Ben

I'm also having this error, attempting to install on a linux box: Linux version 4.19.0-041900-generic (kernel@tangerine) (gcc version 8.2.0 (Ubuntu 8.2.0-7ubuntu1))

Ditto. I'm not familiar with the codebase for bpipe (yet) but if I can help with testing or anything, I'm happy to help.

'pologies for the delay. so my bpipe.config is currently: ``` executor="slurm" queue="bigmem" //walltime="04:00:00" //custom_submit_options="your option here" account="uoa02461" //procs=8 //memory=15 TMP="tmp" modules="BEDTools FastQC cutadapt SAMtools picard BWA" commands { trim {...

Been doing some digging. Not sure how useful it will be. bpipe-slurm.sh, is, I think, only receiving some values into the OPTIONAL_ENV_VARS. I can specify the variables in the named...

That's definitely part of it. I definitely didn't have that. I've added that in, so in my pipeline file I have: ``` trim = { output.dir="data/intermediateFiles" multi "cutadapt -a AGATCGGAAGAGC...

Nope, the new incorrect files are very definitely newly generated. Almost as if it's treating the extra tag in the pipeline file as a 3rd instruction for which a slurm...

Looking closer, yeah, it's definitely generating a 3rd slurm job. I've been looking through the jobs with sacct after running the pipeline, I get something like this:``` 1730112 trim 00:00:02...

So. Here's a thing. It might have something to do with multi. I split my multi command into two exec commands, and added the "trim" tag on to the end...

To clarify, when I specify file extensions, it still doesn't work, but slightly differently. Enforcing *.gz extensions in the input for the trim stage, and *.fastq in the output, and...

It does indeed, sound similar. This is on a node running CentOS Linux 7, Kernel is Linux 3.10.0-693.2.2.el7.x86_64, using a bash shell.