Hey all, I'm new to nextflow coming from Snakemake and trying to get a feel for how nf-core pipelines are implemented. I'm trying to run the smrnaseq pipeline with the following command on a compute node on my institutions hpc

nextflow run nf-core/smrnaseq -profile singularity -params-file params.yaml

I keep receiving a java virtual memory error:

OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x0000144bee000000, 811211948032, 0) failed; error='Not enough space' (errno=12)
  OpenJDK 64-Bit Server VM warning: INFO: os::commit_memory(0x000013a4d8000000, 811211948032, 0) failed; error='Not enough space' (errno=12)

However, in my bashrc file I have added this line and sourced:

NXF_OPTS='-Xms1g -Xmx4g'

I'm not really sure how to get around this and am getting a little lost in all the various logs. I've attached my most recent workflow log.

The log file does not show the Java errors you report, there are a couple of processes failing with exit code

134

, which is in my experience related to Java processes without enough memory, though. In addition you have a crash during the bowtie index creation. That one has several warnings about the sequences (only gaps or empty), so I would make sure you are using suitable reference sequences. I have a hunch that the root of your issues (at the Java ones) are with (lack of proper) configuration. I'll comment more on that at your questions in #CL66GAJBF.