command terminated by signal 9

[csuzhang]

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.

[TimD1]

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.

[csuzhang]

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

[TimD1]

PR #36 added in a --max-supercluster-size option, which should fix this issue.