Mercurial > repos > jdv > gottcha

comparison test-data/test_02.log @ 0:2569a83977f5 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/gottcha commit 5d24210279e26623ae6c98f7551e3565fdc9bc48
author jdv
date Mon, 30 Jan 2017 19:07:21 -0500
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-1:000000000000 0:2569a83977f5
1 ----> ENTRY HEADER:@FOO:13415:1851
2 Threads: 1 (effective) 1 (requested)
3 IDX = 0: reading from 0 to 86912
4 Staggering at 125000 reads; processed 203 reads
5 IDX(0) counted 203 reads
6 GLOBAL READ COUNT = 203
7 Trim Time: 5 ms
8
9 PROGRAM ELAPSED TIME: 6 ms
10 [M::bwa_idx_load_from_disk] read 0 ALT contigs
11 [M::process] read 1226 sequences (40027 bp)...
12 [M::mem_process_seqs] Processed 1226 reads in 0.396 CPU sec, 0.201 real sec
13 [main] Version: 0.7.12-r1039
14 [main] CMD: bwa mem -k 30 -T 0 -B 100 -O 100 -E 100 -t 2 got/db/test_db.species -
15 [main] Real time: 0.206 sec; CPU: 0.400 sec
16
17 Parsing foo/test_temp/test_splitrim.stats.txt... found 203 reads (split-trimmed: 1226) and 39924 bases.
18 ->Retrieving parsed DB from disk [got/db/test_db.species.parsedGOTTCHA.dmp]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
19 ->Parsing SAM file [-] done. Mapped split-trimmed reads: 30; Mapped split-trimmed reads to plasmids: 0; Unmapped split-trimmed reads: 1190; Mapped raw reads: 20; Mapped raw reads to plasmids: 0. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
20 ->Consolidating hits...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
21 ->Retrieving Genome Vitals from disk [got/db/genomeVitals.dmp]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
22 ->Storing coordinates to disk [foo/test_temp/test.replicon.contig.coords.csv]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
23 ->Storing datastructure GI coordinates to disk in BINARY format as "foo/test_temp/test.giCoords.dmp"...done. 0 wallsecs
24 ->Storing datastructure contig length histogram (by entry) to disk in BINARY format as "foo/test_temp/test.replicon.contig.HistoByEntry.dmp"...done. 0 wallsecs
25 ->Storing datastructure contig length histogram (by GI) to disk in BINARY format as "foo/test_temp/test.replicon.contig.HistoByGI.dmp"...done. 0 wallsecs
26 ->Storing parseable contig length histogram(s) to disk...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
27 ->Calculating non-overlapping coverage from mapping results...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
28 ===== REPLICON-level Analysis =====
29 ->Writing REPLICON-level results to disk [foo/test_temp/test.replicon.tsv]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
30 ===== Extended Taxonomic Rank-level Analysis =====
31 ->Pulling replicon GIs from DB entries...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
32 ->Mapping replicon GIs to source organisms...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
33 ->Retrieving Tax Tree from disk [got/db/speciesTreeGI.dmp]...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
34 ->Mapping source organism to its tax tree...done. 0 wallclock secs ( 0.00 usr + 0.00 sys = 0.00 CPU)
35 Congratulations! All organisms have been identified!
36 ->Rolling up results for rank STRAIN [foo/test_temp/test.strain.tsv]...done. 0 wallclock secs ( 0.07 usr + 0.00 sys = 0.07 CPU)
37 ->Rolling up results for rank SPECIES [foo/test_temp/test.species.tsv]...done. 0 wallclock secs ( 0.03 usr + 0.00 sys = 0.03 CPU)
38 ->Rolling up results for rank GENUS [foo/test_temp/test.genus.tsv]...done. 0 wallclock secs ( 0.02 usr + 0.00 sys = 0.02 CPU)
39 ->Rolling up results for rank FAMILY [foo/test_temp/test.family.tsv]...done. 0 wallclock secs ( 0.02 usr + 0.00 sys = 0.02 CPU)
40 ->Rolling up results for rank ORDER [foo/test_temp/test.order.tsv]...done. 0 wallclock secs ( 0.03 usr + 0.00 sys = 0.03 CPU)
41 ->Rolling up results for rank CLASS [foo/test_temp/test.class.tsv]...done. 0 wallclock secs ( 0.03 usr + 0.00 sys = 0.03 CPU)
42 ->Rolling up results for rank PHYLUM [foo/test_temp/test.phylum.tsv]...done. 0 wallclock secs ( 0.02 usr + 0.00 sys = 0.02 CPU)
43 Saving updated table to "foo/test_temp/test.strain.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
44 Saving updated table to "foo/test_temp/test.species.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
45 Saving updated table to "foo/test_temp/test.genus.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
46 Saving updated table to "foo/test_temp/test.family.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
47 Saving updated table to "foo/test_temp/test.order.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
48 Saving updated table to "foo/test_temp/test.class.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
49 Saving updated table to "foo/test_temp/test.phylum.tsv.ABU"...done. (2 taxonomie(s), 1 filtered)
50 ------------------
51 TOTAL SCRIPT TIME: - 0 wallclock secs ( 0.22 usr + 0.00 sys = 0.22 CPU)
52 ------------------
53 Loading STRAIN Lookup file...done!
54 Loading SPECIES Lookup file...done!
55 Loading GENUS Lookup file...done!
56 Loading FAMILY Lookup file...done!
57 Loading ORDER Lookup file...done!
58 Loading CLASS Lookup file...done!
59 Loading PHYLUM Lookup file...done!
60 Loading TAX Lookup file...done!
61 Parsing table "foo/test_temp/test.strain.tsv"...Done!
62
63
64 STRAIN LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
65 Newcastle disease virus B1 366 544 18 0 17 1.48633879781421 1
66 =================================================================
67
68
69 SPECIES LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
70 Newcastle disease virus 366 544 18 0 17 1.48633879781421 1
71 =================================================================
72
73
74 GENUS LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
75 Avulavirus 366 544 18 0 17 1.48633879781421 1
76 =================================================================
77
78
79 FAMILY LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
80 Paramyxoviridae 366 544 18 0 17 1.48633879781421 1
81 =================================================================
82
83
84 ORDER LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
85 Mononegavirales 366 544 18 0 17 1.48633879781421 1
86 =================================================================
87
88
89 CLASS LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
90 Unassigned class - Mononegavirales 366 544 18 0 17 1.48633879781421 1
91 =================================================================
92
93
94 PHYLUM LINEAR_LENGTH TOTAL_BP_MAPPED HIT_COUNT HIT_COUNT_PLASMID READ_COUNT LINEAR_DOC NORM_COV
95 Unassigned phylum - Unassigned class - Mononegavirales 366 544 18 0 17 1.48633879781421 1
96 =================================================================
97 Exporting results to disk [foo/test_temp/test.species.tsv.ABUX]...Done!
98 Done converting 1 files to list.