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