ran into erro

[Huanle]

Hi guylenard:
I ran into this error when running orthomcl_groups_analysis.pl.

'Retreiving: Family1 with 1215 sequences
Can't call method "seq" on an undefined value at ../orthomcl_tools/orthomcl_groups_analysis.pl line 204, <$_[...]> line 61419.'

I used this command:
perl ../orthomcl_tools/orthomcl_groups_analysis.pl -o dollopinput -g groups.txt -p compliantFasta/goodProteins.fasta -a Presence_Absense.grid.txt -c tally.grid -f compliantFasta/

Can you help me out of this?
Thanks a lot for your help and for developing this utility.

Kind Regards,
Huanlee

[guyleonard]

Try writing your command as:
perl ../orthomcl_tools/orthomcl_groups_analysis.pl -o dollopinput -g groups.txt -p compliantFasta/goodProteins.fasta -a -c -f compliantFasta/

Other than that, it's hard to tell what the problem might be without the data - at that point in the script it is trying to retrieve fasta seqs from your compliantFasta directory - so I wonder if you have either extra information in one of your files or a wrong number somewhere...?

The two to double check are the dollopinput and the groups.txt to make sure they are correct

[Huanle]

Hi guyleonard, Thanks for your suggestion.

After I ran
perl orthomcl_tools/orthomcl_groups_analysis.pl -o dollopinput -g groups.txt -p compliantFasta/goodProteins.fasta -a -c -f compliantFasta/

i got the same error.

Can't call method "seq" on an undefined value at orthomcl_tools/orthomcl_groups_analysis.pl line 204, <$fh> line 1181.

....