Stopped at Hmmalign step about big-scape HOT 6 CLOSED

Hello!

I have two questions to diagnose the issues further:

• Could you tell us how long it takes until the job dies?
• How much memory is available on the machine?

It is difficult to say what the issue could be. My intuition is that the hmmalign program crashes after a while, but I am not sure what the reason for that could be.

from big-scape.

Since it stops at the hmm align step, I wonder if it could be that there are ambiguous residues in any of your dataset's sequences (e.g. 'X' characters)?

from big-scape.

Thank you !

• Yes, I am incline to a "time out" situation, since it will crash after many hours , around 4-5 hours after . However I have no ideia how I can solve it.
• I have currently 8 GB RAM allocated for this.
• Also yes, I probably have some "X" characters but in previous(smaller) runs, it always displays some message saying that, but it continues anyways, so I'm not quite sure if this is the issue.

from big-scape.

This is strange. I don't think the ram should be the issue, and the unknown characters case should indeed be handled.

Is it possible that you add a print statement to the code to see which file it crashes on?

from big-scape.

This issue has not seen activity for 14 days and has been marked as stale. Please comment with additional information if this issue is still relevant.

from big-scape.

This issue has been stale for 14 days and has been closed. Please feel free to re-open this issue if necessary.

from big-scape.