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changeset 3:81539b9ae80a draft default tip

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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 9e776e7fab4f
children
files macro.xml test-data/TEST_1/test_1.fna.gff test-data/TEST_1/test_1.fna.is.fna test-data/TEST_1/test_1.fna.orf.faa test-data/TEST_1/test_1.fna.orf.fna test-data/TEST_1/test_1.fna.sum test-data/TEST_1/test_1.fna.tsv test-data/TEST_1/test_1.log test-data/test_2.fna.gff test-data/test_2.fna.is.fna test-data/test_2.fna.orf.faa test-data/test_2.fna.orf.fna test-data/test_2.fna.sum test-data/test_2.fna.tsv test-data/test_2.log
diffstat 15 files changed, 45 insertions(+), 158 deletions(-) [+]
line wrap: on
line diff
--- a/macro.xml	Thu Jan 25 16:32:04 2024 +0000
+++ b/macro.xml	Wed Jul 09 12:49:45 2025 +0000
@@ -1,6 +1,6 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.7.2.3</token>
-    <token name="@VERSION_SUFFIX@">1</token>
+    <token name="@TOOL_VERSION@">1.7.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">21.05</token>
     <xml name="version_command">
         <version_command><![CDATA[isescan.py --version]]> </version_command>
--- a/test-data/TEST_1/test_1.fna.gff	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/TEST_1/test_1.fna.gff	Wed Jul 09 12:49:45 2025 +0000
@@ -2,6 +2,3 @@
 gi|228288719|ref|NC_012624.1|	ISEScan	insertion_sequence	30355	31343	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_1;family=IS5;cluster=IS5_222
 gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	30355	30382	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1
 gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	31316	31343	.	+	.	ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1
-gi|228288719|ref|NC_012624.1|	ISEScan	insertion_sequence	32413	33650	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_2;family=ISH3;cluster=ISH3_198|ISH3||gi|15898236|ref|NP_342841
-gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	32413	32456	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_2_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_2
-gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	33607	33650	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_2_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_2
--- a/test-data/TEST_1/test_1.fna.is.fna	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/TEST_1/test_1.fna.is.fna	Wed Jul 09 12:49:45 2025 +0000
@@ -16,25 +16,3 @@
 TTTTAGGACAAGTGGTTGAGGCTAAGCTCAAGTTCTGGGCTTATGCATGGATGGTCCACT
 TGGCTAATTCTTTAGTTGGTAGAGCTCCGGGTATTAGGGTGTGAGCTTGCGAATAACGTT
 GAAATAAATATTAATTACTGAAAAATTCT
->gi|228288719|ref|NC_012624.1|_32413_33650_- ISH3_198|ISH3||gi|15898236|ref|NP_342841
-CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCTGACAGAATAATATCGA
-TTCATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAG
-CTGAGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCA
-CCAAAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAA
-GAAAGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGA
-AAGCAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCA
-AGGGATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACT
-GAAGGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAG
-ACCGGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGAC
-GACAAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGAC
-TAAGGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAG
-GTTGATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTT
-TAAGTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGA
-TTACGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGT
-GTACAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTAC
-TAATCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCAT
-AGAGACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGT
-TTTCCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAA
-GGGGGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGATGATTT
-ATTCTATCTAAAAGATTTTCTATTTAAATCAATAGAACCGCTTATTAATAATATAGATTT
-ATTTTCAAGGAGGTGATTTTGGGTCTACCGAATAAGGG
--- a/test-data/TEST_1/test_1.fna.orf.faa	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/TEST_1/test_1.fna.orf.faa	Wed Jul 09 12:49:45 2025 +0000
@@ -4,10 +4,3 @@
 TNKGGQYIIAKWGKTKDSKFLKIEIVMDKDQFNVINAEVTSNEVQTAVKTVKDLQDKGKK
 VKKFYGDKAYDANEVYKTGVEVVVPPRENASTRRGHPARRKAVREFKRLGYNRWREERGY
 GVRWRIESLFSAVKRTFGESVRATSFLGQVVEAKLKFWAYAWMVHLANSLVGRAPGIRV
->gi|228288719|ref|NC_012624.1|_32517_33587_-
-MIDNRIYMSIKNSVEERFKLREMWYYHVRSEMVTPVLPHQNNIQQIGYKLLSMLNFKGKK
-GEEVARTLISACLWNDSVESKSRAYGVSPQTVRNYVEEQGMEVIEKLLESARKISLKVLK
-GVKEIDVSIDWTTKTWYGRPVGGLGSSEEGNSWNYATATTKFNGKVLLLAFVTQVKGMTK
-EEIVKALVEQVVAMGFKIRLITLDAGFYTVDVLNFISQFKYIVAVPVGDVKVYEEFDGDY
-ATNSKRHRRDXAGQVQASRVQQGKSEEKEEDVVYFARATNLDLPKGEVLDLYNKVRGPIE
-TSYRNIKAFLPFTSSTKFVXPHVDLRAGRGLLLPVHRVQGGGEEGAVQDTPNTLVF
--- a/test-data/TEST_1/test_1.fna.orf.fna	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/TEST_1/test_1.fna.orf.fna	Wed Jul 09 12:49:45 2025 +0000
@@ -14,22 +14,3 @@
 GGTGTTAGGTGGAGGATTGAGTCCTTATTCTCTGCTGTGAAGCGTACTTTTGGGGAATCT
 GTTAGGGCTACAAGTTTTTTAGGACAAGTGGTTGAGGCTAAGCTCAAGTTCTGGGCTTAT
 GCATGGATGGTCCACTTGGCTAATTCTTTAGTTGGTAGAGCTCCGGGTATTAGGGTGTGA
->gi|228288719|ref|NC_012624.1|_32517_33587_-
-ATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAGCTG
-AGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCACCA
-AAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAAGAA
-AGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGAAAG
-CAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCAAGG
-GATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACTGAA
-GGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAGACC
-GGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGACGAC
-AAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGACTAA
-GGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAGGTT
-GATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTTTAA
-GTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGATTA
-CGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGTGTA
-CAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTACTAA
-TCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCATAGA
-GACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGTTTT
-CCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAAGGG
-GGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGA
--- a/test-data/TEST_1/test_1.fna.sum	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/TEST_1/test_1.fna.sum	Wed Jul 09 12:49:45 2025 +0000
@@ -1,4 +1,3 @@
 # seqid                                                      family         nIS %Genome          bps4IS          dnaLen
 gi|228288719|ref|NC_012624.1|                                IS5              1    2.34             989           42245
-gi|228288719|ref|NC_012624.1|                                ISH3             1    2.93            1238           42245
-input                                                        total            2    5.27            2227           42245
+input                                                        total            1    2.34             989           42245
--- a/test-data/TEST_1/test_1.fna.tsv	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/TEST_1/test_1.fna.tsv	Wed Jul 09 12:49:45 2025 +0000
@@ -1,3 +1,2 @@
 seqID	family	cluster	isBegin	isEnd	isLen	ncopy4is	start1	end1	start2	end2	score	irId	irLen	nGaps	orfBegin	orfEnd	strand	orfLen	E-value	E-value4copy	type	ov	tir
