Comments (3)
jebrosen
commented on August 11, 2024
Can you also report your kernel version / operating system distribution (uname -a)?
Signal 7 on linux is SIGBUS, which indicates a memory access error. It is unusual that it would happen from ProcessRepeats, which is a perl script.
Luckily ProcessRepeats is the last step, so nothing significant has been lost. I first suggest manually re-running that /opt/RepeatMasker/ProcessRepeats -lib consensi.fa.classified -gff -poly ... command again in case it was a spurious error.
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R-Huerlimann
commented on August 11, 2024
Kernel version: Linux version 4.15.0-88-generic (buildd@lgw01-amd64-036) (gcc version 7.4.0 (Ubuntu 7.4.0-1ubuntu1~18.04.1)) #88-Ubuntu SMP Tue Feb 11 20:11:34 UTC 2020
Manually re-running the ProcessRepeats step did the trick. I've run the whole pipeline three times, with some modified parameters, and error happened every time. I also used conda to install RepeatModeler that way, and reran RepeatMasker, and the same error occurs.
At least I have a workaround now! Thank you!
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jebrosen
commented on August 11, 2024
Come to think of it, I believe that error can also be caused by running out of memory. If you do further runs of RepeatModeler it would be a good idea to watch the memory usage and make sure you are safely under available memory / limits.
Closing for now, until there is enough information to reproduce or trace a cause.
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Related Issues (20)
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