Olivia Mendivil Ramos

make_panTE.pl has a sequence limit (>1Kb) that throws a bug of segmentation fault in blastn?

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sh: line 2: 2474030 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query TE_00071658_INT#LTR/unknown TCTGGTATCAGAGCAATCATTCCAGGGGATTTGTTCTATGTCTTTTTTTTCAACATAATCAAGCAATCACTCCATCACCATTTTCCCTTCATCGTAGTCTCGCATCAAACAAACATCCACCACCTGACGCTACACACGCAATAGAAATAACAGAACTCGCTGCATAGTGAAATAAAAATACCCATAATCTACGTGCGTAGAAGACACAGTGAGCTACTTAACGAAGAATTCATAGATAACTAGCAATTATCGATGTGGTAGAAGTGAGTTAAAAATAATTCTAGATCTTCCACTTGCAAAAAATCATATCGACGAATATTTTTCAAAGCGATTCAACACTCAATTCTCGGCACAAACATCATCTCCGATGAATAACCCAAGAAATTGGTGAAAATAAAATAAAAATTAAAAATAAAACTAAGGTTTAATATTTTTCTATTCATTGGCTCGTATTTTTTGATGTCAAAATTATACGAGTAAAAGAATTGTGTTAATTCTATGGGACAATAGTCCCACATCGACAACAAAAAGGAAGTTTTCAAGTTTAAATATGCCAAGGCACGTACAAGACATCGTGACTTAGATCATGTCCTCCCTCCCATGCCTCATGTTATGCTTGCTACCTATCGTTGTTCCCTCACTACCTCAATCTTGTTGTTGTTGACTTTTCCACCCCCTGCCTGCCTGTTGACACCCCCACCTTGTGGTTATTGCTATTGACTGCCCCATGTTGCGTTATCTATCTCGTATTGCATGCCACCCTGTCTACTGTCTGCCTCATGTCCCACACTGCTCTTGTCCACCTTCCACCTCATGTCCCACTGCCTTGTCACTGACTTGTCTCGCCATGTCATCCACACTAATATTAACCATTTAAGGGGACAAAACTAAAGTTGCAACAACCAAATTTTTGACATGTTCAACAAAATTGCCAAATGGTTTTGACAAAATATTGTTCAAAATTACCCAATTACAAAATTGATGAAAATTCTTATAATTATTTTTGCACATAATTGACACAAATTTGCGATAAAATTTCTGACAATAATTCTTGTAACCATTTTTACAAAACTTTTGTCAACTTTTATGCTGCCCAATTTTGATGACGACTTTTAGCAACTTTTGTCAATTTTTTCACGATGGTTTTTGTGACGATTTTCAACAAAATTAGTGATAACCTCCAACAATGACTACACAAATGGCCATCGATGGAATATCTCATGATCCCAATATACTTTCATCGATTAATCTCACCACCCTTAGTCAAATTACTTTCATGCATGCATATAAAAATCAGTGCCAGGATATCATCAATTACATCTCTGGGTTAGATGAATCATTTCTCATAAGTTGCTTTGTCAATGGATTAAAGGATGAGATTAGGAAGGAGGTGGAAATATTCAATCCTTGCACCCTAATGCAGACCTTTGGATTAGCTTTATTAGCTAAAGATAAACTCAATGTTCAACGTCGATTAGGAAAACCACCTATGGGGAAATCACAAACCACTTACACCATCCCCAAACCTAACCAAACTTTACCAATTTAATTTCTTAGATTTAAGGAGAAGAAGGAACGATGAGTGAAATATCTTTGCGATACTTGTGATGAGAAATTTGGAACCCACCATAAATGCGCTACACAAACATTGTATTTATTGAAGGTAGTTGATCCTTGTCAATCCATAAAGGGTGAATATGAGGAAGATGAGCAAGAAATAACTGAAACACCTAATCAAATCTATGGAGACAATGATATTGAGGTGCAAGAAGTAACCAAAGCACCTAATCAAAAAAATAAATGCAATAAGGTTGATGTGCAATAAGTGATCGATTTCCCAGGAAAATATAAGGTAGACATAGAAGACGTGACCAATGAAGGCTACACATACACTCTAAAAATACTACCCATAAGTTCATCACAAATAGTGAGTTCTCACCACATGGTAAAACCTATCTAAAAATAAGGTAGAAAGTTGACTGCACACTTAATTTTTGTTGACTCTCTCAGGGAACAACCAAAAGATGTGGGAGTGTTACCACCATTTTTGATGCATCCTTCCAAAGTGTTTGAGGAGTCCCAAGGGTTACCCCCCCATCATCATCACGATCCTACTATTCTTCCTGGAAACCCCCCACTAATGCTTTGATCCTCAAGATATCCCTACCTCCAAAAAAGTGATATTAAACTTGTGCAAATACTACTTGGAAAGCACCTCATCAAT ") -db data/omendivi/TREES_2020/TE_WN_v3/merge/TElib.list.panTE.raw.iter8 -word_size 7 -evalue 1e-5 -dust no -outfmt "6 qseqid sseqid pident length mismatch gapopen...

with TIR/Sola2 TE_Sorter chokes?

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Hi Shujun, Thank you for EDTA it is a nice tool. I have run EDTA on a large genome split in chunks. One of the chunk ran EDTA_raw.pl without an...