Mercurial > repos > pimarin > isescan

view test-data/TEST_2/test_2.log @ 0:cecb2758ec26 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
line wrap: on
line source

/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
Using 1 threads.
no. of seqs: 1
Clock time used (by 1 threads) = 0.00 mins
prepare gff file..
Time elapsed: 0 hours 0 minutes and 0 seconds.
ISEScan starts at Tue Aug 23 09:40:26 2022
predict and translate genes from genome sequence into protein database using FragGeneScan program

Begin to translate genome into proteome.
Translating genome into proteome for /tmp/tmpjm077o6o/files/8/9/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat , return  0

Finish translating genome into proteome. Tue Aug 23 09:40:26 2022

Begin to phmmer search against proteome database. Tue Aug 23 09:40:26 2022
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

Finish phmmer searching against proteome database. Tue Aug 23 09:40:45 2022

Begin to profile HMM search against proteome database. Tue Aug 23 09:40:45 2022
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

Finish profile HMM searching against proteome database. Tue Aug 23 09:40:57 2022
pred begins at Tue Aug 23 09:40:57 2022
Begin addNonORFcopy at Tue Aug 23 09:40:58 2022
Finish addNonORFcopy at Tue Aug 23 09:40:58 2022
Begin addNonORFcopy1 at Tue Aug 23 09:40:58 2022
Finish addNonORFcopy1 at Tue Aug 23 09:40:58 2022
getFullIS() begins at Tue Aug 23 09:40:58 2022
Start removing partial IS elements
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
Finish removing partial IS elements
Begin removeOverlappedHits at Tue Aug 23 09:40:58 2022
gi|228288719|ref|NC_012624.1|: no intersected hits found
Finish removeOverlappedHits at Tue Aug 23 09:40:58 2022
Begin reading protein database at Tue Aug 23 09:40:58 2022
Finish reading protein database at Tue Aug 23 09:40:58 2022
Write IS elements from all sequences in d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat into one result file under results
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
Write summarized result to results/d/dataset_89de31f8-93d7-43e1-a4d5-1b0757afa41d.dat.sum
End in pred Tue Aug 23 09:40:58 2022
Only complete IS elements are reported.
ISEScan ends at Tue Aug 23 09:40:58 2022