uy2v/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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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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168 saved to /tmp/tmplvd_uy2v/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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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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170 saved to /tmp/tmplvd_uy2v/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
45924fa8d8c5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 9e4867db42282a980f1149711159fa811b2d8414"
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173 NOTICE: Genes are not predicted by default. Use --gene-finding or --glimmer option to enable it.
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174
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175 2024-11-12 11:21:56
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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..
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178 1 of 3: Creating PDF with all tables and plots...
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179 2 of 3: Creating Icarus viewers...
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180 3 of 3: Creating Circos plot...
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181 /usr/local/bin/circos -conf outputdir/circos/circos.conf > outputdir/circos/circos.log \
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182 2> outputdir/circos/circos.err
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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 2024-11-12 11:22:00
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186 RESULTS:
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a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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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
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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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
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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189 HTML version (interactive tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.html
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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190 PDF version (tables and plots) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/report.pdf
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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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)
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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192 Icarus (contig browser) is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/icarus.html
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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193 Log is saved to /tmp/tmplvd_uy2v/job_working_directory/000/12/working/outputdir/quast.log
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194
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195 Finished: 2024-11-12 11:22:00
a3b35edea53a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit 975a3b77e7a54e4c61e8bf4cd883cde01b16f0fd
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196 Elapsed time: 0:00:07.048981
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197 NOTICEs: 3; WARNINGs: 4; non-fatal ERRORs: 0
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198
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199 Thank you for using QUAST!