findPPG_parsealn.py

[leyanKk]

The command used is python findPPG_parsealn.py -o PPGFparse -t32 gene.12bed ref.fna aln_SV.paf The error message is I pulled out the line that ran the error and found it was the same as the other lines. SV1995 2281 89 2143 + gene-Dlg2|protein_coding|Dlg28 701329 380171 632540 219 2076 0 NM:i:1857 ms:i:124 AS:i:18 nn:i:0 ts:A:- tp:A:S cm:i:17 s1:i:73 de:f:0.1275 rl:i:160 cg:Z:7M1807I20442N3M1D9M2I16M2D5M3I9M231666N6M5D5M1I11M1I11M1D29M11D1M2D60M1I67M cs:Z::7+gggggggggggggggggggggggggggggggattaaatccaggcccttgtgaatgctgggcaaccactctctctccgaaccaccgaaccatacccatagctcagtttttaaaattcatttctaatatgtcttagagcttcgtgaatcaggaccttgcaaacttccctcatcttcacacagcctgatgcttgccttccaagctgcccactaggggtcatgtctggggattaggagcctttctggttttcctgaggctggctcagtcagagacaatgggacagcctacgatgggacagcctggagaacacacacaggccctgcttgtctgccagaggccagggttcctcaccaatgatgtccccactgtctgcttcagcctgtggaggctctaacgattgttcttctgccactaccccaccaagacagcattgcctctcagtctaggaagcaacagtggacagtcctggacacactgttagtttctccctggagcccaccccattgcccgagatacaatttcacataagaaactcatttctttccgtgcagtatgaaggcagacaagttagcagaatggtctctactgtcttcctgattgtgcgtttgtggttagaactcgggctttgtacaatggagagggaagcctgtcctctgttctagaaagacaagtatttgctcaggagtcagcgtgtgtgaaactgcatagtggaatgggcagctggtggttggctcttttcccgttttgtttttattttatataaatgggtgttttgcctccatgtatgtctgtgccccatgtgtgtgcagtccttagggtgaccagaaaggggcatcaggtttcttggaactggagtcactgtgagctaccgtgtgggtgctgggaaccaaactttggtgctttacaggagaatctggggctcacaaccgctcatccccctctccggcctgtggggtcagcttctgctcatccctccggcctctggagccagctgttgttcatctctccagcctgtggagtcgacttttgcatctctccggcctgtgaggtggactttggctatgtttctttcattctcctctttcccccacctcaaatgtatcagaaagtctgggaaggtgtaccgaccgtcctgagatgctgcaggcacggtgacccactggcagttctgagatgtctgaagagtgggtacacatatctcctggaagtgaggtataatgaggacccttcatgtttcaaaggttcctaaggaaacgtggcagacattaacatccccagggaatcaagttcctgtacagatgtgccgggatttgaggtgctccctccaaagttcttacactaatcccactaagggatgttgagctgggcagtgttagtctcaggaggtctctgtctgcatgagtggactgggtgccctgggaagggccagaggggctggagttggtccattttgcacttttcctgtctgtcacatgagaacccaggatttcttccccctgaaaggcactatcctggaagcagaaatgagctcagtccaaacactgaagaaccatcgggctgatcttctacttttgccttccagagctatgagaaatgaatttctgctgattgtaaattgcctgctcttgggtatcttgttacagcacacagcctgtgatagatcttcttaaagacatagaacatcagctgaaaactcagtgggacccttccacagccacgtggcagtgagcaggggtgtgcctctctgcccatcccacaccaggagagcagaaatcaagctcgacctctctgatcccacagtgggaccag~gg20442ac:3-a:3*ta*ga:1*gc:2+tc:16-aa:2*at:2+aat:4*ta:4~at231666ac:3*ta:2-aaaaa:5+a:11+a:11-a:6*ac:1*ga:6*tg:6*ag:6-tgcctgcaggc:1-ag:1*at*gt*at:1*gt:2*cg:37*ag:2*tc:10+t:52*ga:6*ct:3*gt:3 I hope you can help me see what the problem is

Thank you

[xfengnefx]

Is gene-Rere|protein_coding|Rere in the gene.12bed file? And what were the commands that you used before this step?