Received signal: 11 while running fq2bam on the sample dataset

Healthcare & Life Sciences Parabricks
1

I have installed Parabricks using Docker with a trial license. When running fq2bam as described in the manual (https://docs.nvidia.com/clara/parabricks/v3.2/text/getting_started.html) to test the installation the program aborts with an error reading “Received signal: 11” while in GPU-BWA mem, Sorting Phase-I, version 3.6.1-1.ampere.

When trying to reproduce the error, I sometimes get “Received signal: 7” or “Received signal: 6” with the additional error message
PARABRICKS: /dnabricks//sortcommon/inc/compressfile.h:283: size_t LoopReader::LRread(int, char*, size_t): Assertion `size < 32 * BLOCK_BYTES' failed.

Is there anything I can do to fix this?

2

Hey @mnutsua,

Thank you for trying out the Parabricks software. Can you send the exact command you used and the full terminal output?

I would also recommend using the latest version of the documentation, which can be found here: https://docs.nvidia.com/clara/parabricks/3.7.0/index.html