 gi|228288719|ref|NC_012624.1|	IS5	IS5_222	30355	31343	989	1	30355	30382	31316	31343	24	20	28	0	30399	31298	+	900	1.7e-37	1.7e-37	p	1	AGAATTATACAAAAATTTATAAATAATT:AGAATTTTTCAGTAATTAATATTTATTT
-gi|228288719|ref|NC_012624.1|	ISH3	ISH3_198|ISH3||gi|15898236|ref|NP_342841	32413	33650	1238	1	32413	32456	33607	33650	48	34	44	0	32517	33587	-	1071	2.3e-147	2.3e-147	c	1	CCCTTATTCGGTAGACCCAAAATCACCTCCTTGAAAATAAATCT:CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCT
--- a/test-data/TEST_1/test_1.log	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/TEST_1/test_1.log	Wed Jul 09 12:49:45 2025 +0000
@@ -1,43 +1,42 @@
 /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 15:18:46 2022
+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 Aug 31 15:18:46 2022
+Finish translating genome into proteome. Wed Jul  9 09:57:43 2025
 
-Begin to phmmer search against proteome database. Wed Aug 31 15:18:46 2022
+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 Aug 31 15:19:05 2022
+Finish phmmer searching against proteome database. Wed Jul  9 09:57:55 2025
 
-Begin to profile HMM search against proteome database. Wed Aug 31 15:19:05 2022
+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 Aug 31 15:19:17 2022
-pred begins at Wed Aug 31 15:19:17 2022
-Begin addNonORFcopy at Wed Aug 31 15:19:18 2022
-Finish addNonORFcopy at Wed Aug 31 15:19:18 2022
-Begin addNonORFcopy1 at Wed Aug 31 15:19:18 2022
-Finish addNonORFcopy1 at Wed Aug 31 15:19:18 2022
-getFullIS() begins at Wed Aug 31 15:19:18 2022
+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 Aug 31 15:19:18 2022
+Begin removeOverlappedHits at Wed Jul  9 09:58:03 2025
 gi|228288719|ref|NC_012624.1|: no intersected hits found
-Finish removeOverlappedHits at Wed Aug 31 15:19:18 2022
-Begin reading protein database at Wed Aug 31 15:19:18 2022
-Finish reading protein database at Wed Aug 31 15:19:18 2022
+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 2 IS copies to results/input.csv and results/input.tsv and results/input.raw
+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 15:19:18 2022
+End in pred Wed Jul  9 09:58:03 2025
 Both complete and partial IS elements are reported.
-ISEScan ends at Wed Aug 31 15:19:18 2022
+ISEScan ends at Wed Jul  9 09:58:03 2025
--- a/test-data/test_2.fna.gff	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/test_2.fna.gff	Wed Jul 09 12:49:45 2025 +0000
@@ -1,4 +0,0 @@
-##gff-version 3
-gi|228288719|ref|NC_012624.1|	ISEScan	insertion_sequence	32413	33650	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_1;family=ISH3;cluster=ISH3_198|ISH3||gi|15898236|ref|NP_342841
-gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	32413	32456	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1
-gi|228288719|ref|NC_012624.1|	ISEScan	terminal_inverted_repeat	33607	33650	.	-	.	ID=gi|228288719|ref|NC_012624.1|_IS_1_TIR;parent=gi|228288719|ref|NC_012624.1|_IS_1
--- a/test-data/test_2.fna.is.fna	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/test_2.fna.is.fna	Wed Jul 09 12:49:45 2025 +0000
@@ -1,22 +0,0 @@
->gi|228288719|ref|NC_012624.1|_32413_33650_- ISH3_198|ISH3||gi|15898236|ref|NP_342841
-CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCTGACAGAATAATATCGA
-TTCATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAG
-CTGAGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCA
-CCAAAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAA
-GAAAGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGA
-AAGCAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCA
-AGGGATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACT
-GAAGGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAG
-ACCGGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGAC
-GACAAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGAC
-TAAGGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAG
-GTTGATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTT
-TAAGTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGA
-TTACGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGT
-GTACAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTAC
-TAATCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCAT
-AGAGACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGT
-TTTCCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAA
-GGGGGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGATGATTT
-ATTCTATCTAAAAGATTTTCTATTTAAATCAATAGAACCGCTTATTAATAATATAGATTT
-ATTTTCAAGGAGGTGATTTTGGGTCTACCGAATAAGGG
--- a/test-data/test_2.fna.orf.faa	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/test_2.fna.orf.faa	Wed Jul 09 12:49:45 2025 +0000
@@ -1,7 +0,0 @@
->gi|228288719|ref|NC_012624.1|_32517_33587_-
-MIDNRIYMSIKNSVEERFKLREMWYYHVRSEMVTPVLPHQNNIQQIGYKLLSMLNFKGKK
-GEEVARTLISACLWNDSVESKSRAYGVSPQTVRNYVEEQGMEVIEKLLESARKISLKVLK
-GVKEIDVSIDWTTKTWYGRPVGGLGSSEEGNSWNYATATTKFNGKVLLLAFVTQVKGMTK
-EEIVKALVEQVVAMGFKIRLITLDAGFYTVDVLNFISQFKYIVAVPVGDVKVYEEFDGDY
-ATNSKRHRRDXAGQVQASRVQQGKSEEKEEDVVYFARATNLDLPKGEVLDLYNKVRGPIE
-TSYRNIKAFLPFTSSTKFVXPHVDLRAGRGLLLPVHRVQGGGEEGAVQDTPNTLVF
--- a/test-data/test_2.fna.orf.fna	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/test_2.fna.orf.fna	Wed Jul 09 12:49:45 2025 +0000
@@ -1,19 +0,0 @@
->gi|228288719|ref|NC_012624.1|_32517_33587_-
-ATGATAGATAACAGGATTTATATGAGTATTAAGAATTCAGTTGAAGAAAGGTTTAAGCTG
-AGGGAGATGTGGTATTACCACGTGAGTAAGTGAGATGGTAACACCGGTACTCCCTCACCA
-AAATAACATTCAACAAATAGGATATAAATTACTTTCCATGCTGAACTTCAAGGGAAAGAA
-AGGGGAAGAGGTGGCGAGAACCCTCATCTCAGCGTGTTTATGGAACGATTCGGTGGAAAG
-CAAGTCGAGGGCGTATGGCGTGTCCCCACAGACCGTGAGGAATTACGTGGAGGAGCAAGG
-GATGGAAGTTATTGAGAAACTCTTGGAAAGCGCCAGGAAGATATCCTTGAAGGTACTGAA
-GGGAGTCAAGGAGATAGACGTCTCAATAGACTGGACAACCAAGACCTGGTACGGGAGACC
-GGTGGGAGGGCTCGGGAGTTCGGAGGAGGGAAACTCTTGGAACTACGCAACTGCGACGAC
-AAAGTTTAATGGGAAAGTGCTCCTACTGGCCTTCGTCACTCAAGTCAAGGGGATGACTAA
-GGAAGAGATCGTGAAGGCCCTCGTGGAGCAAGTCGTCGCGATGGGGTTCAAGATAAGGTT
-GATAACTCTTGACGCAGGTTTCTATACTGTTGATGTGCTCAACTTCATTTCACAGTTTAA
-GTATATAGTTGCTGTGCCTGTTGGGGATGTTAAGGTTTATGAGGAGTTTGACGGGGATTA
-CGCAACTAATAGTAAGAGGCATAGGAGGGATGAGCAGGTCAAGTTCAGGCTTCTCGTGTA
-CAGCAAGGAAAAAGTGAGGAGAAAGAAGAAGAGTGTTGTTTATTTTGCTAGGGCTACTAA
-TCTAGACCTACCGAAGGGGGAGGTGTTGGATTTGTACAATAAGGTAAGGGGTCCCATAGA
-GACCTCTTATAGGAACATTAAGGCTTTTCTTCCATTTACTAGTTCTACTAAGTTTGTTTT
-CCGCACGTTGATCTTCGTGCTGGCCGTGGCCTTCTACTCCCTGTACACCGTGTTCAAGGG
-GGAGGTGAGGAGGGAGCAGTTCAGGATACTCCTAATACTCTTGTTTTCTGA
--- a/test-data/test_2.fna.sum	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/test_2.fna.sum	Wed Jul 09 12:49:45 2025 +0000
@@ -1,3 +0,0 @@
-# seqid                                                      family         nIS %Genome          bps4IS          dnaLen
-gi|228288719|ref|NC_012624.1|                                ISH3             1    2.93            1238           42245
-input                                                        total            1    2.93            1238           42245
--- a/test-data/test_2.fna.tsv	Thu Jan 25 16:32:04 2024 +0000
+++ b/test-data/test_2.fna.tsv	Wed Jul 09 12:49:45 2025 +0000
@@ -1,2 +0,0 @@
-seqID	family	cluster	isBegin	isEnd	isLen	ncopy4is	start1	end1	start2	end2	score	irId	irLen	nGaps	orfBegin	orfEnd	strand	orfLen	E-value	E-value4copy	type	ov	tir
-gi|228288719|ref|NC_012624.1|	ISH3	ISH3_198|ISH3||gi|15898236|ref|NP_342841	32413	33650	1238	1	32413	32456	33607	33650	48	34	44	0	32517	33587	-	1071	2.3e-147	2.3e-147	c	1	CCCTTATTCGGTAGACCCAAAATCACCTCCTTGAAAATAAATCT:CCCTAATACGGTAGACCCAAAATCGTATTATGAAAAATAATTCT
--- 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