--- a/test-data/test_2.log	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/test_2.log	Wed Jul 09 12:49:45 2025 +0000
@@ -1,43 +1,41 @@
 /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..
+Clock time used (by 1 threads) = 0.1 sec
 Time elapsed: 0 hours 0 minutes and 0 seconds.
-ISEScan starts at Wed Aug 31 15:19:29 2022
+ISEScan starts at Wed Jul  9 09:58:18 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 Aug 31 15:19:29 2022
+Finish translating genome into proteome. Wed Jul  9 09:58:18 2025
 
-Begin to phmmer search against proteome database. Wed Aug 31 15:19:29 2022
+Begin to phmmer search against proteome database. Wed Jul  9 09:58:18 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 Aug 31 15:19:48 2022
+Finish phmmer searching against proteome database. Wed Jul  9 09:58:30 2025
 
-Begin to profile HMM search against proteome database. Wed Aug 31 15:19:48 2022
+Begin to profile HMM search against proteome database. Wed Jul  9 09:58:30 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 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
+Finish profile HMM searching against proteome database. Wed Jul  9 09:58:38 2025
+pred begins at Wed Jul  9 09:58:38 2025
+Begin addNonORFcopy at Wed Jul  9 09:58:38 2025
+Finish addNonORFcopy at Wed Jul  9 09:58:38 2025
+Begin addNonORFcopy1 at Wed Jul  9 09:58:38 2025
+Finish addNonORFcopy1 at Wed Jul  9 09:58:38 2025
+getFullIS() begins at Wed Jul  9 09:58:38 2025
 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
+Warning: no valid hit found for gi|228288719|ref|NC_012624.1|
+Warning: no valid hit after removing short IS element candidate for gi|228288719|ref|NC_012624.1|
 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
+Begin removeOverlappedHits at Wed Jul  9 09:58:38 2025
+Finish removeOverlappedHits at Wed Jul  9 09:58:38 2025
+Begin reading protein database at Wed Jul  9 09:58:38 2025
+Finish reading protein database at Wed Jul  9 09:58:38 2025
+No IS element was found for ['input']
+End in pred Wed Jul  9 09:58:38 2025
 Only complete IS elements are reported.
-ISEScan ends at Wed Aug 31 15:20:01 2022
+ISEScan ends at Wed Jul  9 09:58:38 2025