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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
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/usr/local/bin/FragGeneScan -s input -o results/proteome/input -w 0 -t illumina_5 -p 1
Using 1 threads.
no. of seqs: 1
Clock time used (by 1 threads) = 0.1 sec
Time elapsed: 0 hours 0 minutes and 0 seconds.
ISEScan starts at Wed Jul  9 09:57:43 2025
predict and translate genes from genome sequence into protein database using FragGeneScan program

Begin to translate genome into proteome.
Translating genome into proteome for input , return  0

Finish translating genome into proteome. Wed Jul  9 09:57:43 2025

Begin to phmmer search against proteome database. Wed Jul  9 09:57:43 2025
Finish phmmer searching /usr/local/bin/pHMMs/clusters.single.faa  against results/proteome/input.faa , output results/hmm/clusters.single.faa.input.faa

Finish phmmer searching against proteome database. Wed Jul  9 09:57:55 2025

Begin to profile HMM search against proteome database. Wed Jul  9 09:57:55 2025
Finish Profile HMM searching /usr/local/bin/pHMMs/clusters.faa.hmm  against results/proteome/input.faa , output results/hmm/clusters.faa.hmm.input.faa

Finish profile HMM searching against proteome database. Wed Jul  9 09:58:03 2025
pred begins at Wed Jul  9 09:58:03 2025
Begin addNonORFcopy at Wed Jul  9 09:58:03 2025
Finish addNonORFcopy at Wed Jul  9 09:58:03 2025
Begin addNonORFcopy1 at Wed Jul  9 09:58:03 2025
Finish addNonORFcopy1 at Wed Jul  9 09:58:03 2025
getFullIS() begins at Wed Jul  9 09:58:03 2025
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 Wed Jul  9 09:58:03 2025
gi|228288719|ref|NC_012624.1|: no intersected hits found
Finish removeOverlappedHits at Wed Jul  9 09:58:03 2025
Begin reading protein database at Wed Jul  9 09:58:03 2025
Finish reading protein database at Wed Jul  9 09:58:03 2025
Write IS elements from all sequences in input into one result file under results
Write 1 IS copies to results/input.csv and results/input.tsv and results/input.raw
Write summarized result to results/input.sum
End in pred Wed Jul  9 09:58:03 2025
Both complete and partial IS elements are reported.
ISEScan ends at Wed Jul  9 09:58:03 2025