EDTA
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oushujun
make_panTE.pl has a sequence limit (>1Kb) that throws a bug of segmentation fault in blastn?
sh: line 2: 2474030 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00057433_INT#LTR/Copia GGTATCAGAGTAGAATAGATTTTGCTAGCATCCTCTCTTGAAGATTCTAGGAGTTGGTTCTTTGTATCCTTTGTTGGCTTCTCCTTTTTTGTTTAAGCCTTCAAAAAAAATTATATATAGTTTTTATTTTAGCTATATTTTTTTGAAATATATGTATGTGGGTTTTTCTAAAAAATATTTGTCTCCTTCAGGAAGGGAAGATTCATTGTCTTCTAGTATAATTTTTTTAAGAAATATTGCCCTTTTTTTTCCATAGATTTGTTTTTTTTGAGAAAAAACTCTCTTCTATGAAAATATTCATACATAATATTTTATAAGGAAAAAAAAAACTCTCCTCTTCAAGCGATTATATTTTTCAAAAATATATATTTGAAATTTTTTAAGCTTGATATAATAGGATAATTTTTCCTATCATTAGTTTTTTTTCCTTGCAGGAAAAATTTCACTTCGCTAATCACAGAGACAAAATTCAGGCTTGCAAATCATCCACAGGGCACCTTTTTTATGGGCATTGTCATCGTTCTTGTGTCACCTCTCTTCCGCCTCTCCATCTGAGTTTAAAATCTCCATTGGCGCAACTATCAATTGATGCATTATCAAACGAATGTTGTTGAGATTTTCTAATTTTTTAGTTTACCTTCATGTGCTTGAGAAGATGTCTTCTATAGTTGCATTAATACATTTTTTTTAACATTTCATAAAGAACTGTTCTTTTTACACGTCTCTCACTTCAACATCGGTGAACGTCGTGAAGCCTGCTAAAGTCAAAAGTTATTTCTTTTGGTGATGGCTAACGAATATCTTTAGAATCCTTTAAATCTCATTCAACACCTCTTTCTTTCACATTGCAATCATTTTTTCTCTTATGCTCGAAAATATTGTTTTAAATCTCTACAAGTTTAAAGCTCATTTGATTTGCATATATTTTTCATATTGTTATATTTTTTTGCAAGATAGTAGGCAAAAATTTTCTCTATTATTCGTTCCTTGTTGTCTTATCATCTACAGGTTTATCCATTCTTAGGGGGGCAAGGATCTTGGACTGTAATTTACAAGTGATAGATAGCCTTTTTCGAAGGCCTCTATTTCTTTTATGAATCATTGGGTCTGCATCTTCATTTCGAAACAATCCAACCTTAGTTGAAGACTCTCATTTCAAAGCATCTCAAAGAAAAGCTAGCCTTCTACGAAGACAACCACCTAGCTTCTCATTCTTCAGCGATGCGTTGGGTCTACGACATTGAAAATATTCATCTTCGCTTGAGGCACTCTATTCTTTTGTTACCTATCTTTTTTTGTAGGGTATCCAGATTGTATACAGAGGAGTATTATTCTTTTGCCTTGTTCTAGCTTTCTGCATGTGCCTTGGTTGCCATGAATAAATCATCCTTCTTTCAGGCTATTTTTTATTGCTTTATAAAATACCTTCAATATCAAAGGGTTTTTTATTTTTTTGACTCCCTTTTTCACTAAGCCTTTATTTTCCCAAAGGCTATATTCAAAAGTGAAAAGCATCTTTTGTAATCAAAGTAATACAAAGTCTATTTACGGGGGGGTTAGAGGTGCTAATTATTGCACCATTGTCTATTTTATCTTTTGAGGGGGGTCATCTTTCATGTGTCCTTTTTCTTTATTCTAATTCCTTTTTTTAGTAACTATAATAATAATTTAAGTGCATAATTTTTTAATATATGATAAAAGTACTCACTAAAATTAAAAAGGGAAATCTCAAGTTGTAAAACCTTTTTTTCTCTAAATCTTCCCCTTTAAATGTAATTTTTTTATCATAATCTTGTTGGTTTTTAAATACACTTATTTTCAGGTTAATTCATAAGATATAGATAGAAAAATAAATAAAACCATTTTTCAAGCCCTCAATACTAATATAGTTTTTTTTGGCTTGTTGCTTCTTAAAATTAAATTCTTTTCTATCTATTCCTTTTTTTTGAATACTAAATAAATCTATTTATAATTAAGCAATCCTATTCAAAAACTTATAGTTTCTTAATTTTTTCAAGATATTTTACCTACGTTCCACGTACCAATATCTTCCATAAACTTATAGTTTCCCTCAAGTTAGGGTAGGTTTTTTTAAATACTTGGTATACAGGTCTAGCATATATTTTTTGATCACCTTATTTCCAATATTGGATATCTCTATTACTTATATTTTCCCTCTCGTAAGGGCGAGTCATTGAGATATTCCAATATCTAAATCTGGCTGATCCTACTTGCATTTCAAGCCAATCTTCCAAATATTTTTTCTACTCATTACTTACAGTTTCCCTCAAGTAAGGGCGGGTAATTGAGAAGAACGATATTGGGCTTGGAAACTGTTTCTAAGCTAATTTTAATATAACAACACTCTATTACTTATAGTTTCCTCTCATTAGGGTGGGTAATCTGAGGGTTGTGACATTAAAAAAAATCTTGCATTCTTCTTTAAATTGCACTAATATAAACTTGAAGTTGACAAAATGAATACAATTGATCTTTTCACCCCTCATAACTATCACACTTGGAAACCCAGAATTTTAAATCTTATATCTCAAAAAGGGCTCACTCATTTGCTAGAAGAAAAGCAACCTAAATTTGAGAAATAATATGAAAAAAATGTTCATAAAGGAAAGATGTATGAAACAATGGGTATTATAAGCACTAATGTTTATGAAAGCTTATGGTTTCACATTAAATTTTTTAAAAATCCTCATGAAAGTTGGGAAAAATTAAATATTTTGTTTGGGAAAGTAGATCAAATAAGATCAATGCAATTAGAGGCAGAATTAACAACTTTATCTCCTAAAGACTTCAACAATATTGTTGAATTTCTCACCAAATTCAAAGAAGTCCTCACTCAATACAAAGGCAGTGGGAAGACTAAGACTGAAGAAGAATGCATTTATCTAATTATTTATAAACTAAATGGTGTATTTCAAATATTTTCAACCACCTTTCTATATACAAAAGATGTTGTTGGTGCAACCTTTAAAATGCCCTCTTTAGAATAATTTTGTGATAGAATAACTAGGGAAGAAACACAACTTGAAAGATATGAAATCTCTTCCTCAAAATCCTTAGTGGCCTCCACCTCTTCTAAAGAAAAATTCAAAAAGAAAGAAAGGAATCCCATAACTTGTACTCACTGCAAAAAGAATGGTCATTCGACAAACAAATGTTGAAAAATATTACAACAAATAGAGGTAGCTATGAAGGATAAAAATATAGACAACAAAAACCAGATAGGAAAAGCCCTAAATGTTCAAAGGAAAACCACCAATTCCTCTTCTAATTACTGGGTCCTAGATTCTGGAGCAACTCATCACATGACTGCTTCAGATGAGTCCTTCTCTTCTATCTCCTCAAGTTCAACATGTAGCATAGAAGTTTGTGACTCTTCCTTTATCCCAATCAAAGGAAAGGGTAACATATCCATTGATGATACTCTATCAGTAATGTTCTCTATATTCCAAACATTGCAAAAAATCTCCTCTCTGTCTATCATATTTGTACTTTTGGAAAGGGGAAAATTGTTCTCTTCTCTCTAATAGGAGTTGAGATAAGAGACTTTCAATACCCCCACTCTCTTATAGCAAAAGGAGATATTGATCACAATACTAGTCCATTTCACTTCAAAGGATTAAAAAATCCAAAAGGGGCCTCCTATTTTGTGGCTCATGGAGATAGTCTACCTCAATTTTATTATTTTTTGTATTAAGAGGACAATGTTTGCAAACCGAAGACAAGCCTCTTCCTTTTATATTTTTTGATAGATGGTTTTTCCCATGGGGTTTTTACCATCTCTTCATAAAAGAAACCATTGTACATGAGTACCTAATTAGGCTCTATTTCTAGGACTCATCAACACAATACACCTCTAGTATCACTTAAGGGGGG ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2484204 