Comments (8)
I solve this by shuting down multiprocessing (--cpus "0"
) using the following command
postprocess_variants --cpus "0" --ref "/input/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta" --infile "/tmp/call_variants_output.tfrecord.gz" --outfile "/input/{OUTVCF.gz}"
But I still not sure what cuase Broken pipe lipe.
I also tried less core like --cpu "12"
still get BrokenPipeError: [Errno 32] Broken pipe
.
from deepvariant.
Is it possible for you to share /tmp/call_variants_output.tfrecord.gz
(you can send it to [email protected])? I would be very interested in trying to reproduce the issue myself. I have a theory as to what may be the root cause.
from deepvariant.
@lucasbrambrink Thank you for you response, I do kept those files but there are 16 of them, listed as below
call_variants_output-00000-of-00016.tfrecord.gz
call_variants_output-00001-of-00016.tfrecord.gz
call_variants_output-00002-of-00016.tfrecord.gz
call_variants_output-00003-of-00016.tfrecord.gz
call_variants_output-00004-of-00016.tfrecord.gz
call_variants_output-00005-of-00016.tfrecord.gz
call_variants_output-00006-of-00016.tfrecord.gz
call_variants_output-00007-of-00016.tfrecord.gz
call_variants_output-00008-of-00016.tfrecord.gz
call_variants_output-00009-of-00016.tfrecord.gz
call_variants_output-00010-of-00016.tfrecord.gz
call_variants_output-00011-of-00016.tfrecord.gz
call_variants_output-00012-of-00016.tfrecord.gz
call_variants_output-00013-of-00016.tfrecord.gz
call_variants_output-00014-of-00016.tfrecord.gz
call_variants_output-00015-of-00016.tfrecord.gz
each is about 200 MB due to the high coverage of the sequencing, do you want all of them?
from deepvariant.
Yes please, that would be great!
from deepvariant.
@lucasbrambrink The file you requested is sent to your email just now.
from deepvariant.
@LogCrab Thank you for providing the files. We've tried to reproduce this in various ways without success. Could you provide the specs of the machine you ran this on? Thank you for your patience!
from deepvariant.
@lucasbrambrink Sorry the the dealy. My machine is running Ubuntu 22.04. The cat /proc/version
output is
Linux version 6.2.0-35-generic (buildd@bos03-amd64-016) (x86_64-linux-gnu-gcc-11 (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0, GNU ld (GNU Binutils for Ubuntu) 2.38) #35~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Oct 6 10:23:26 UTC 2
In terms of hardware are dual Intel Platium 8352Y, dual RTX 3090 and 512 G of RAM and full HDD array.
Hope this can help.
from deepvariant.
Related Issues (20)
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from deepvariant.