Errors when using T-coffee to align 1.5 million DNA sequences

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Mann, Carla M

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Sep 20, 2022, 4:31:05 PMSep 20
to tco...@googlegroups.com, Ramanathan, Arvind
Hi,

We are trying to use T-coffee to align 1.5 million viral genome sequences, but keep getting fatal errors during our attempts, and hoping to get some assistance to get this running.

We are using the recursive process described in the manual. When attempting to use mbed/Clustalo, we get the message: "ERROR: UNSPECIFIED UNSPECIFIED." To get around this, we also tried using the Mafft options, but get the error message: "

ERROR: Could not produce/read parttree tree." 


Both Clustalo and Mafft are installed, and recognized when running "t_coffee" by itself to list available modules.


We also initially got the MAX_N_PID error that has been detailed in the GitHub issues, but with a combination of modifying the default value in the installation files and setting the environmental variables were able to get around this issue.

Do you know what we can do to fix this issue? 

Thanks,
Carla

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Carla M. Mann, Ph.D.
Data Science and Learning Division
Argonne National Laboratory

Cedric Notredame

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Sep 20, 2022, 5:12:01 PMSep 20
to tco...@googlegroups.com, Ramanathan, Arvind
Dear Arvin

T-Coffee is not really the right tool for this kind of tasks. What you want is more of an hmm aligner like Covid align. 

Cheers 

Cedric 

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Dr Cedric Notredame
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On 20 Sept 2022, at 22:31, 'Mann, Carla M' via Tcoffee <tco...@googlegroups.com> wrote:


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