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mptrsen / Orthograph

Orthology prediction using a graph-based, reciprocal approach with profile hidden Markov models
GNU General Public License v3.0
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Slow orthograph-analyzer #34

Closed KristinaGagalova closed 4 years ago

KristinaGagalova commented 4 years ago

Hi, I am using orthoDB plants to group my own sequences in orthogroups. I managed to do all the steps but now orthograph-analyzer is taking a while. Attched the log file for the alignments Do you maybe have any sugestion on how to speed it up? Thank you in advance alignment.zip

mptrsen commented 4 years ago

How long is "a while"? Generally, with a new ortholog set, the first orthograph-analyzer run will take loooong because it needs to create alignments and HMMs. Once these are done, subsequent analyzer runs can use those and will be much faster.

You could give Orthograph more threads with --num-threads (can also be set in the config). This will also be passed on to MAFFT and HMMER.

What alignment program are you using? It looks like there are so many sequences that the alignment takes ages.

mptrsen commented 4 years ago

Closed, could not reproduce