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comparison test-data/logfile_test_1.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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-1:000000000000 0:0c094ece2c73
1
2 Starting Polypolish (2022-09-14 14:05:31)
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 /tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat
16
17 Settings:
18 --fraction_invalid 0.2
19 --fraction_valid 0.5
20 --max_errors 10
21 --min_depth 5
22 --debug /tmp/tmpacfaqf7s/job_working_directory/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat
23
24
25 Loading assembly (2022-09-14 14:05:31)
26 contig00001 (5,513 bp)
27 contig00002 (3,532 bp)
28 contig00003 (3,227 bp)
29 contig00004 (3,138 bp)
30
31
32 Loading alignments (2022-09-14 14:05:31)
33 /tmp/tmpacfaqf7s/files/0/e/6/dataset_0e63b923-512f-4f9b-b6fa-8c6ead4a29db.dat: 75 alignments from 72 reads
34
35 Filtering for high-quality end-to-end alignments:
36 25 alignments kept
37 50 alignments discarded
38
39
40 Polishing assembly sequences (2022-09-14 14:05:31)
41  For each position in the assembly, Polypolish determines the read depth
42 at that position and collects all aligned bases. It then polishes the assembly
43 by looking for positions where the pileup unambiguously supports a different
44 sequence than the assembly.
45
46 Polishing contig00001 (5,513 bp):
47 mean read depth: 1.0x
48 2,496 bp have a depth of zero (54.7252% coverage)
49 0 positions changed (0.0000% of total positions)
50 estimated pre-polishing sequence accuracy: 100.0000%
51
52 Polishing contig00002 (3,532 bp):
53 mean read depth: 0.3x
54 2,629 bp have a depth of zero (25.5663% coverage)
55 0 positions changed (0.0000% of total positions)
56 estimated pre-polishing sequence accuracy: 100.0000%
57
58 Polishing contig00003 (3,227 bp):
59 mean read depth: 0.2x
60 2,818 bp have a depth of zero (12.6743% coverage)
61 0 positions changed (0.0000% of total positions)
62 estimated pre-polishing sequence accuracy: 100.0000%
63
64 Polishing contig00004 (3,138 bp):
65 mean read depth: 0.1x
66 2,842 bp have a depth of zero (9.4328% coverage)
67 0 positions changed (0.0000% of total positions)
68 estimated pre-polishing sequence accuracy: 100.0000%
69
70
71 Finished! (2022-09-14 14:05:31)
72 Polished sequence (to stdout):
73 contig00001_polypolish (5,513 bp)
74 contig00002_polypolish (3,532 bp)
75 contig00003_polypolish (3,227 bp)
76 contig00004_polypolish (3,138 bp)
77
78 Per-base debugging info written to /tmp/tmpacfaqf7s/job_working_directory/000/3/outputs/galaxy_dataset_0fff3b6a-ddab-4999-b6a2-78a6dff1a4bc.dat
79 Time to run: 0:00:00.029839
80