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00025015_LTR#LTR/Copia TGTTGGAATTATTAAACCAACTTTCACGCCATCCGCAAACGCTTCACCGTGAAGCAGTAAAAACATGCCTCTTGAAGGTGCTTCACTGCGAAGCAACAAAATTATGCCCCCTAAAGATGATTCGCTGTGAAGCAACATAAATCCGAGAGTTCGCCCATCAGATTTGCAAAGCAGTGTCCAGGCACGGGAAACGAGCGCCTGACATCACACATGTGAGTAGGTGGGGTTGTTTGGCGTTTTGTGGAAAACCCTCTTCGGCATTTAATTTTTTGTCAGCCGATTGGTGAATTATTCCCACCTCTTGTCTTCATTCTTCGTCTATAAATACCGGACCATATGTCATTTAGAAAAAGAGAGGAATTGCAAGTGCAAAGCAGCCACAGCAGCTAGGGTTTCGAGCGCAGAGCAGTAGAACAGTAGATACCCAGAGCAAGGAGCAACAGCCTCTAGGAAACTATCTCTTTTGTGTTTATCCTGCAATTTTAACTTGCAGATGTTTGTAACCGCTTCATTGAAAGAAGCCTTGTAAATCCGGTTATATTTCAATATATAAAATATTTGTCTTGCAACTTTGGGTCCCTTTGTTTTTGTTCTCTGCCTCGAAGTATTGTTTATCTGAAGACGAACTTCAGGGAGGTTTTGCCCCGAAGTGGTAAAACACTCTTTCCATCCTGAGGGTAAATTTGTTTATTTGTTTGTTGTGTCAAAGAAGCACTTCAGCACTTTATTTCCCCGAAGTGGGATTTTGGAGCCACTTCGCCCGAAGCTGCCAAATTGCCGTGAACTTGTGCTTCGCAACCTTCTTGGACGAAGCTGCCACTTCGCTCGTATTTATTGCGAAGCACCCTCCACCTACCTAAAACTTGCGAAGTTTGATTTTCTTTGGCGCTTCGCAATTTAACCCAGCGAAGTAGCCACTACACTGCCTTCTGCCTAAACCTGCGAAGCTCCCATCCGCATGTCAATTCCTCCAAAGCTCCCAAAGCTAGTTGTGCAAAGCGTTTTTATTTAACGCGTTTTTAATTCCTTCACCA ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2489281 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00072609_INT#LTR/Copia TGGTACCAAAGCAGGATATATTTTGCTAGTATTCTCTCTTGAAGGTTCTAGGATCTGATTCATTTAATTTGGATAATTTTCTTTGGCTATCTTACTTCAAAGTTTATAGTAGTCACATTTTATCCATAGTTTACTCTTTCAACATATTTATTTTTTATGAAATATATGTTGTAATATTTTTTTTAATCAAATCTGTGTTGAATTCGTGCTTGAGGGATTTTTTTTTTAAAAAAAAAGCTCTTATTTTTCTTTAAACACAAGGTTTACCCTATGTGCATGGCACTATTCTAGCCCATGTTAAAAAATAAGAGCCTCTTAAATTTTTTAAATACTTTTTCCCTCTCTTCGATATTCATTTAAACAGTCTCTTTGTGGTCCACCAGAACTAGAAATATCATTTACATTTTTGCTTAATTTTTTAGCGCAAATATCATTATATTTCTAACCACTATATTTTTCAATATATTGGTAAGTAGTGGTTTTTTAAATTCTTTGAGATTTTATTCGATCCTCAGGACAACGGGTCTCCTCATTCCCATTTCAACTCGGTGCTCATGACATTCTCTCTAGTCGCTTTATGATATGAATCCTTGGTCCTTGGCGCCATTCGCAACGTCTCTCCATTGCCATTTTTTTTGTTGTTCCTGTCTCAGAGTTTAGAATATTATTCAAATATTTTTTTCAATCCCCCCAATGCTCTCTTTGTCGGTCTTTAAATATCCTCTCCCTGCAAAGTTTTAAAGTGCCAAGACTTGCTATTCAATTTAAAAAAAAAAAACTCAATATCATATTGCTCATTCTAAATATTTATTTTTTCATATATTTCTGATAGTTTTTGTAGGGGTCACTGGTTCGTTTTCCCATTTACGTTTTCTGCAGAGGTCGTTGTCTTTTAAGTAATGTTTTGTGCAGGTTTTGTTGGTTCGTCTGAGGAAAATATATTTTTATTCTTAAAAATTCCACAGGTGCATAGTCAAGCATCACGGACCAAAGTGCTCTTCCATATGCCCATACGCGTCCTCTTCTCTCGATGAAATCCTCTGCTCCAAAATGAAATATATATATTTTATATATTTATCATCCTATTATCAAGAGGCACTGATTCCTTTTAATTAATGATTTCTGTAGAGGCATTAACATTTTGTGCAAGGGTCGTTGGCATGTTATAATATATTTTTTATTTAACATTCTCTTCTGTAGGGTAAGATCATTATGTCCTCTCGAAGACGTCCTCTGCTCTAGACGATTCCAGATTGTGCAGGTAATAGAAAATATCATTGCAGATGCCTCATCATCTTCGTTCGAACCTCTTCTCTACTATGTTTTCACCTACAGAGATCGAAGCTGCGTCTTCCAATTTAAAAGTGCAGGGAAATTTAAAAGGGCTCTTCGCCTATCCTTTTATGAGACTCAGAGTTTGTAATTTTTTTCTTATATTCCTCCTCATATCTTTTATTTAAGTTATTAGGTTTCTTTTGAATCCTTGTGTTTCAAAGAAACACCTTTGTCTCCTTTTTTAGAAGCCATTATTTATTTTATGGCTCTCTTCAAACGTGAGACCCTATTGTAACCATTATAATAAAATAATTCTTTTCAGGGGGTTGCGTACAAGTAATTGCACATCTGTGTTTCAAAGGGGCGTTGCATTTCTTATTTTTGCCTATCTTCTTCTATAGTTTTTACTTGCTTTAAAGTAAGTCATAATTATAAGGATATAATTGTTGATATTTCCTTTAAATTTTCATAGAAAAGTTACTTACAAAAAAAGCATCACCCATATACATAAATTTTTTCTTAAAAATTACAATTATAATATTTTAAGGGGGGTTGAATCTTCTTATTTAAAATATTTCATTTAAATTATTATATTTAAAGGTATTTGTTTATAATATATTTCTTTATATTTCATTAAGAAGATAACTCTACACCTCTTCATTTTTTTAATTAATATTTTTTCATTAATCTTTATGTATGTCACATTGTTGGTATTTTTTTTACAAATTATAAACTTCTATAATTGAAAACCTCTGTTAAAATAAATCTCTATTTTTTTCTAAATTCTAATAAAATTTTCCCTCAAAATATATTTGCCTACGTTCCATGTATCACTATCTCTAAAACTTACAGTTTCCCTCAAGTAAGGGTGAGTTTTTTGAGACTATTGGTATAAAGGCCTGGCATATATTTTCTCGTATCAACCTTACTACATATTGAATATATCTCTTACTTATAGTTTCCCTCTAGTAAGGGTGAGTATTGAGTTATCCATATTTAATTCTGGTTGATATCTTTGCATTTCAAGCCTAACTTCCTTTAAAGAACTAATTGGCATTTATTTAAGAAAATAATATGAAAACATCATTATACTTATAGTTTCCCTCTAGTTAGGGCAGGTATATTGAGTTGTTATATATTGAACAACTTCATTCTTTCCCTCTAAATTGCATAAATTTGAAGTTCTTTATCAAAGGAATAGGGGATATAACCATTGGTGGTGGCTCTATTAACAATGTTCTCTATGCTCCAAACATTGCCACTAATATCCTCTCCGTCTACCAAATTTGTACCTCTAGAAAGGGGAAAAATTTTCTCTTCTCCCCAATAGGAGTTGAGATAAGAGATTTTCAAGATTCCAAATCTCTTATAGCCAAAGGGAATATTGATCACAACTCTCATAGTTTTCACTTCAAAGGTTTTCAAAATCCAGAAGGAACCTCCTATTTTGTGGCTCATAATGATCTATATTATGAAGATCCAACTCTTGAAGTTAACTTGGTTATTGATAATCAAGAAAGAAGCCTCAGATATAAAATAATGGGATGATGCCATGGAAAACAAATTTTCTTTCTTGATGAAAATATAGACTCCGTCCTTCTTTCAGCAAAATTTTCTCATTGTGAGTCTGATAACATAGTTTAAATTTGGAGAAGTAAAGGTAATATCACCATTCTTGTTCTTTATGTTGATGATCTTCTTCTCACTAGTAGTAACTTCACTCACATTCAAACTATAAAAGACTCCCTCTTTAAAAAATTTGAAATGGCTAATCTAGGTCTAGCTCATTACTTCCTTGGGATTCAAATAAGTCAAAAAAATGCAGGAATTACCTTGTGTCAACAAAAGTACACCCTAGATCTCCTTCAAAAGTTTAAAATGATAGATTGCAAACCTTCTCCTACCCCTTTTCAATCTAGAATTAATCTCAATACTTATTGCTTATACCCTTTATGTGATGCAACTCTATATCGTCAGCTTGTAGGAAGCCTGTTATACCTTACTCATACTCACCCAGATATATCATATGTTATTGGGCTCATATCCAGATTATCTCATAACCCTCATTTCAGTCATTAGAAAGCAACTAAAATAATTCTTCATTATTTTTAGGTCAGTACACACTTTGGGCTCATCTATAAGGGAGACTCCATGCATATCATTGGCTATATATATTCAGATTGTGTAGGATCATTAGATGATAGATGTTCAACCTTTGGATATGTTTTTTGCCTTGGTTCTTCACCAATAGTCTAGTTATGCAAGAAACAACAAGCAGTAACATTATCTTCTATAGAGGCAGAATACAAAGTAGTAGTTTCAGATAGTCAAGAAAATATTTGGCTTTGTTAAATTCTAAAAGAATTTGGTTTGTTACATAAAGAGCCTATAACTCTTTGGTGTGACAATTAGAGCATAATTCATATTGCACATAATCCATTTGATCATCAGTGCACCAAAAACATTGAGATACACATGCACTTCATCAGGCAACATATTCAGAATGGGGATATACACTTGGACTATATTCTGACTGAGAATCAAATTGCAGACATCTTCACCAAGTCATTTCCTTCTTTGAGTTACCTTCAGTTGCGAGGAAAACTTGGAGTATTACAACTACATTGATACATAGGTCTCCCACCTCTCATTATATTATAAAAGAGTACCTCATCAGACCTTGTTGCTGGGACTCATCATTCTTTTGTATAAGAGAACAATCTTCTCCATCCGAAGATAAGCCTCTTTCATTCTTCTTTATTTTTTATTGATGGCTTTTCCCACTGGGTTTTTACCATCACTTCAAAAAAAAGAGGTGATAGTTGGCTTTTTCCCACAGAGGTTTTTTCCACCAACTATCTATATTATACATGAGTACCTAATCAAGCCTCGTTGTCGAGACTCATTTGTAAAAATCTCCCCTAGTATCACTTAAGGGGG ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2490848 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00043536_INT#LTR/unknown GTCCGCCCTTCCCAAAGATTGCTTGTCCTCAAGCAATACTCCAATATACTCTAGTCAAATATCTGCTCCTGGCTGTAGTCACAAAAATACTAGGATCCCAAACAATCCTCAGGAGAAATCCACCATGCTGACGCTGCGCCACTCTGATCTCAACAGGAAATCCATTGTGCACCAACTGCACTCCCTGCTTCGGTGAACCGATGAAAGCACTGATCAATCTCCAACAAGAAGCTGATATAGAAGTGGGTTGCAATGTCAATTCTACGAATAAGCATCTCGGGAATGCTTTCGCTAACAAGGTCTGAGAACATCAAGCTATTACTCAACCTCCAAGTGATCATATATTCATTCCAGGAGTAACCACACACTCGAACAACAATGAATCTCAAAGCAGAATCAAAAATTGGGAAATCTATCAACATGAGTTGACTGACAAAATTCTTACCCGAAGGCTGAATGACCCGAAAATGATCAAAACTAAAGCTGTCCAAGTCTGAAATTTGCATCTCAAAGTCTGATTTTAGAAGAATCAGCGTTCCATGAGAAGCATAACTGCTGCAAATCAGAGACCTACCAAATAGAATGCAAAGTTTGATCATACCATCAACTGAATTAGCCTCCCAGAGAGTCACCAATCCAACAAACCTCTGGTTCATCTTCAGAATCTCCCTCCAATCCATATAGTCATTCAAAAAGCAAACAACAACATCCCTTTCACTCTTTTGGCTAACCAACTCCCAAGGCACGCACCTTCCATCGTTCTCAATGCCTGGAAACACCAACATGCAATCTTGGGTGTAGAAATTCACCTCCTCAAAGGCTCTGACATACTGAGGCTGCACCATACCAAACATCATATGAATGTCATCTATATAGGAATTAGGAATGTTTGTTGGTACATCACAAAGCCTCTCCATCACATCAGTTGTTGAATCTTTATTAATCTCCTCTCCCTGTGGTGAATCCACAAGGTTCAACACCATGTCACAAAGATTCGACCCAACATGATCCGTCAAAGGAAGTAAATCATCATCATGATGCATCTCAAAGAGTGGATTGTTACAGGTTGTCTCACTATCCACCTCAAACAATAGATTGCCAATCCACTGGATCTCATTACTGTCCTCATGCTCGAACCAATCAACCTGCTGCTCTAAAATAGTGTCTTCTGATTTCGTGGGACAGTGGACTAATTCAAAGTCCTCCTGAATGCTATCAAGCTCTTCAACCAACTGCCCAATCTCCTTGGCTCTTTCCTGATTCTCTTGTTTAGTGGAATCTATTACAGCAGCAAGTTTCATCTTTGTTTCATGCAATGAAATGTGTGCCTCTGACAAAGAACTTCTAGAAGACTTAAGCTCCGCAGTGAGCCTATCAACCTCTTCCTCTTTTCCTTTTAATGCACTATGGGTCTCTTCAGCAAGCCTGATATAATGGTCCCTGTCTGCAAGTATGTTCATGAAATCTGATTTCATAGTTCCCAAGGCTGCTATTAATGTCTTCAAATCTGCAATAGTGACTAACCCTTCAACACCCTTCTTCCTCTTCTCAATTTGGACCTTCCAATATAGTTCTTCAGTGAATTTGTGGGTGTCATCAAAACGAGTTAATGCAGCAACAATTATGTCTTCACTAGTTCTGACATCAAAATCAGATTTATACATTAAGTTTCCAGAATTATTTTCCTGATGATATTCTGCAAAATCAACATCTACTGGGGTTTCCTCTTTGCACATTATATGCTCCATTGTTTGTTCTTTACTTGGGATAAGAGGAATTTCACTCCCAAGCGTTTCTTCAACAGTATTAGGTGTCAACACACCCGGATCCCAAGGCACTGAGAGCTGATCTCTTAATTCTGCTTCATCATGCATGTCTATCTCAGTACGTAAATCGCTCTGTAGATCATCAAAGAAAATGAAGTTACCCGACACACTTACTTTCATAGGTTTAGTTTCGAAACTAAACCCACATCCATCTGTACTGTCATCACCGAAGTGTGATAGGGAAGTGTCATCATGTGCTGATTGGAAATCTATATCACCTTCAACATGCTTAGCATCTGAAAAAGCATTAGTGAACTCATCATAATAAGCTGCTGTAACAAATTCATCATTCTTTGTCTCTGCATTGGCATTAGTAAACTGAACAAATTTGTCATCATTAGCACCAATTCTAATAGTGCCATCAAAGCATTGGTCAACCTTAGAGCTTCCTTTTGAGTGGTCTAAATCAGCAACAAAGTTTACTGTAGTGTTCTTTTCCCCTTGTTCAGTTTCATCAACAATGAGTGCATGCATGTTATTAAAATCAATCCGAGACTCATCCATACATACCTTATGTGTGGTGTCATTGCCTTCATGAGAATTTTCTGATTTAAGCTCCTCTTCTTCCCTGTGCTCATCAATCACACACAAATTTTCAGGGTTCCTTTTCAACTTCCGATCATACTTTACCATCATATCCATGAAATCTGCAAATGATATTTCAGCTTGATACATGGCTCCCATTGATTGGTATGTTTTATAATCTTTCCAAAAAATCTCTTCTTCACTGAGTGGCTCCATGGAGCTGCCACTAAATATTAACATGCAACTGTTGCAACTTCGTTATGGAAACATAAATTTGAAGACCATGCAACAAATATCAACTTCCCAACAGGCTGGCAGGGAAACCTGCTCTGATACCAC ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2495246 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00073208_INT#LTR/Copia