Comments (6)
Hi Matteo,
I've looked into the issue with Ghost processes and this should be fixed in the next update.
All the best,
Michael
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What was the input problem, and were you able to fix it?
Nothing script-related, I didn't index the FASTA files. I was more concerned with finding 28 ghost processes with top
after 30 minutes that it had crashed!
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What was the input problem, and were you able to fix it?
I circumscribed the problem: I have a GTF file where cds sequences are not all multiple of 3, one where some coordinates are duplicated, and one where some of the coordinates are not found in the FASTA file. The multiple of 3 seems to be the last warning arising, so probably the reason why it gets stuck.
This time I didn't have any time
output so the process is still ongoing. However, none of the 20 cores is using cpu or ram, they seem idle!
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Follow up on this topic:
If the tests on the consistency of the files are passed, the program continues normally and (if crashing) there will be no ghost processes later on.
If the tests are not passed, then the threads stay up as ghosts without doing anything. Maybe the .join() function is not invoked yet?
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Related Issues (12)
- Dependencies HOT 2
- Augustus config path obtained from wrong variable HOT 1
- Sequences not multiple of 3: poor stderr information HOT 1
- proposedGenes file not found HOT 5
- Several issues HOT 5
- Error in gff_to_gtf_safe.py HOT 2
- Version of Orthofinder? HOT 1
- IMPORTANT DEPENDENCY VERSION INFORMATION HOT 1
- $genome not recognized in reference tdv file HOT 4
- orthofiller's hmmer commands raise a makehmmerdb bug that may lead to memory reallocation errors HOT 1
- Error opening HMM files for writing HOT 2
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