naming of jobmanager templates, `*.template` versus `*.template.example`

[jbloom]

When I try running cellranger version 2.1.0, I get the following error:

ls: cannot access /fh/fast/bloom_j/software/cellranger/martian-cs/2.3.0/jobmanagers/*.template: No such file or directory

The problem appears to be that the relevant files are named *.template.example, not *.template.

For instance, ls martian-cs/2.3.0/jobmanagers/ yields:

config.json              retry.json            slurm.template.example
lsf.template.example     sge_queue.py          torque.template.example
pbspro.template.example  sge.template.example

[wflynny]

Not a developer, but where in the run do you encounter this problem?

Looks like the only place that check arises is during sitecheck, and stderr should be piped to /dev/null during the check. What do the last two entries in the _sitecheck file for that job look like?

[adam-azarchs]

What is the command line you are using to run? Are you setting --jobmode? If so, you need to have the corresponding template configured.

[jbloom]

Here is an example. It appears that the problem does only exist during the sitecheck.

The problem exists with version 2.1.0, but not version 2.0.0:

This works:

jbloom@rhino3:/fh/fast/bloom_j/software$ cellranger mkfastq --version && cellranger sitecheck > sitecheck.txt
cellranger mkfastq (2.0.0)
Copyright (c) 2017 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------

But this does not:

jbloom@rhino3:/fh/fast/bloom_j/software$ ./cellranger-2.1.0/cellranger mkfastq --version && ./cellranger-2.1.0/cellranger sitecheck > sitecheck.txt
/fh/fast/bloom_j/software/cellranger-2.1.0/cellranger-cs/2.1.0/bin
cellranger mkfastq (2.1.0)
Copyright (c) 2017 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------

ls: cannot access /fh/fast/bloom_j/software/cellranger-2.1.0/martian-cs/2.3.0/jobmanagers/*.template: No such file or directory

[adam-azarchs]

I can't reproduce this on a fresh install, and that error should be getting suppressed and ignored. So something weird is going on here. Was this actually stopping progress or just a warning message?

I'd theorize that there might be something unusual about your .bashrc which would alter the behavior. If you could share the output of shopt and alias that might clarify things.

This information would be helpful to make a more permanent fix, but as a temporary workaround if this is blocking your work, you can comment out that part of the sitecheck (https://github.com/10XGenomics/cellranger/blob/master/tenkit/bin/sitecheck#L82). If you have further problems you should contact support@10xgenomics.com.

[jbloom]

It's just a warning, not an error it turns out. So maybe not worth worrying about...