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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
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/usr/local/bin/FragGeneScan -s /tmp/tmpjm077o6o/files/6/a/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat -o results/proteome/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.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 09:39:42 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/6/a/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat , return  0

Finish translating genome into proteome. Tue Aug 23 09:39:42 2022

Begin to phmmer search against proteome database. Tue Aug 23 09:39:42 2022
Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa  against results/proteome/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa , output results/hmm/1/clusters.single.faa.dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa

Finish phmmer searching against proteome database. Tue Aug 23 09:40:02 2022

Begin to profile HMM search against proteome database. Tue Aug 23 09:40:02 2022
Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm  against results/proteome/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa , output results/hmm/1/clusters.faa.hmm.dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.faa

Finish profile HMM searching against proteome database. Tue Aug 23 09:40:14 2022
pred begins at Tue Aug 23 09:40:14 2022
Begin addNonORFcopy at Tue Aug 23 09:40:14 2022
Finish addNonORFcopy at Tue Aug 23 09:40:14 2022
Begin addNonORFcopy1 at Tue Aug 23 09:40:14 2022
Finish addNonORFcopy1 at Tue Aug 23 09:40:14 2022
getFullIS() begins at Tue Aug 23 09:40:14 2022
Start typing IS elements
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
Finish typing partial IS elements
Begin removeOverlappedHits at Tue Aug 23 09:40:14 2022
gi|228288719|ref|NC_012624.1|: no intersected hits found
Finish removeOverlappedHits at Tue Aug 23 09:40:14 2022
Begin reading protein database at Tue Aug 23 09:40:14 2022
Finish reading protein database at Tue Aug 23 09:40:14 2022
Write IS elements from all sequences in 1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat into one result file under results
Write 2 IS copies to results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.csv and results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.tsv and results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.raw
Write summarized result to results/1/dataset_6a1f68ad-940d-4e7c-9736-cf5a2ce9fd9e.dat.sum
End in pred Tue Aug 23 09:40:14 2022
Both complete and partial IS elements are reported.
ISEScan ends at Tue Aug 23 09:40:14 2022