vcfdist
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TimD1
command terminated by signal 9
I use vcfdist to evaluate a phased assembly of HG002. The variants are called by dipcall. The command terminted by signal 9. Vcfdist was ran on a server with 1.5Tb RAM using default command where bed file is generated by dipcall.
Since the command terminated with signal 9, it most likely ran out of RAM. Limiting the maximum variant size with -l 1000 should do the trick.
Are you sure that there is 1.5TB of RAM, and not 1.5TB of disk space? If you're running Linux, what does the command lshw -c memory show?
Can you please provide the exact command you used to run vcfdist? The inputs (including the BED file) would be helpful for me to reproduce the error.
I'm sure that the memory is 1.5TB. Here is the output of the command lshw -c memory
WARNING: you should run this program as super-user.
*-memory
description: System memory
physical id: 0
size: 1534GiB
*-memory UNCLAIMED
description: Memory controller
product: Lewisburg PMC
vendor: Intel Corporation
physical id: 1f.2
bus info: pci@0000:00:1f.2
version: 09
width: 32 bits
clock: 33MHz (30.3ns)
capabilities: bus_master
configuration: latency=0
resources: memory:92210000-92213fff
WARNING: output may be incomplete or inaccurate, you should run this program as super-user.
The vcfdist command is vcfdist hg002.dip.vcf.gz GRCh38_HG2-T2TQ100-V1.0.vcf.gz GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -b hg002.dip.bed -p hg002 -t 80 -v 0. Here is the input hg002.dip.vcf.gz, hg002.dip.bed.gz and GRCh38_HG2-T2TQ100-V1.0.vcf.gz can be downloaded from here
PR #36 added in a --max-supercluster-size option, which should fix this issue.