Hello,

I am trying to run this command line in the terminal from Mac OS, which is copied from a protocol:

FEELnc_codpot.pl –i <unannotated_transcript.fa> -a <mRNA_sequence.fa> -g <reference_genome.fa> -m ’shuffle’ –o <unannotated_transcript>

However, I get the following error: command not found, probably because I am not using perl, so I entered:

perl FEELnc_codpot.pl 

which gives me the following error:

Can't locate Bio/SeqIO.pm in @INC (you may need to install the Bio::SeqIO module) (@INC contains: /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/site_perl/5.26.2 /opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/5.26.2 .) at FEELnc_codpot.pl line 14.

So I copied seqio.pm from the bioperl directory which I had downloaded and placed it in /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level directory.
However, this does not resolve the error.
When I tried to run this command:

perl seqio.pm

I get this message:

Can't locate Bio/Factory/FTLocationFactory.pm in @INC (you may need to install the Bio::Factory::FTLocationFactory module) (@INC contains: /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/site_perl/5.26.2 /opt/anaconda3/lib/5.26.2/darwin-thread-multi-2level /opt/anaconda3/lib/5.26.2 .) at seqio.pm line 339. BEGIN failed--compilation aborted at seqio.pm line 339.

So I copied FTLocationFactory.pm into /opt/anaconda3/lib/site_perl/5.26.2/darwin-thread-multi-2level.

Again this did not resolve the error. But gives the message that I also need Simple.pm in @INC. Which I copied into the correct directory (darwin-thread-multi-2level)

However, again this is not sufficient.

Does anyone know how to get FEELnc_codpot.pl working and resolve this error?



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