| Previous changeset 2:9e776e7fab4f (2024-01-25) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/isescan commit e2191246bc1ccd70c05fe0dac45d39cf8dd621d3 |
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modified:
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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a macro.xml --- a/macro.xml Thu Jan 25 16:32:04 2024 +0000 +++ b/macro.xml Wed Jul 09 12:49:45 2025 +0000 |
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| @@ -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> |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/TEST_1/test_1.fna.gff --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/TEST_1/test_1.fna.is.fna --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/TEST_1/test_1.fna.orf.faa --- 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 |
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| @@ -4,10 +4,3 @@ TNKGGQYIIAKWGKTKDSKFLKIEIVMDKDQFNVINAEVTSNEVQTAVKTVKDLQDKGKK VKKFYGDKAYDANEVYKTGVEVVVPPRENASTRRGHPARRKAVREFKRLGYNRWREERGY GVRWRIESLFSAVKRTFGESVRATSFLGQVVEAKLKFWAYAWMVHLANSLVGRAPGIRV ->gi|228288719|ref|NC_012624.1|_32517_33587_- -MIDNRIYMSIKNSVEERFKLREMWYYHVRSEMVTPVLPHQNNIQQIGYKLLSMLNFKGKK -GEEVARTLISACLWNDSVESKSRAYGVSPQTVRNYVEEQGMEVIEKLLESARKISLKVLK -GVKEIDVSIDWTTKTWYGRPVGGLGSSEEGNSWNYATATTKFNGKVLLLAFVTQVKGMTK -EEIVKALVEQVVAMGFKIRLITLDAGFYTVDVLNFISQFKYIVAVPVGDVKVYEEFDGDY -ATNSKRHRRDXAGQVQASRVQQGKSEEKEEDVVYFARATNLDLPKGEVLDLYNKVRGPIE -TSYRNIKAFLPFTSSTKFVXPHVDLRAGRGLLLPVHRVQGGGEEGAVQDTPNTLVF |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/TEST_1/test_1.fna.orf.fna --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/TEST_1/test_1.fna.sum --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/TEST_1/test_1.fna.tsv --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/TEST_1/test_1.log --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/test_2.fna.gff --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/test_2.fna.is.fna --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/test_2.fna.orf.faa --- 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 |
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| @@ -1,7 +0,0 @@ ->gi|228288719|ref|NC_012624.1|_32517_33587_- -MIDNRIYMSIKNSVEERFKLREMWYYHVRSEMVTPVLPHQNNIQQIGYKLLSMLNFKGKK -GEEVARTLISACLWNDSVESKSRAYGVSPQTVRNYVEEQGMEVIEKLLESARKISLKVLK -GVKEIDVSIDWTTKTWYGRPVGGLGSSEEGNSWNYATATTKFNGKVLLLAFVTQVKGMTK -EEIVKALVEQVVAMGFKIRLITLDAGFYTVDVLNFISQFKYIVAVPVGDVKVYEEFDGDY -ATNSKRHRRDXAGQVQASRVQQGKSEEKEEDVVYFARATNLDLPKGEVLDLYNKVRGPIE -TSYRNIKAFLPFTSSTKFVXPHVDLRAGRGLLLPVHRVQGGGEEGAVQDTPNTLVF |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/test_2.fna.orf.fna --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/test_2.fna.sum --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/test_2.fna.tsv --- 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 |
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| @@ -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 |
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| diff -r 9e776e7fab4f -r 81539b9ae80a test-data/test_2.log --- 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 |
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| @@ -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 |