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2.3 years ago
1012254696
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Dear all ! I've successfully run the KisSplice2RefTranscriptome workflow according to the documentation, I got 30 reads.fq and finish Transdecoder with a reference fasta file (Using Pacbio Seq to sequence and create）like this :
>Gene.103793
ATGTGTGACGACGAGGAAAGCACTGCCCTTGTGTGTGACAATGGATCAGGACTGTGTAAG
GCAGGCTTCGCCGGGGATGATGCTCCCAGAGCGGTGTTCCCCTCCATAGTGGGTCGTCCC
AGACACCAGGGAGTGATGGTGGGAATGGGGCAGAAAGATAGTTATGTTGGCGATGAGGCG
CAAAGCAAAAGGGGAATCCTGACCCTCAAGTACCCTATCGAGCACGGCATCATCACAAAC
TGGGACGACATGGAAAAAATCTGGCATCACTCTTTCTACAATGAGCTCCGTGTGGCTCCA
GAGGAGCACCCCACTCTGCTGACAGAAGCCCCTCTCAATCCCAAAGCCAACAGGGAAAAG
ATGACCCAGATCATGTTTGAGACCTTCAATGTTCCAGCCATGTATGTAGCTATCCAAGCG
GTGCTGTCCCTGTATGCTTCTGGACGTACAACAGGCATTGTCCTCGACTCTGGTGATGGT
GTCACCCACAACGTGCCCATTTATGAGGGCTACGCTCTTCCGCATGCCATTATGCGTTTG
GACTTGGCCGGCCGTGATCTCACTGACTACCTCATGAAGATCCTAACTGAACGAGGCTAC
TCATTCGTCACCACTGCTGAAAGAGAAATTGTCCGAGACATCAAAGAGAAGTTGTGCTAT
GTGGCGCTGGATTTTGAGAATGAGATGGCCACTGCAGCCTCTTCCTCCTCCCTGGAGAAG
AGCTATGAGCTTCCCGATGGACAGGTCATCACCATTGGCAATGAGAGGTTCCGCTGCCCT
GAGACACTCTTCCAGCCATCCTTCATTGGAATGGAATCTGCTGGCATCCATGAAACCACT
TACAACAGCATCATGAAATGCGACATTGATATCCGTAAGGACCTGTATGCCAACAACGTG
TTGTCTGGTGGTACCACCATGTACCCTGGCATTGCAGACAGGATGCAGAAGGAGATCACT
GCTTTGGCCCCCAGCACCATGAAGATCAAGATCATCGCCCCACCTGAGCGCAAGTACTCA
GTATGGATTGGCGGCTCCATCCTGGCCTCCCTCTCCACCTTCCAGCAGATGTGGATAAGC
AAGCAGGAGTATGACGAGGCCGGGCCATCCATTGTGCATCGCAAGTGCTTCTAA
the error occur in this step:
python3 kissplice2reftranscriptome -b NJLFY.transdecoder.cds.fa.bed -k results_coherents_type_2.fa -t type_coherent_2.psl
the problem is:
Opening all files and formatting tables...
Collecting data...
Traceback (most recent call last):
File "kissplice2reftranscriptome", line 577, in <module>
main()
File "kissplice2reftranscriptome", line 443, in main
blatbd.lowerPath, kSize)
File "/home/xuweitong/software/kisSplice/kissplice2reftranscriptome-1.3.3/kissplice2reftranscriptomelib/dataAnalysis/snpPositionFinder.py", line 54, in getMultipleSnpPositionInBubbleWithBlat
if upperRowNucleotide[i] != lowerRowNucleotide[i]:
IndexError: string index out of range
the file results_coherents_type_2.fa is :
>bcc_92143|Cycle_0|Type_2|upper_path_length_91|C1_0|C2_0|C3_0|C4_0|C5_0|C6_0|C7_0|C8_0|C9_2|C10_0|C11_0|C12_0|C13_0|C14_0|C15_0|C16_0|C17_0|C18_0|C19_0|C20_0|C21_0|C22_0|C23_0|C24_0|C25_0|C26_0|C27_0|C28_0|C29_0|C30_0|rank_1.00000
AACTGTATTTTGAAATTCAGAAATAGACAACTTATCACTTGTACAAACTAATCACTTGCACAAACTTATCACTTGTACAAACTTATCACTT
>bcc_92143|Cycle_0|Type_2|lower_path_length_74|C1_1|C2_1|C3_0|C4_0|C5_1|C6_0|C7_0|C8_0|C9_0|C10_0|C11_0|C12_0|C13_0|C14_0|C15_0|C16_0|C17_0|C18_0|C19_0|C20_0|C21_0|C22_0|C23_3|C24_3|C25_0|C26_0|C27_0|C28_0|C29_0|C30_0|rank_1.00000
AACTGTATTTTGAAATTCAGAAATAGACAACTTATCACTTGCACAAACTTATCACTTGTACAAACTTATCACTT
and the file type_coherent_2.psl is :
psLayout version 3
match mis- rep. N's Q gap Q gap T gap T gap strand Q Q Q Q T T T T block blockSizes qStarts tStarts
match match count bases count bases name size start end name size start end count
---------------------------------------------------------------------------------------------------------------------------------------------------------------
34 0 0 0 0 0 1 30 + bcc_75492|Cycle_50|Type_2|upper_path_length_86|C1_0|C2_0|C3_0|C4_0|C5_0|C6_0|C7_0|C8_0|C9_0|C10_0|C11_0|C12_0|C13_0|C14_0|C15_0|C16_0|C17_0|C18_0|C19_0|C20_0|C21_0|C22_0|C23_0|C24_0|C25_4|C26_0|C27_0|C28_0|C29_0|C30_0|rank_1.00000 86 52 86 Gene.94817 1809 1429 1493 2 17,17, 52,69, 1429,1476,
39 0 0 0 0 0 2 71 + bcc_75492|Cycle_50|Type_2|upper_path_length_86|C1_0|C2_0|C3_0|C4_0|C5_0|C6_0|C7_0|C8_0|C9_0|C10_0|C11_0|C12_0|C13_0|C14_0|C15_0|C16_0|C17_0|C18_0|C19_0|C20_0|C21_0|C22_0|C23_0|C24_0|C25_4|C26_0|C27_0|C28_0|C29_0|C30_0|rank_1.00000 86 35 74 Gene.80066 1245 1085 1195 3 13,12,14, 35,48,60, 1085,1113,1181,
Appreciate for any info! Thanks in advance!
