questions about results from orthomcl_groups_analysis.pl

[wsuplantpathology]

Hi @guyleonard

Thanks for your nice tools. I have some questions about the results from orthomcl_groups_analysis.pl. Now I attached the first 10 lines from my groups.txt, and from count_list.csv and presence_absense_grid.csv. Please check them out.

Basically my first question is: totally I have 16 taxa which are listed in the header of count_list.csv, my understanding is, count_list.csv contains how many proteins are presented in each group for each taxa, so there should be 16 columns for each group. However, I found there more than 16 columns for many groups in count_list.csv. For example, for first group, there are 21 numbers, instead of 16. Is there something wrong?

My second question is: during orthomcl_groups_analysis.pl runing, I got error message like this:

Use of uninitialized value $accession in hash element at /data/chen/software/orthomcl_tools-1.0/orthomcl_groups_analysis.pl line 155, <$_[...]> line 36816.
Use of uninitialized value $accession in hash element at /data/chen/software/orthomcl_tools-1.0/orthomcl_groups_analysis.pl line 155, <$_[...]> line 36817.
Use of uninitialized value $accession in hash element at /data/chen/software/orthomcl_tools-1.0/orthomcl_groups_analysis.pl line 155, <$_[...]> line 36818.
Use of uninitialized value $accession in hash element at /data/chen/software/orthomcl_tools-1.0/orthomcl_groups_analysis.pl line 155, <$_[...]> line 36819.
Use of uninitialized value $accession in hash element at /data/chen/software/orthomcl_tools-1.0/orthomcl_groups_analysis.pl line 155, <$_[...]> line 36820.
Use of uninitialized value $accession in hash element at /data/chen/software/orthomcl_tools-1.0/orthomcl_groups_analysis.pl line 155, <$_[...]> line 36821.
Use of uninitialized value $accession in hash element at /data/chen/software/orthomcl_tools-1.0/orthomcl_groups_analysis.pl line 155, <$_[...]> line 36822.

There are lots of this message. What happened, is there something wrong? Thanks.

Best regards,
Chongjing Xia
groups_head.txt

count_list_head.txt
presence_absense_grid_head.txt