--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/TEST_2/test_2.log	Tue Aug 23 10:01:31 2022 +0000
@@ -0,0 +1,43 @@
+/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