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comparison test-data/test_2.log @ 3:81539b9ae80a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3
author iuc
date Wed, 09 Jul 2025 12:49:45 +0000
parents debe9c750cdd
children
comparison
equal deleted inserted replaced
2:9e776e7fab4f 3:81539b9ae80a
1 /usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1 1 /usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1
2 Using 1 threads. 2 Using 1 threads.
3 no. of seqs: 1 3 no. of seqs: 1
4 Clock time used (by 1 threads) = 0.00 mins 4 Clock time used (by 1 threads) = 0.1 sec
5 prepare gff file..
6 Time elapsed: 0 hours 0 minutes and 0 seconds. 5 Time elapsed: 0 hours 0 minutes and 0 seconds.
7 ISEScan starts at Wed Aug 31 15:19:29 2022 6 ISEScan starts at Wed Jul 9 09:58:18 2025
8 predict and translate genes from genome sequence into protein database using FragGeneScan program 7 predict and translate genes from genome sequence into protein database using FragGeneScan program
9 8
10 Begin to translate genome into proteome. 9 Begin to translate genome into proteome.
11 Translating genome into proteome for input , return 0 10 Translating genome into proteome for input , return 0
12 11
13 Finish translating genome into proteome. Wed Aug 31 15:19:29 2022 12 Finish translating genome into proteome. Wed Jul 9 09:58:18 2025
14 13
15 Begin to phmmer search against proteome database. Wed Aug 31 15:19:29 2022 14 Begin to phmmer search against proteome database. Wed Jul 9 09:58:18 2025
16 Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa 15 Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa
17 16
18 Finish phmmer searching against proteome database. Wed Aug 31 15:19:48 2022 17 Finish phmmer searching against proteome database. Wed Jul 9 09:58:30 2025
19 18
20 Begin to profile HMM search against proteome database. Wed Aug 31 15:19:48 2022 19 Begin to profile HMM search against proteome database. Wed Jul 9 09:58:30 2025
21 Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm against results/proteome/input.faa , output results/hmm/clusters.faa.hmm.input.faa 20 Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm against results/proteome/input.faa , output results/hmm/clusters.faa.hmm.input.faa
22 21
23 Finish profile HMM searching against proteome database. Wed Aug 31 15:20:01 2022 22 Finish profile HMM searching against proteome database. Wed Jul 9 09:58:38 2025
24 pred begins at Wed Aug 31 15:20:01 2022 23 pred begins at Wed Jul 9 09:58:38 2025
25 Begin addNonORFcopy at Wed Aug 31 15:20:01 2022 24 Begin addNonORFcopy at Wed Jul 9 09:58:38 2025
26 Finish addNonORFcopy at Wed Aug 31 15:20:01 2022 25 Finish addNonORFcopy at Wed Jul 9 09:58:38 2025
27 Begin addNonORFcopy1 at Wed Aug 31 15:20:01 2022 26 Begin addNonORFcopy1 at Wed Jul 9 09:58:38 2025
28 Finish addNonORFcopy1 at Wed Aug 31 15:20:01 2022 27 Finish addNonORFcopy1 at Wed Jul 9 09:58:38 2025
29 getFullIS() begins at Wed Aug 31 15:20:01 2022 28 getFullIS() begins at Wed Jul 9 09:58:38 2025
30 Start removing partial IS elements 29 Start removing partial IS elements
31 Remove single-copy partial IS element with evalue > 1e-50: isLen=989 IS5 bd=[30355, 31343] orf('gi|228288719|ref|NC_012624.1|', 30399, 31298, '+') evalue=1.7e-37 30 Remove single-copy partial IS element with evalue > 1e-50: isLen=989 IS5 bd=[30355, 31343] orf('gi|228288719|ref|NC_012624.1|', 30399, 31298, '+') evalue=1.7e-37
31 Warning: no valid hit found for gi|228288719|ref|NC_012624.1|
32 Warning: no valid hit after removing short IS element candidate for gi|228288719|ref|NC_012624.1|
32 Finish removing partial IS elements 33 Finish removing partial IS elements
33 Begin removeOverlappedHits at Wed Aug 31 15:20:01 2022 34 Begin removeOverlappedHits at Wed Jul 9 09:58:38 2025
34 gi|228288719|ref|NC_012624.1|: no intersected hits found 35 Finish removeOverlappedHits at Wed Jul 9 09:58:38 2025
35 Finish removeOverlappedHits at Wed Aug 31 15:20:01 2022 36 Begin reading protein database at Wed Jul 9 09:58:38 2025
36 Begin reading protein database at Wed Aug 31 15:20:01 2022 37 Finish reading protein database at Wed Jul 9 09:58:38 2025
37 Finish reading protein database at Wed Aug 31 15:20:01 2022 38 No IS element was found for ['input']
38 Write IS elements from all sequences in input into one result file under results 39 End in pred Wed Jul 9 09:58:38 2025
39 Write 1 IS copies to results/input.csv and results/input.tsv and results/input.raw
40 Write summarized result to results/input.sum
41 End in pred Wed Aug 31 15:20:01 2022
42 Only complete IS elements are reported. 40 Only complete IS elements are reported.
43 ISEScan ends at Wed Aug 31 15:20:01 2022 41 ISEScan ends at Wed Jul 9 09:58:38 2025