Error running pbrun fq2bam: No space left on device

Question

[Ritu]

I am running the pbrun fq2bam command from NVIDIA Parabricks on a 25 GB FASTQ file from the 1000 Genomes Project. Despite using the --low-memory and --memory-limit flags, the process is abruptly terminated with the error:

Process terminated with signal [SIGKILL: 9]. SIGKILL cannot be caught. A common reason for SIGKILL is running out of host memory.

However, a larger 48 GB FASTQ file from another dataset (e.g., NCBI) runs successfully using the same configuration.

What are the possible causes for this behavior? How would you debug and resolve the issue?

Answer 1

[DBScan]

Did you specify the temporary directory? If it's not specified, the directory points to you current directory where maybe a quota is in place. So I would try ‑‑tmp‑dir /scratch or something like this.

Answer 2

[Pierre Lindenbaum]

it's unrelated to memory

The No Space Left on Device error on a Linux system means that the partition you are trying to write data to or save files on lacks sufficient space for the operation.

[Ritu]

I know about this but why this is happening with 25 GB1000 genome project dataset not for 48 GB NCBI fastq dataset.