ClustalW using Biopython

0

I want to make a clustalw alignment using biopython on a fasta file that have many reads converted from fastq format to fasta format (the reads have different lengths). when I run clustalw on this file I got this error:

Traceback (most recent call last):
  File "F:CIT656pythonProjectsCIT656_Spring21Project_Script.py", line 33, in <module>
    stdout, stderr = clustalw_cline()
  File "F:CIT656pythonProjectsCIT656_Spring21venvlibsite-packagesBioApplication__init__.py", line 574, in __call__
    raise ApplicationError(return_code, str(self), stdout_str, stderr_str)
Bio.Application.ApplicationError: Non-zero return code 1 from '"C:/Program Files (x86)/ClustalW2/Clustalw2.exe" -infile="E:\Courses\Bioinformatics Diploma\Programming to bioinformatics\Project\CIT656-project\Balkans\Balkans_reads_extracts\merged_raeds\merged_fasta_file\merged_reads.fasta"', message 'There was an exception in the PearsonFileParser::getSeqRange function.'


clustalw


biopython


fasta


fastq

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