TTAAGCATACCTCTGGAATTGTACCTCTAGGTCTATCTCGGGATCTTCCTGTGAAACTGCCTTTGGATCATTGCCTTTGGATCTGCCTGTAGATCTGCCTCTGGAACTTTGTCTCTGGGTCTGTCTTTAGGTCTGTCTCTGGGTCATTATCTCTGGGACTACCACTTGGTCTGTCAGTGATTGCAACAATGCTTTTTAGGAGTTGTAGGAGATTTAGGTTTTACAAACATAGAATTACTGGTACTTGCATGTCCAGTATAGCCAAGGCCTTCATGCTTTGCCCTGACATTTAGCATTATAGGAGTTTTAATGCCTTGTTCTTGTTTACCTAATCTCTCACCATTGAATCCCATTTTCTTCATCATTTTGGAACCAAATCCTTTGGTGTGCTTTTAAAAACACCCAATTTCATCATCTTCATCAATGCTTTTAACAATATTGCATTTGTCGTTATTAATGAGATTATGGAGCTCTTTTTTAGGAGGTTTAGTTTTTAAGTCACTAGTGTCACAAGCAAAATCTGCTATTGAAATGAGATCACTTGTGCTATAATTGATATCTACCATAGAAGGTATGAGGTCACCTGTATCACAACAAGCATGTGCCACAATGGGCTAAAGGTCACTTGTGTCACAACAAGCGTTCGCCTTTAGGACCTCACTTTCCTTATTTATTTCCAATTTACGTTGGGCACGGTCAAGTGCAACAAATACCAGGTATATGCCCCTTAGAACGCCAATAGGAACTTGAGAACAATTTGTCTAAAGGTCTATACAAGACTCAGAATCATCGAGGAGAGCTACTAAACCATTGTTTAGTGTGAGGAATGTGCCCTCCTCATAAAAATCCAACCCATCCATCTCTGGTGGAAAGTATGGGTCTTTAACTGATTTAGCAACATCGGTTTTAGGGCTATCTTTTTCTTTGATCTGCCCATTTTTAAGGTGTCGGTCTCTGCCGAAAATGCACCTTTTACAATAAAATTTTGCAAAATAATTTGACTAAGGTGTCGGTCACTGCCGAAAATGCACCCTTATAAGTCTTCCCCCCTTGGTTTTGCAAAATTATATCCTCCTTTTGATGCAAAAATAGGAGATAGTGGAGAGAGAAAAAATGTTATCCCCCCCTTTTGTGCAAAAAAAAATGCAACAATTAAACCTAAAAAAAGGCTCTTACAAAGCTTGCCCTGTAGGCATATTAGCACAATATATCACCAAAAAAAATCCCCCTATGTGAAGTACTTCAAACAAAAAATTGCTATTTATGAAGTCTAAAAAAACAGGTTTGGAGGTTTGATGATTTTATGCCTCTTTAATTGCTTTGATGGTGGAGAGAAAAAAATCTATCCCCCCTTGAAAAAAAATAACTCCCCCTTTAAAATTTTCCTTTATAAAGCATTTTAAAACATTTTATATTCTAAAGTTTAAAAAAATTATTATTCCTAATAGCAAAAAAAAAAAAAATTTAAATAATTTTAAACTATATAAAAGAAATAATTTAAAAATTTTAATTTTAACTTTAGAAAAAAAATATTAAAAAATAACTTAAAAAAAAAAATTGTTTTACCTTTGTTTGGGGGGGGTCGGCGGGTTTTGATCCCCCAACCTCACGGGCGCTAGCCTGGCGCTCCTGCCAGTTGGGCTAGCCCGCCCGATGAGAGGGAGAAGGGAAGATTTTCCCTTTCTCCCCTTGCGACCCTCGCGGGGAGCAAAAAAAATTGTGGGACTTTAGTCCCACATTGCTCCCACGGGGTGCATGAGGGGGGAATAAAAGGGAAGATTCCCCCCTTTGTACATTATTGCCTTCGGGTAATTACGACACCCATTTTTCTGCGCCACGCGACAGGGGTCAGGTCCGCGTCGGGTCACATGGCGGCCATGTCAGTCCACGTGGCGGCCACATCAGTCCAGCGTCCAGTCAGCTGCCACGTCAGTCCATGTGGCGGTCCAGTCCATTCCAGCGTTAGTCAACTGCCACATCAGTCCAGTCCAGGTGGTGCCACGTGTCAGTCCAGGTCGTCGCCACGTGTCAGTTCAGGTCGTCACCACGTGTCAATTTACCTTGAATTTCATGCCCAAGTCAGCCACCTGGGCTCCATGCCAGATCCAGGGTCTGTCAGGTCGCTATGTCCAGTCAACCACAGTCGTCAGATCTCAGGATCTATGCCCAGTCAAGCCAGTCCAACCGCCCTCGTTCCGAGTGCAGGTCTAGTTTCGATTCCTCGGGATGCATGCTCGAGCAGGTCCAGTTCCTATGCCTCAGGATGCATGCTCGAGCAGGTCCAGCCATGCCTCGAGAAACATGCCCGTGTCTTTGTCTACGCTAGTCTCCTTAGATATCGAAAAGTGTGCCCAAGCAAACCTTGCTCTGATACCA ") -db data/omendivi/TREES_2020/TE_WN_v3/merge/TElib.list.panTE.raw.iter8 -word_size 7 -e/grid/mccombie/home/omendivi/value 1e-5 -dust no -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2495250 Segmentation fault bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00063580#DNA/DTM GACAAGTGTCATTTTCATCATATAGGCCTTCTGCCTATATATGTAACACATTTTTATCAATAAAACATTTCTTAGAGTGATTGAGAGGAAATGCAACGGACGTTTGAATATTTGGTCGAGGAAATGCATCAGCTCAAAATAATTCATGTTATGACCTGAAAATGGAAGGATGAAAACCAAAAATACATAAAGAGGAGAAGAACACCATTTTTTGTCCAGCAAAGATCATGCGAAATGAAATATTCTTCGGTTTTAGAAATCCGTCGGGCTAAGTGCTATTGTGGGAATGGCATTCCAAGCGATCAATGTCCACAATTTCCTTGAATTTGGATGACTGTAGCAATATTATTTTTCAGAGCGGCATGGTGCAGATCGAGCATGATTTTTTATGTATGTGAGTAGCTGGGAATCGATAAGGCCACCGTCGAAGAAGGAGGAGTGGTGTGGATCAAGCGCAGGATGGTGGCGTCCAACGAGGGGAAGCCGCAGGTGACCGCCATCAACCACTGCTCCATCGGGGATGCACCGTTGTGCCACCACATAAAATTTTTACCCAGGCGGAGCACATCCACCAAGATCCATCACAAGCCGACGCAGGGCAGATGGTTCGCGTTGGGAGAAAATTTCAGCTAAGTCGCCGAAGAATGCAACAGTTGTAGAGAAATTTGTGGAGCTTGGACATGGAGGATTTTTGGATAACGTGTTCCAGTGAATTAGGCGATGATCCCATCAAAGACGATGCTGATAATTAGTTACAATGATAGAACTTAATTGATACTATTGTGGAAGTCCGAGCACCAAATCCAGTTCTTGTGGCTGTGTGCTCGTCGCTAAAATATCCTGAGGCTCCCGTATGCCCTGACTGTTATTTATCCCACTATGGATAACAACACCATACCAAAGATGTTGAAGTAGGTGCCTCTCGCTAGGGCCTGTGTGGCGGAGCCCTCGCGCCTGGCAGAGCAAGTCATTTGTCATTAGTGGGTAGGGTAAAATATTTTAATCATGTTAAAATTTGTATTGGCCGACAAGTCCACTCTTCGTTTTGAAGATGACAGTGTTGAGGGGGAATTGTTTTTAAATTGAAATTTGAAATTTTAGTGGGATATGGCTATTGGAGATGGCCCATTACTTGTGAAAAGTATTTTCGACAGCCACAATGTAATGGGGGAAGCAATTTATGGACAGGCAGTTTTTTCGGATTTCTTCTCTCATCCTATATGGATCTATGGCTCAGGATGACCTGGAGAGGCAACAGACCCAGATGTGGCTGACCTTGAGGCACCCATGATGACCCTGAGGCACTTAGAAGGCTGACCCAGTGGCAACAGACCCGTTGAAGTGGCTGACCCTGAGGCAATAGACCAAGATGTATACATAGTGGATCTAGCATTATTCATAGTTGGAGAGCCAAGCGCAAAGAAGAATTCAACATTAAGGGGGAATGTTAACCTAATACTTTAAGAGGGAATGTTAGAGTTAAAGTGCACTATGCCTTCAGTTTGACACTTGTC ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2502502 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00042576_INT#LTR/Gypsy CTAGTAGAAGAGCACCACAATGGTGTACACCCATAGCCAAGCCCAATCAAGGGCGGATGCTGCGGAAGGTGCACAAAGAGAGGGCGTTGGTCACCTTCGCTTTAGCCCTGAGGACTTGGCCATACCGCCTTGGCGGTCTGGCCTACAAGAGAGTCCACATCAGGCCACATCAAGAAGGAATTATTGGGACCCCCCTCTGTGGGGTATGCCCATTCAACACAGCCCCTTTCGGGAAGAAGCTTTACATGTAGCACTCAACGTAAATAGAAAACCGCCTTTTGAGGCTAGATCTGAGTGGCCACAACATGATGAAGCGCTAGAGAGGCACAATGTCCATGAGGAGAGACAACGTGAATACGACACCTCTCCTTTGCCTCCCATTAGAACTGAAAGACAAAACCCAGAGCGCAGGGCTCTCCACACAGGGCGAGCTAACTCCGCCCGCCCCTTTCACACCCATGAAAGGGAGTACGAGGAAGACCATCGCATTCCTCGAGAACAACATACAACGTGGGAACCTTGCATTTCCGCACCTGCTAGATATCATGGTCACCCATCGAGGCCAGAGCCTCAAGTAAATGCCGCCGACCTCGACAGAGGGAAGCGACCCATTGAAATCTCGGATCATCAAGACCGAGGCAAATACATAGGAGAAACATTCAAGCCTCCTGAGCAAAATATGGCAGACCAAATTGACCCGGCAGTCACCAGACATGCCGCCCGCCAAGCCCGAATCACGCGGCTTGAGCAAGGTCATCAGGAGTTAGAGTACTTATACCGCCTTAATAAAGAGCGCATGCAGCGCGAAGCGGATGAGCTGCATTATAAACTACCTGAGAGGGGGCCAACCCCTCGCACCCAAAAAGTAGAACAATATGAGAGGTATAATCCTTTGGTGCAGGACAGGTCTCCGCGACCTCGTCAAGCTTTGCCTCCGAGACCTTATAGACCCGAGAGGGAGGCCACTCCCCGAAACAATGATGGGTACCCTCGACAGGGACTCACTCAGGGTCATAGGTCTCGCCCAGAGACTCCTCAGGAAGTTTATGAGGAATATGAACCAGAAATAGAATGGGCCAAAATGCCCTATCAAGGCGGGAGGGCTGCCATTCGGCCACCCCCCATAGGCCTCCAGTCTCCCATAACTCACAATGGGAGCAAACAAAAGAGGAAGAAATTAAATCTTTCGATGCATACAAAGCGCTATTAGAGCGTTTGGAGTCTATGGAGACAAAAGCTTCTGGGCAGGCAAAACCTCTTCGAGTCAATGAGGTGCGACAGAATCTTCCCATGCAAGGATTTGTGGGAATGATCAGCATAGTGACCAGGAACAAAAAGTACCCAGGGAGTTGCCCTCGAGGCAGCTACAAGAGAAGTTCCAACAACGTCGCAACCTCAACAACGCCCTGTGCAATTGCCTCCGCCTAGACCCGAGGTCATGATACGGACCAAACTCACGCAGAGTTTGCGGACCACATCGGCTAGGCTTTTCGGACACTAACTCCCAAGGAGAGCATAAACGGTGTCCAGAGATCTTTTTGAAACTGTTCCCTTTAGAGGTTCCAATTGAGCCAATGCAGTGTCAAGAGAATCAGGTCCCTCCACCAAGAGTGGAACAACCGCAATGGGATCAGATTAATTTGCTCGAACAAGGTGAACCCTTATATTTCACAAACAGTTGTGGAAGAAAATGAACATTTTTGGATCTCCGATAGTGATTCGAAAGATGAGACTGAGATGGCTTATCTCAATCACATGTGACAAATGCAACAAAGGCAACAAGTGCAACAACGATGTCCCTTAGGGATTGATGACTTATTTGCATAGATGGGCATACTGCTAGGGCATGAGTGGTATGTAGACCCAGCGGGGTGGGACCAAGTGTTGGATCCATGGCTCCAAATTTATGATGAGCACCGTCCACCCCGAGACCCTATAATGACATCAGTGTCGAGGGAAGACCCTGTCTTCCTATCAGCACATAGGGCAGATCCGTTCGTGCCCGTTCCCCTAGAGCCAGATCCAGAGTATAGGGAGCATCCAGAATGTTCGAGTTATCATACCCACGGTAATGGAGACCAAATTCATTCCATCCACATGATCTCCATTGATTTGACCGCACCCATCCGCAATCCGGCCGATCCAACATGGTCATTGCATCTAGACATAGATGCCATCGACTGGGATCACGTCAATTCACCTCTCTCACCATCAAAGTACTGGCCTTTCGATAAGATGCCTCATTTTACCCCAGGGACAACTCAGGATATTTTTTAGGCTGAAGAGGAACCCGAGGTTCCCAACATAGACTTAAATTCAGCTGGCTAGAAATCTTGGAATCAATTAGGAAAATGCAATCCCAGGATGCTCTAAAAATCCCATTTGGTCTTGGTCAAATCCTTGCCCGATGAGAGTGTTGTTGCACTTGACATCCCGGGC ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2502489 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00072125_INT#LTR/Gypsy AGTGGTATTAGAGCTATGTTCCTGTGTGCAAATATTTTTTTCTCTGGTTTATAATTTCCAACCGTAGTCAGCTTGCTCCAACGTATAGAAAATATGTTCTCCAAGAAGTCCCAACACAATCGTTTAGTATTTGTAAAGACTTTGAGCATTATTTGACGTTTATCTTCACATTAAGGTAGAATAGTTGGCAAAAGGTGATATTATGGTTCCGACGAATAAATTTCCTTGTTCAACATTCCTGCTCAAAAGTTCAGTGAATGTGTCTACGAGTTTCTCCTCACATGCATCAAAGTGATGCCAATAAAATTAATTAATTACTAAGGTTCATAAGTGAACATAAAAAAATCTTCGTTTATTTTGCATTCGAGCATATATTAACAACAACAATTTGTAAGGTTTATATAGATTTTTCATAGTGATTAAAATCCTATGATGAATCAAATCTAGCAAATAAAATTACCAGTTGATTTGAGTGACTGTTATGATGAAGAAAATTAGTGGTCGTAGCCCTAACAAAATAAAAAAGTATCTTCCAGATATGTAGGCGCTAGGTGTTCATTAAGTAATTAATTCAGAAATCATGTCCACTAATTGTTAGGACCCACAATTGAAGAGCAATAAAGCATCAGTATTAAAATTGTTATAAGAAAGAGAGAAGTCTGTGCAAGCAATAATTCTCATATGTTCATGATAAAGATATTAATTCATTCGAAAATTAATTTTGAAAAATCACCACCTTTTTGAATGATCTGACTCCAACCATGGAAGGTAGAATCCCTAACATTGCCATCCATTAATTTGGAGGTGATTCAGAGTAATTCAGTCTTAATCAACCACAAAACCCTAAATTTTCCATTCCCACCCACCAACCAAATCACGCGATTTAATTTATTAATGCATTGAGGCTAAGGTTTATTCATGATTTATTTGACTATTGATAAAATACAAGGATTTTTTTTAATTTCTTCATGCAGATATCCCACACAGGTTGTGTGGATAACACGAAGGGAAATATATACAATAAAGAATGCTATTTTAAAACATTTCTTAGCATGGTAGCTCTCCTCAAACCACGTGTCTTTGATCGACTTTTTTGATTAGCTTGCATCATTTACAATCCAATGTTGTCCTGTATTATCTTGTTCACATGTTGGTCTCTTTGTCTCTTGTTGTGTTAGTAGCCTCATAGGTAGTGCATCCATTGTTTAGTTCATTGGTAAAAGTGTGCATTTGCCTGTTGTGTCAGTAACCTCATAGGTAGCATGTTTATCATTTAGCCCATGTTAAAATCATTAACATTTGTTCATCTGCTAGTGCCCAAATAACCATCGTATATGGTCATCCACAAGTGCTAAGTAACCATTGTAAAGGTTCAAACAAATTCAAATTTCTAGATGTTGCAAAAAATAGTTGTTGGAGAAATAAATTCAAATTCTAAATTATAGTTATTACAGAAAATAGTCATTGGAGAAAGGAATTCTAATTCTAATTTCGTAGATGGAGCGACATATTGGTCAATAAACATTGACAATTTTTTTTTCTTCTACCAAAATTAAGAAAATTATCTTGTCCTATTGTTTGTAAAGCAAGTATAAAATTATCTTGGTTGTAAGGCAAGTGCATGAGAGACAGGTGGAATAGAGGACCAAACAAAATATTAAATAGTGCAAATAAACCAAATGAAGGGCCATTAAATTCACCAAGAAGACCTTTGTAAAATAAAGGTATGCAACATAATTCTCCTTTATGCATTAATAGTTTTAATCCCAATCACTCTATCCTTAACTTCATGGTTCCTTCCAACTCATCCCATGCAAATCTCAAACATGAGGAAGTAGTAATCCCTACTACATGCAACCAAGAATTACAAGAGTGCCTGTCTAAAATAACTACTAATATGAACAATATGTCAATAGTTCTTGGACAACTATTAAATAAATAAAACCTTAAACCTCCTTCGTCTCCAACTAATTCCTATAGACAAAATGATACTACGGATCAAGATTCTCCCATAAGTCACAATGATCCTAACTCAGATACAGGGGAAGCTACTCAATATTTAAAATGACCAATAGGTGTTAAAATCCTAATGTACGTCATTATCAATACCCTCAACCTCAAAAAGTAAAAATTGAAAATATTTTCTAAGAACTATTATAACATGGAGTCATTTGTCATAGCACTAGTCTTTATTCATCACTAGTGGTTTTGGCCCATCGTAAAGATAATTCTTGGCATATGTGTCCTGATTTTCATCCCCATAATTATGATAAAATTGCAGCTCCTCTCACCACCCTCACAAAAAAGGATGCCTTTCATTGGTCAAATGCTACCACTCAAGATTTCATGGCACTAAAAGAAGCTATGTGTACTACTCCGATTTTGGCAACTCCAAATTTTCACAAACCATTCGCTATCGAATGTGATGCTTTGGGTACAAGTATTGGGGTGGTATTAACAGGTGAAAATTTGGAAAGGTCCACATATGAGAAAGAAATGTTGGCTATCCTACATGCAGTCAAGAAATGAAGACATTACTTACTCAACAGTCGCTTCATCATAAAAATAGGTCATAGTAGTCTTAAGCACTTTATCGAACAACGTTTCTTCTATATAGAGCAAAATAAGTGGAAGACAAAGTTATTGGGATATGATTTCATCATTGCATATAAGAAGGACAAAGAGAATGTAGTAGTAGATTATTTATCCCATAAATATGAAGATGAAGTTTCCATCGTTCTCAATGGGTTGCTCAACTTCAAGAAGAATGGTTGGCGAACATCGAAACTGCTCAAATTATTCAAGATATGATTCTTGGATCATCAAAGCATCCTTATTTTTCATATATTGACAAGGTGTTACAAAATAAATATCACATTTACATTTTGTAAGGTTCCACTATTAAATAGATGATCCTTGAAGAATCACATGCTTCTCCATCAGTAGGACACTCAAGATTTTTGAAAACATATCAACGGGTGAAACAATCATTTTATTGGAAATGTTAAATCTGATGTCAAGACTTTTATGGCCGAATGTGAAGTATGTCATCATAATATAGGTGATACAATCAAATATCTAGGACTTCTTCAACCATTACCAATTCTTGACCGTTAGTGGGAACGCATACCAATGGATTTTATTGAAAGTCTATCCAAGTCTGAAGGAAAAATAGTGATTTTTGTAGCAATAGATCGTCTTTCTAAGCATGTTCACTTCAGTGCTTTACAACACCCATATTCAACAAGCAAAATGACCAAGGTATTTATGGAATCCATTTTCAAGTTACATGGAATGCCCAAAACTATTGTAAGTGATCGTGATCCCATATTTACTAGCAATTTTTGGAGATAATTATTCCATCTCAGTGATACCAAATTAAATATGTCTTCTACATACCATCCCCAAATTGATGGTTAAACTAAAATTATTAACAAATGCTTGGGTATCTATCTGCGCTACTTTGCTCAAAATAAGAAGTATCAATGGAGTCACTGGATTTCATTAGCAGAATGGTGGTATAACACTTCTTACCATTCTTTCCTCAAGATGTCCCCATTTGAAACATTGTATGGATTAAAACAACCAAAAATAATAAATTATGTTTCAGGATCTTCCAAAGTTGCTCAAGTAGATGATTGGTTCCAACATCGACAAAAAATGCTTAACATTATTAAAGATAATTTGATCCAGGCACAAAATCGTATAAAACAACAACATAACTCACACTGTTCAGAGTGTCAATTCTATATTGGAGATATGGTTTTCTTACGTCTACAACCTTACAAACAACTAACATTGAAGATCAAGACTAGTCAGAAGTTGGATCCAAGATTCAATGGTCCTTACAAGATAGTTCGTCGAGTAGGTGAAGTAGCATATCAACTAGAGGTTCCTCCCTCATCCCGTATACATCCATTTTTTTATGTTTCATGTCTCAAAAAGGTGATTGGTCAAAGAGTACACTCCCAATCAGAGCTTCTAGTACTTGATAAAGAAAGGACATAAATATTTAGCCAAAAGTAATATTGTAAAGTATATCACATAATATTCGATCTCACCACATTAAAGAATTTCTTATCAAATGGCATGACCTACCAGTAGAAGATGCTACATGGGAAACAAAAAGTATTTTTGAGTCATTTCGCATTTAAGGACAAAGCTTTTCGAGGAGGGGAGACA ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2505784 Segmentation fault bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00054691#DNA/DTM GTATTCCTCTAACATTAACACCAATGAAATATATTTATTTCTAGTATATTTCACCACCATTTAAATCAATATAATATTTATCCCTTTAACATTATCACCCACATCTCCATTTAAATCAAATTAACATATTCATTAGAGAAAAGGTATATGTAATCCTGAAAATGCCATAGTTATATCCACAAATACGTATCTTAGAAGACAAAAAAATCACTATAAAATAAAATACCAATCAAGAATTTTAGAAATTATTGTGTCCACCATAGTCCCTTCGACAAATGCAGTTAGTATGCTAAAAGGTGACTTAGTGCATTGTATGTCCAGACACACCTCTCTGCTAGCAAACCACTACAAATAAAATATGGCCCTCCTGACCATAGATGCATCATCCATAATTATAGGAAGAAATCCTTTTAAAGAAAACCTTAACACTATAATGACTAACAAAGAATCTACTCCACCTAATGAATATTAAATTGCCAATCTGCCTAAGAAGAACCAACATTGATACAAAGATAGGCAAATATTCAAAAGACACATACAGGTCAACCTCTTTGGAGACTAATTTAATAAAATTATAAATGCAACAAATTAAATACTTTTGAAAGAAAGGAAAATGTTTCAAGTTGAAAGGCAATGCCTTTACATCAGTAGCAATGCAACAATGCAATAAAGTATGAGCATACCAAAAAATAATGATGAAAGGATTCCAAATATTCAAATTATCATAGTTTCCAACAATAGTGCAAGTATAGGAACTGGCTACTAATGTTCATATGAGAGGAAGTGCCTCTCAAAAAGCATCAGGCTTATCAAAATACAATGTATTTTCTTAAATGTTTTCAAAGTGAGTAAAGAATATATTATTAAAAAATAAATGACTTGAGAAAAGGAAAAATCACCAAAATTTGAACTCCATGAACAAATAACAACTCAAAACAAGCAAAGCAATTAGCCCCAAAATCCTTTCAACATTAGTAATGCCAAAATACGTTATCAAAAATGTGTCTATTTTTATCCTTTTCCCAAAAATAATTGTTAAACAAGAAACAGAATCATGAAAAATTGAACTCCACACACATTTAACAACTTGAAATAGCCAACGTGATTAGCCCCAAAATACCTTAAAATAAAATAATATGTTCCTATGATGCAGATCTAAGGTTTGGGAATAGCAAGTCATCCATGATTATGGTGCTCTCTTGCACCTTGTGGGTCCAACCTCTTGAGAATTTTTGCAAGGTCACTGGCCATCCTCACACTCTATAAATGGTACTCTAAGCTGCATTTATAAAAATAATAATTTTCCATTAGTTTCAGCATTTCTATTATGTAGCTTGCTTGCTTTCTTCCCCCTTCTCGTCCTTCAAAATCACATCTGATTCTATACACCTAGTGTGATTTCACCGCTACCACCCAAGGTGAAATCACGGTCGGGCTATGAAATCATGTCTAGATCATACAAAGCGAAACCACTTATTTTAGTAGAAAACCACCCAAAAAGCATAAATGTTTTGAAAATTTTAGAAATGCTAGGATGGTTTTAGATCCTACCTCTACCCACTCTGCCTTTGTTTCTGTCTCACCCCTTGCAATCATCGAATGGTGCACCGGTAGCATAGTCTCCAATTTTTCCCTAAAACTCCTTTTTCCTCTTTTGTGTGGTAAAAATGAATTAGGGGTCCTTTTTTCACCTCTCTTATTTAAAAACACCCTAATTATTTGCATTTGGCATGTTTTGCATCATCCCTCCTCATTTTTTTTCCCATCTCACCTTCAAATCTACTATATAAGGAGGGTTTGAATTCATTTTCTAGAACACGATAATAAGTAATGATCACAACATATCACAATTATTATTGCAAAGTGTTTTTGTGTTCACAACTTGGTCTACATCCTTCTTCGTCTCCCACAAGAAATATAACTCTAAAGTGTGAAGTTTAATTTATTCTTTTCTACATTATAGTTGCTCGCTTTGGTAGATTTGTGTTGAAGCTCTAAGGAGAGATCAAATATTTTGGGAGGTCTCAACACTTCTGCTTATTTCCTCGCTCTCTACTAGGTAAATTAATTCTATTACATTCATATTTTAGTTCATTTCATCTAACATTTATTATTTTTAATTGATCTAATATGTTTCACCTTACTTTTGCAAAATCACACATGAATCTCTACATAGGCTATTTTTTGGATGTCTTCTATTTTTGTTGTAAACCTATATATGATTTAAGAGAAATAC sh: line 2: 2505794 Segmentation fault bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">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 qstart qend sstart send qlen slen"' 2> /dev/null ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 2507035 Segmentation fault bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00011177_LTR#LTR/unknown TGTTGGCAATTTTGGGTACCTTGGGTACATTGCCTTTGCTCAAGTGTTGATGTTGTCATTGATGTCAAGAAGCTTTTGAAGGAATTTGATTTGAGGTCAAAAGGATCTAAGTTCAAGGAAGGGTTTTTGTGAAAACCAAGGCAGATAAAATAAAAGGTTTTATTTAAAACCATGGACAACAGATTTGAAATGGGTTTTTCTTAAAACCCAAGTTGGCTCTTCGTTTCGTTGAAAAAGGTGCCCCGGTGATGAAGATATTTAATTTTAAATATTTAGTTTAAATTTTATTTATTTAAAATTTAAATTAAAATTTTAAATTAAATTAAAAGGGCCGACGTGTTTGGATATGCATCAAAGTGCATATAAAATAAGGCAATTAAATTCATTAAGTTTGAGGGATGGTGTTTCGACATTAAGCGCAATCAATTCGATTTCGGAAGGAGCAGAGAAGAGTGTTAAGCATTTCGTTCGATCAGCGAAGGAAGGGAATAAATAAAAGCGGCGGTGGAAGACTTTCCACGTGGGTGGCTAGCCCAACCGGTCGTGAGGCTAGCGCTAGAGCGTTGGTGGAAGGGAGATCTCGTGTTCGAATCTCGCGGATGCTTTTTGTAGAGCAAGATAAAGTGAAACACGTTTTCAACGGAGAGAAGGTATAAGATAAAGTGTGGGCAAGACTCTTTCCAAGCGGGTGGCTAGCCTAGCTGGTCGCTAGGCTAGCGCTAAGGCGTTGGCAGGAAGAGAGTCACGGGTTCAAACCTCGCGATCGCCGTTTTGCTAGATAGAAAGGACAAGTTGTTCGTGTGAGCACGTTTGCAAGCGGAGAAGGAATTTTTCCAAGGTATGAGGACTTAATTTTTATTAGAAAAAGTTAAAAGGTTATATGGTATAGGAGAAATAAGGAATTGTAAGGTTTTATTGGGTTATGATTTTTGAAGTCAAATATTGGAGTTATAAGGTGTAGAAAAGGAATATTATTTTGTAATATGTTGAATGTTAGGTTGAGGAATGGAGTAGATAAGGTGAATATAAGAAATATGTTATGTATGATTTGTTGAATGAGGTTGAAAGAAGAAGACATAGAACCTTGATTATATTTGGACCAAGGAATATTCTTGAGGAAATATTAAAGAAATATGTTGTCTACTAACCTTCTTGAGTTTGGCAAAAAGGTGGTTATGGTTATGACAAATTTGTGAGATCTTCTTCATCTTCAATAAGGTATGGGCACTTTCTTCTTATGAGTATGATTGGTGTATGTTTTCCTGAAATAAGATTGGAGTGAAAAGGTATTCAACTAGGTTTCCTTTGGTTGGGTGTAAATCCTATTTTCTGGTTTGTTGAAGACTACTTATGCATTGTTATCCTTGATGAGAGTTTTGGTGAATGCATAATTCTGGTTTGAGGTAGTGGAAGCATTGTGCACTAGGGTGTATGTTTGTAAGTCTTGCTACTTGCATTGAGATGGTGAAACCCTTAGTTGGTTGTTTTGATATTAATGGATGAGTTGCTTCCATAGAGGTTGTTTTGATCAAGTTAGTGCTTTACTTGATTCATGATATTGGGCTTACTCCATTGAGTTGATTTGAGCAAGTTATTCTTTGCATTTGGTGATATTGTGTTGGTGGTTGTTTTGTTCAAATATCTTTGGAGGGAAAAGGATTTCTACTTGTTTCCTTTTCTTGTGATGATTGGTTGAATGCTTCAAGGTTGATGTTGAGTTGAATGTTGTTGGTTAAACCTTGTCTATGAGCATTGTTGTTGAAGCCCTAATTGGTTGAGAAAAGATATTGGTTGTGGAAAGAACATGAGTAGCATTGTTATATGAGATATTGCATGGTTGGCAATTGTTGGGTTGTGTTTCATGTTCTTGAGAAAAGCATACTACATCTATCTTAGTCTTTTAAGATTTGAGATTGAGTTGAGATTGAGATTGGGAGTTAAGTATAGAACATATTGAGTCTCTAACAATTCTCTTTATGCTTCTATGAGGTTGATGAATCACATTGGGTCTCTAACCATTCTCTTTGTGGGTTCATGCCAAGCAAGTTTTTCTTGATGAACTTGTGAGCAGGTTTTGGATAGGTTCCGTTGGGGACTTGTGAGCAAATTTGGACAGGTCCTAGCAGAGGACTTGTGAAGCTGAGTTTGATAGTTCTATCAGAGAACTTGAGGACAGAGGTGCATTGGTTCTATGAGAAGAACCCGAGGACATTTGTGCTAGACCGAAGGACTATGTTTAGTGCAAATTCGAGGACCAACTTTGAGGTGATAGAGTTGAGGACAGAGGTCTCCAGCCAGAGCAGGGAAGACAAGTGTCTTCTGTGGATAGAGTTCCATTTTCTAAGGGCAGCGGAGGCAGAGGTCTTCTAGAGGATCACCAACGAGAGCAGAGGTAGGGGAAGGTATCTCCTTTGAGCAGAGGCTCATAAATTTATATTGGGGGAAGGTATCTCCTTTGAGCCGAGGCTCATAAACATTGTAATTGGGAAGGTTTCCCAAAGAACTTTGAGATAACTTTTAGAGAAAAGTTTTGTGGATGAACCACGTTAAAATTGGTGTCACTTTGTGGATGATCTTGTGCATTGTTTTGATATTGCTTTGGATATATTGCTTTATTGTTTTGAAGTATAAAAGAAAAGTAAAAAGAGGTCTTATACTGTTCACCCCCCCTCTCAGTATAAGCTTGTGTTCTTCA ") -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 qstart qend sstart send qlen slen"' 2> /dev/null sh: line 2: 3264476 Aborted bash -c 'timeout 188s /home/omendivi/.conda/envs/EDTA_1.9.9/bin/blastn -query <(echo -e ">TE_00050706_LTR#LTR/Gypsy