Error codeml_reader

[michoug]

Hi, When I try to run the codeml_read command on my samples. I got this error :

Output::load failed: invalid Codeml output file header in 'Codeml_Setup_Inferred_Genetree_Map_Gaps_metAl_compare_Prank/similarity_group_1974/similarity_group_1974/m3Discrtk3/Omega0/out', exiting; at /Library/Perl/5.18/CodemlWrapper/Job.pm line 775.

I attached the out file as an example Any ideas Thanks Greg

out.txt

[bede]

This may relate to a change in output file format associated with recent PAML versions. @aewebb80 perhaps you could you take a quick look?

Bede

[oconnmar]

The other important point is that the number of sequences this user has are below the lowest threshold for codeml to be accurate...

M

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On 22 Nov 2018, at 11:34, Bede Constantinides notifications@github.com wrote:

This may relate to a change in output file format associated with recent PAML versions. @aewebb80 perhaps you could you take a quick look?

Bede

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[aewebb80]

Sorry for the delay. Was on break for Thanksgiving.

Mary does raise a valid concern. The codeml_setup will by design not create the PAML directory (for the codeml analysis) and return the following error for this reason: 'Number of sequences (N) in 'myfile.aln' is below minimum number (7)".

That being said, @bede is likely right that the error is due to changes to PAML output. We use Tom's PAML reader, which would have been designed around v4.4d.

From my perspective there are three solutions: 1) Someone would need to update Tom's code - it's in perl, so I'm clueless unfortunately 2) We recreate the function in python 3) Restrict the analysis is specific version of PAML - Likely a reasonable temporary solution until we finish 1 or 2

Andrew