Mercurial > repos > iuc > isescan

comparison test-data/TEST_1/test_1.log @ 3:81539b9ae80a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 15:18:46 2022 6 ISEScan starts at Wed Jul 9 09:57:43 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 15:18:46 2022 12 Finish translating genome into proteome. Wed Jul 9 09:57:43 2025
14 13
15 Begin to phmmer search against proteome database. Wed Aug 31 15:18:46 2022 14 Begin to phmmer search against proteome database. Wed Jul 9 09:57:43 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 15:19:05 2022 17 Finish phmmer searching against proteome database. Wed Jul 9 09:57:55 2025
19 18
20 Begin to profile HMM search against proteome database. Wed Aug 31 15:19:05 2022 19 Begin to profile HMM search against proteome database. Wed Jul 9 09:57:55 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 15:19:17 2022 22 Finish profile HMM searching against proteome database. Wed Jul 9 09:58:03 2025
24 pred begins at Wed Aug 31 15:19:17 2022 23 pred begins at Wed Jul 9 09:58:03 2025
25 Begin addNonORFcopy at Wed Aug 31 15:19:18 2022 24 Begin addNonORFcopy at Wed Jul 9 09:58:03 2025
26 Finish addNonORFcopy at Wed Aug 31 15:19:18 2022 25 Finish addNonORFcopy at Wed Jul 9 09:58:03 2025
27 Begin addNonORFcopy1 at Wed Aug 31 15:19:18 2022 26 Begin addNonORFcopy1 at Wed Jul 9 09:58:03 2025
28 Finish addNonORFcopy1 at Wed Aug 31 15:19:18 2022 27 Finish addNonORFcopy1 at Wed Jul 9 09:58:03 2025
29 getFullIS() begins at Wed Aug 31 15:19:18 2022 28 getFullIS() begins at Wed Jul 9 09:58:03 2025
30 Start typing IS elements 29 Start typing IS elements
31 The 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 The 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
32 Finish typing partial IS elements 31 Finish typing partial IS elements
33 Begin removeOverlappedHits at Wed Aug 31 15:19:18 2022 32 Begin removeOverlappedHits at Wed Jul 9 09:58:03 2025
34 gi|228288719|ref|NC_012624.1|: no intersected hits found 33 gi|228288719|ref|NC_012624.1|: no intersected hits found
35 Finish removeOverlappedHits at Wed Aug 31 15:19:18 2022 34 Finish removeOverlappedHits at Wed Jul 9 09:58:03 2025
36 Begin reading protein database at Wed Aug 31 15:19:18 2022 35 Begin reading protein database at Wed Jul 9 09:58:03 2025
37 Finish reading protein database at Wed Aug 31 15:19:18 2022 36 Finish reading protein database at Wed Jul 9 09:58:03 2025
38 Write IS elements from all sequences in input into one result file under results 37 Write IS elements from all sequences in input into one result file under results
39 Write 2 IS copies to results/input.csv and results/input.tsv and results/input.raw 38 Write 1 IS copies to results/input.csv and results/input.tsv and results/input.raw
40 Write summarized result to results/input.sum 39 Write summarized result to results/input.sum
41 End in pred Wed Aug 31 15:19:18 2022 40 End in pred Wed Jul 9 09:58:03 2025
42 Both complete and partial IS elements are reported. 41 Both complete and partial IS elements are reported.
43 ISEScan ends at Wed Aug 31 15:19:18 2022 42 ISEScan ends at Wed Jul 9 09:58:03 2025