Non-zero return code 127 from Needle
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4 months ago
Park • 0

I am struggling with running Needle. What did I do wrong?

from Bio.Emboss.Applications import NeedleCommandline
needle_cline = NeedleCommandline("/opt/anaconda3/envs/SmartBioCode/bin/needle", asequence="needle1.fasta", bsequence="needle2.fasta", gapopen=10.0, gapextend=1.0, outfile="needle.txt") print(needle_cline.outfile)
stdout, stderr = needle_cline() print(stdout + stderr)
ApplicationError: Non-zero return code 127 from '/opt/anaconda3/envs/SmartBioCode/bin/needle -outfile=needle.txt -asequence=needle1.fasta -bsequence=needle2.fasta -gapopen=10.0 -gapextend=1.0', message 'usage: dirname string [...]'
Emboss Needle Biopython • 316 views
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