Mercurial > repos > pimarin > isescan
comparison test-data/TEST_2/test_2.log @ 0:cecb2758ec26 draft
planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit df153ded9cba1e4a89cf3ea554183e7344e01c5d-dirty
| author | pimarin |
|---|---|
| date | Tue, 23 Aug 2022 10:01:31 +0000 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| -1:000000000000 | 0:cecb2758ec26 |
|---|---|
| 1 /usr/local/bin/FragGeneScan -s /tmp/tmpjm077o6o/files/8/9/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat -o results/proteome/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat -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 Tue Aug 23 09:40:26 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 /tmp/tmpjm077o6o/files/8/9/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat , return 0 | |
| 12 | |
| 13 Finish translating genome into proteome. Tue Aug 23 09:40:26 2022 | |
| 14 | |
| 15 Begin to phmmer search against proteome database. Tue Aug 23 09:40:26 2022 | |
| 16 Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa against results/proteome/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.faa , output results/hmm/d/clusters.single.faa.dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.faa | |
| 17 | |
| 18 Finish phmmer searching against proteome database. Tue Aug 23 09:40:45 2022 | |
| 19 | |
| 20 Begin to profile HMM search against proteome database. Tue Aug 23 09:40:45 2022 | |
| 21 Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm against results/proteome/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.faa , output results/hmm/d/clusters.faa.hmm.dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.faa | |
| 22 | |
| 23 Finish profile HMM searching against proteome database. Tue Aug 23 09:40:57 2022 | |
| 24 pred begins at Tue Aug 23 09:40:57 2022 | |
| 25 Begin addNonORFcopy at Tue Aug 23 09:40:58 2022 | |
| 26 Finish addNonORFcopy at Tue Aug 23 09:40:58 2022 | |
| 27 Begin addNonORFcopy1 at Tue Aug 23 09:40:58 2022 | |
| 28 Finish addNonORFcopy1 at Tue Aug 23 09:40:58 2022 | |
| 29 getFullIS() begins at Tue Aug 23 09:40:58 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 Tue Aug 23 09:40:58 2022 | |
| 34 gi|228288719|ref|NC_012624.1|: no intersected hits found | |
| 35 Finish removeOverlappedHits at Tue Aug 23 09:40:58 2022 | |
| 36 Begin reading protein database at Tue Aug 23 09:40:58 2022 | |
| 37 Finish reading protein database at Tue Aug 23 09:40:58 2022 | |
| 38 Write IS elements from all sequences in d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat into one result file under results | |
| 39 Write 1 IS copies to results/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.csv and results/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.tsv and results/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.raw | |
| 40 Write summarized result to results/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.sum | |
| 41 End in pred Tue Aug 23 09:40:58 2022 | |
| 42 Only complete IS elements are reported. | |
| 43 ISEScan ends at Tue Aug 23 09:40:58 2022 |