TGTTGACAATTTTGTCACATTTCACAATGGGATTGAAAATTAAAACTTGTACAGTGTTCTTTGTTGTAAAGTATTTTTGGCGGTTGTTTTTTGGAAATATTTGTAAGAAGTTGATGAAACAGGCATTACCGAAAAAGAATACAAGGAAAGAAAAAGAGCTTTAGGCTCGAAGTTCCTCAAAATACTACTTCGGGTGAAAAGGTTGCGAAGCAGCATTGCCGAAACAGAAATTCTTGCAAGGCATAAAGAAGAGCTTCGCACCCGAAGCAGTTCTAGAAACTACTTCGGGCAAAAGTTCCACGAAGCAGAATCCAAGTAGCATTTCAAAAGAGCAGCCATGGACCAAATTAGCCAAGGCAAGAAAAACCACTTCGGGCCCGAAGCATTTCAAAAGGCAGCTTCGGGTGAGTTTTTTGCAAAACAGTTTTGTCGAAGGAAAAATGTCATTTCTACTTCACCGAAGTTCGTTGCGAAGCATCTGCTTCGGCCATCTTTCATGCAAAGTACTTTCACCCGAAGTAGTGACAGCCATAAAGAATGCAACATCTTTTGAAGGCAATTGCTTCGGCTAAAACCGTCCCGAACCTTAGTCTTGAAAGAGGATCGTAGCGAAGCATTTCTCCAAGGCATCAGCGAAGTAATTTTGTCAGCGAAGCGGCGAAGAATGAAGAGGCCCATTTTGCAAAGGAAATATGCTTCGACACTCATGCCCCCAAAGCAGTTTTGTGAAGCTCCATTTTGTGAAGTACAAATCAAGGAGTTATTGCTTTGGCACAAGTCCATTGTGAAGCAAATTTTCAAGAAAACATCTCGCAAGGCACTTCAAAGGCATGATTTCCAATTCGAATATTTTCTCGAGGCAATCAAGTGCCTCATAAATGCATTTTTACGTGCCTGGTAAGACTGCTGCCCTAGAAGGATAACCTAACAAGCATGGTAGTCACTCGAGCATCACACCCAAAAGTTGAGGACGTTCAAGTGGTCCATTAATGTGTATTTCCTTGGTTTACCCGGCCGCAGCTGTTAATTTTGGCAAAGTATATGAAAGCTTAGTCATGAGGACCGTAGAGGGCCAACTTCTCAGCTTCTGAGGATGTACTTTGCATTCTGTGTAATAATGATTCAGAGGGTCGGGTCCTCTATAAAAACCCAGGCATTGTAACGAAATAAGGGGGGAGGAACTATCTGCTAGAAAGCTATTGTAACTTGATGTCCTGCGATTAATACTAAAGAGATTTGGGCTCAATTTCTCTCTTTTATGCTGCCTTTTGTGCTTGATTATTTTGTCTTTCTTCATTTGTATACTGAGACTCTGAACTCTGAATCTGGTGTGCGATTGGGGATTGTTCCCTGAAACTCACCTGAAGGATACATAGGAGAGGAAAAATGTAATATTGGTTTTCTTTTATGCTGCCTGGTGGGTTGTGGTTTATGTTACATTCACTTGTCCTAATCATCTTTACTCTGAACCCTGAATTTCGATGAAAGGGAGAAGCAGAATCCCTGTGAGCTCACCCAGTAGATACATAGGAAGGTTAATGTTTTGTTTATTTCGTTTATTCTTGGTGTTCCTTGCTGCTATTCAAGTTTTCAGTTAGTGATCGTGCTTCCTGTTCTTTCCCACCTTAAATCATCGATCTCTCTTCCCTTACCCTTATTTATTTATTTCTCTAACCCTAACTCTTTTATCTCTTTCCTGCACCCTTATCTCAAAACACAAAAGTAGATTAGCATAGGAGTCGGCCTTTCTTCAGAGATTGGCATGAGGGGCATCTCTTCCCTTCGGCATTTCAATGTTGGTCCAGGTCTAGGGTGCATACATTTACCCAAAATCCTTTCCTAGGCAGATTTGATGACCAACA ") -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 qstart qend sstart send qlen slen"' 2> /dev/null
I don't think it's the length issue because it has reached the 8th iteration as suggested by the file name TElib.list.panTE.raw.iter8. Something might have changed in your environment or system. Please check further. - Shujun
@oliviamr can you elaborate on how you work around it? Others may benefit from your experience. Thanks! - Shujun
Hi Shujun,
Happy to! So I erased some of my logs and hence the delayed response. However, it gave me the chance to rerun some of the code and this, in particular, peaked my attention:
I ran pante.pl 3 independent times the log came out clean no issue like before and the ending results (number of TEs sequences) are these:
run 1: 61947 --> logs with error profile above run 2: 62094 --> logs with no errors run 3: 62182 --> logs with no errors
I understand there is a degree of stochastic error however, could you indicate any possible downstream filtering I could potentially do?
Thank you, Olivia
Hi Olivia,
Thanks for your update. This is quite a stochastic process and sometimes it will have warnings but I have not encountered this type of error by far. So probably your way to rerun it again is the best solution...
To check the quality of the annotation, you may use the --evaluation 1 to see the annotation consistency. The original paper has more descriptions and discussions. I recommend to manually prepare a SINE/LINE library of your species (by searching NCBI or other studies) and give it to EDTA. This way will significantly improve both SINE/LINE and other TEs. For downstream filter, you may filter out those single copy elements. Please check the wiki page for more info.
Best, Shujun
Hi Shujun,
Thank you so much for your comments and advice. I am going to overextend your kindness by asking if you know any good resources of SINES/LINES from Gymnosperms? If not happily would take any good resources of SINES/LINES from Angiosperms?
Thank you for your great patience, Olivia
Hi Olivia,
You may need to search around. There is a SNIE database that collects some sequences. NCBI is a also good place to look at. There is a nice annotation pipeline for SINEs recently published. Or a more generic google search.
Please share your efforts here or in your publications, so that others can benefit from them.
Best, Shujun