Error while running CPC2

Question

[Princy]

Hello, I am trying to run CPC2 after finding ORF from the Trinity fasta file. But this is giving me an error. I have searched but did not find anything. Pl, let me know how I can solve this?

head ORF.fasta
>lcl|ORF1_TRINITY_DN74697_c0_g1_i1:93:185 unnamed protein product
MEFLNRNCESDPRCCIRSVDAAIDAPLKRS
>lcl|ORF2_TRINITY_DN74697_c0_g1_i1:330:434 unnamed protein product
MWECGCPWADSLIVTTGHTVPNTAGELRGCGLGA
>lcl|ORF3_TRINITY_DN74697_c0_g1_i1:513:620 unnamed protein product
MKRMRSMQHMTSSQNLTKSVLKTAKMQNGRKLLGG
>lcl|ORF4_TRINITY_DN74697_c0_g1_i1:1140:1286 unnamed protein product
MHSFACLLLYYSRGSLKFPFLLDSYSFCLVLMEKPNSTMRSVAPWPQL
>lcl|ORF5_TRINITY_DN74697_c0_g1_i1:1479:1559 unnamed protein product

Error - 
    [INFO] read file 'ORF.fasta'
    Traceback (most recent call last):
      File "/opt/software/applications/CPC2-tool/bin/CPC2.py", line 315, in <module>
        sys.exit(__main())
      File "/opt/software/applications/CPC2-tool/bin/CPC2.py", line 38, in __main
        if calculate_potential(options.fasta,strand,options.outfile):
      File "/opt/software/applications/CPC2-tool/bin/CPC2.py", line 261, in calculate_potential
        seqprot = mRNA_translate(seqCDS)
      File "/opt/software/applications/CPC2-tool/bin/CPC2.py", line 236, in mRNA_translate
        return Seq(mRNA).translate()
      File "/usr/lib64/python2.7/site-packages/Bio/Seq.py", line 1194, in translate
        cds, gap=gap)
      File "/usr/lib64/python2.7/site-packages/Bio/Seq.py", line 2744, in _translate_str
        "Codon '{0}' is invalid".format(codon))
    Bio.Data.CodonTable.TranslationError: Codon 'GQR' is invalid

Answer 1

[Mensur Dlakic]

Bio.Data.CodonTable.TranslationError: Codon 'GQR' is invalid

You are steadfast in your refusal to read error messages, even though they are as clear as day. I have no idea what CPC2 does, but that error message is clear: the program is expecting codons to translate - meaning DNA/RNA sequence - but it is getting amino acids.

Maybe try the website directly:

http://cpc2.gao-lab.org/

Please read error messages line by line as the answer is usually there.