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comparison test-data/logfile_test_4.log @ 0:0c094ece2c73 draft

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planemo upload for repository https://github.com/mesocentre-clermont-auvergne/galaxy-tools/tree/master/tools/polypolish commit 95f351736787f04c65e830cd9daf9c9c8521893a
author iuc
date Thu, 22 Sep 2022 07:50:58 +0000
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1
2 Starting Polypolish (2022-09-14 14:06:52)
3  Polypolish is a tool for polishing genome assemblies with short reads.
4 Unlike other tools in this category, Polypolish uses SAM files where each read
5 has been aligned to all possible locations (not just a single best location).
6 This allows it to repair errors in repeat regions that other alignment-based
7 polishers cannot fix.
8
9 Polypolish version: 0.5.0
10
11 Input assembly:
12 input_data
13
14 Input short-read alignments:
15 paired_collection/forward_input0forward_filtered.sam
16 paired_collection/forward_input1forward_filtered.sam
17 paired_collection/forward_input2forward_filtered.sam
18 paired_collection/reverse_input0reverse_filtered.sam
19 paired_collection/reverse_input1reverse_filtered.sam
20 paired_collection/reverse_input2reverse_filtered.sam
21
22 Settings:
23 --fraction_invalid 0.2
24 --fraction_valid 0.5
25 --max_errors 10
26 --min_depth 5
27 --debug /tmp/tmpacfaqf7s/job_working_directory/000/20/outputs/galaxy_dataset_a267d150-242f-43e2-b91d-3a230d92a70f.dat
28
29
30 Loading assembly (2022-09-14 14:06:52)
31 contig00001 (5,513 bp)
32 contig00002 (3,532 bp)
33 contig00003 (3,227 bp)
34 contig00004 (3,138 bp)
35
36
37 Loading alignments (2022-09-14 14:06:52)
38 paired_collection/forward_input0forward_filtered.sam: 75 alignments from 72 reads
39 paired_collection/forward_input1forward_filtered.sam: 75 alignments from 72 reads
40 paired_collection/forward_input2forward_filtered.sam: 75 alignments from 72 reads
41 paired_collection/reverse_input0reverse_filtered.sam: 64 alignments from 62 reads
42 paired_collection/reverse_input1reverse_filtered.sam: 64 alignments from 62 reads
43 paired_collection/reverse_input2reverse_filtered.sam: 64 alignments from 62 reads
44
45 Filtering for high-quality end-to-end alignments:
46 144 alignments kept
47 273 alignments discarded
48
49
50 Polishing assembly sequences (2022-09-14 14:06:52)
51  For each position in the assembly, Polypolish determines the read depth
52 at that position and collects all aligned bases. It then polishes the assembly
53 by looking for positions where the pileup unambiguously supports a different
54 sequence than the assembly.
55
56 Polishing contig00001 (5,513 bp):
57 mean read depth: 5.7x
58 1,751 bp have a depth of zero (68.2387% coverage)
59 0 positions changed (0.0000% of total positions)
60 estimated pre-polishing sequence accuracy: 100.0000%
61
62 Polishing contig00002 (3,532 bp):
63 mean read depth: 2.0x
64 2,280 bp have a depth of zero (35.4473% coverage)
65 0 positions changed (0.0000% of total positions)
66 estimated pre-polishing sequence accuracy: 100.0000%
67
68 Polishing contig00003 (3,227 bp):
69 mean read depth: 0.8x
70 2,652 bp have a depth of zero (17.8184% coverage)
71 0 positions changed (0.0000% of total positions)
72 estimated pre-polishing sequence accuracy: 100.0000%
73
74 Polishing contig00004 (3,138 bp):
75 mean read depth: 0.6x
76 2,699 bp have a depth of zero (13.9898% coverage)
77 0 positions changed (0.0000% of total positions)
78 estimated pre-polishing sequence accuracy: 100.0000%
79
80
81 Finished! (2022-09-14 14:06:52)
82 Polished sequence (to stdout):
83 contig00001_polypolish (5,513 bp)
84 contig00002_polypolish (3,532 bp)
85 contig00003_polypolish (3,227 bp)
86 contig00004_polypolish (3,138 bp)
87
88 Per-base debugging info written to /tmp/tmpacfaqf7s/job_working_directory/000/20/outputs/galaxy_dataset_a267d150-242f-43e2-b91d-3a230d92a70f.dat
89 Time to run: 0:00:00.024238
90