Mercurial > repos > iuc > isescan

comparison test-data/test_2.log @ 0:b18e9d02e503 draft

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planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379
author iuc
date Thu, 01 Sep 2022 09:29:16 +0000
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-1:000000000000 0:b18e9d02e503
1 /usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1
2 Using 1 threads.
3 no. of seqs: 1
4 Clock time used (by 1 threads) = 0.00 mins
5 prepare gff file..
6 Time elapsed: 0 hours 0 minutes and 0 seconds.
7 ISEScan starts at Wed Aug 31 15:19:29 2022
8 predict and translate genes from genome sequence into protein database using FragGeneScan program
9
10 Begin to translate genome into proteome.
11 Translating genome into proteome for input , return 0
12
13 Finish translating genome into proteome. Wed Aug 31 15:19:29 2022
14
15 Begin to phmmer search against proteome database. Wed Aug 31 15:19:29 2022
16 Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa
17
18 Finish phmmer searching against proteome database. Wed Aug 31 15:19:48 2022
19
20 Begin to profile HMM search against proteome database. Wed Aug 31 15:19:48 2022
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
22
23 Finish profile HMM searching against proteome database. Wed Aug 31 15:20:01 2022
24 pred begins at Wed Aug 31 15:20:01 2022
25 Begin addNonORFcopy at Wed Aug 31 15:20:01 2022
26 Finish addNonORFcopy at Wed Aug 31 15:20:01 2022
27 Begin addNonORFcopy1 at Wed Aug 31 15:20:01 2022
28 Finish addNonORFcopy1 at Wed Aug 31 15:20:01 2022
29 getFullIS() begins at Wed Aug 31 15:20:01 2022
30 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
32 Finish removing partial IS elements
33 Begin removeOverlappedHits at Wed Aug 31 15:20:01 2022
34 gi|228288719|ref|NC_012624.1|: no intersected hits found
35 Finish removeOverlappedHits at Wed Aug 31 15:20:01 2022
36 Begin reading protein database at Wed Aug 31 15:20:01 2022
37 Finish reading protein database at Wed Aug 31 15:20:01 2022
38 Write IS elements from all sequences in input into one result file under results
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.
43 ISEScan ends at Wed Aug 31 15:20:01 2022