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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
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UnboundLocalError: local variable 'seqid' referenced before assignment #46

Closed IRSINGH27 closed 2 years ago

IRSINGH27 commented 2 years ago

ISEScan starts at Tue Aug 23 17:43:29 2022 use NCBI protein database

command : isescan.py --seqfile GCF_013415905.1_ASM1341590v1_genomic.gbff --output result/ --no-FragGeneScan

Traceback (most recent call last):
  File "/home/aswin/irsingh/miniconda3/envs/isescanner/bin/isescan.py", line 87, in <module>
    isPredictSingle(args4isPredictSingle)
  File "/home/aswin/irsingh/miniconda3/envs/isescanner/bin/isescan.py", line 25, in isPredictSingle
    isPredict.isPredict(filelist, args['output'], args['removeShortIS'], args['translateGenome'],
  File "/home/aswin/irsingh/miniconda3/envs/isescanner/bin/isPredict.py", line 208, in isPredict
    proteome_files = proteinFromNCBI(dnaFiles, path_to_proteome)
  File "/home/aswin/irsingh/miniconda3/envs/isescanner/bin/isPredict.py", line 195, in proteinFromNCBI
    tools.gbk2fgs4protein(fnaFile, gbkFile, fgsFile)
  File "/home/aswin/irsingh/miniconda3/envs/isescanner/bin/tools.py", line 1450, in gbk2fgs4protein
    seqid = rdGbFna(fnaFile)
  File "/home/aswin/irsingh/miniconda3/envs/isescanner/bin/tools.py", line 1298, in rdGbFna
    return seqid
UnboundLocalError: local variable 'seqid' referenced before assignment
xiezhq commented 2 years ago

Hi,

ISEScan does not support using NCBI protein database. The option '--no-FragGeneScan' does not make much sense.

Xie