comparison test-data/test_2.log @ 0:debe9c750cdd draft

planemo upload for repository https://github.com/pimarin/tools-iuc/tree/isescan commit d9d88c043b2d45877e3b0bffba6e709c9a0f0379

0:debe9c750cdd

/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) = 0.00 mins
prepare gff file..
Time elapsed: 0 hours 0 minutes and 0 seconds.
ISEScan starts at Wed Aug 31 15:19:29 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 input , return  0

Finish translating genome into proteome. Wed Aug 31 15:19:29 2022

Begin to phmmer search against proteome database. Wed Aug 31 15:19:29 2022
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 Aug 31 15:19:48 2022

Begin to profile HMM search against proteome database. Wed Aug 31 15:19:48 2022
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 Aug 31 15:20:01 2022
pred begins at Wed Aug 31 15:20:01 2022
Begin addNonORFcopy at Wed Aug 31 15:20:01 2022
Finish addNonORFcopy at Wed Aug 31 15:20:01 2022
Begin addNonORFcopy1 at Wed Aug 31 15:20:01 2022
Finish addNonORFcopy1 at Wed Aug 31 15:20:01 2022
getFullIS() begins at Wed Aug 31 15:20:01 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 Wed Aug 31 15:20:01 2022
gi|228288719|ref|NC_012624.1|: no intersected hits found
Finish removeOverlappedHits at Wed Aug 31 15:20:01 2022
Begin reading protein database at Wed Aug 31 15:20:01 2022
Finish reading protein database at Wed Aug 31 15:20:01 2022
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 Aug 31 15:20:01 2022
Only complete IS elements are reported.
ISEScan ends at Wed Aug 31 15:20:01 2022