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

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

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test_2.log	Thu Sep 01 09:29:56 2022 +0000
@@ -0,0 +1,43 @@
+/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