failed to create hard link ‘pbmc10k_data.SCANPY.hvg_scaled_output.h5ad’ => ‘tmp’: Operation not permitted

[vagabond12]

centos7.7
nextflow version 20.10.0.5430
vsn-pipelines Version 0.25.0

nextflow -C pbmc10k.vsn-pipelines.complete.config
run vib-singlecell-nf/vsn-pipelines
-entry single_sample
-r v0.25.0

Describe the bug

[pbmc10k_data, /home/jxx2/Tutorials/SCENIC_pbmc/pbmc10k_data/outs, 10x_cellranger_mex_outs, h5ad]
Error executing process > 'single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:PUBLISH_H5AD_HVG_SCALED:SC__PUBLISH (1)'

Caused by:
Process single_sample:SINGLE_SAMPLE:SCANPY__SINGLE_SAMPLE:HVG_SELECTION:PUBLISH_H5AD_HVG_SCALED:SC__PUBLISH (1) terminated with an error exit status (1)

Command executed:

mv pbmc10k_data.SCANPY.hvg_scaled_output.h5ad tmp
if [ ! -f pbmc10k_data.SCANPY.hvg_scaled_output.h5ad ]; then
ln -L tmp "pbmc10k_data.SCANPY.hvg_scaled_output.h5ad"
fi

Command exit status:
1

Command output:
(empty)

Command error:
ln: failed to create hard link ‘pbmc10k_data.SCANPY.hvg_scaled_output.h5ad’ => ‘tmp’: Operation not permitted

Work dir:
/home/jxx2/Tutorials/SCENIC_pbmc/work/7d/7c3d7ff02cdf4adc14c4b8d1062342

Tip: when you have fixed the problem you can continue the execution adding the option -resume to the run command line
WARN: Killing pending tasks (4)

[cflerin]

Hi @vagabond12 ,

This should be fixed in the develop branch. You can update your local copy using:

nextflow pull vib-singlecell-nf/vsn-pipelines -r develop

[Ijoanito]

Hi @cflerin,
I also experience similar problem but on different file:

I then try your suggestion to use the develop version, but I get another error:

"Unknown error accessing project vib-singlecell-nf/vsn-pipelines -- Repository may be corrupted: /home/ubuntu/.nextflow/assets/vib-singlecell-nf/vsn-pipelines"

This is how I run it (my nextflow version is 20.10.0):
nextflow -C single_sample.config run vib-singlecell-nf/vsn-pipelines -r -entry single_sample

[cflerin]

Hi @Ijoanito ,

It seems like your local copy was corrupted somehow. Best thing to do would be to remove it and re-pull it. See the comment here for how to do this.

Keep in mind that if you are switching from a release to the develop branch, you may have to re-generate your config file (nextflow config ...) as we have changed some parameters since the last relase.

[Ijoanito]

Hi @cflerin

Thanks for your prompt reply.

Yes I have tried that one too. This is how I run it:

rm -rf ~/.nextflow/assets/vib-singlecell-nf/vsn-pipelines
nextflow pull vib-singlecell-nf/vsn-pipelines -r develop
nextflow config vib-singlecell-nf/vsn-pipelines -profile tenx,docker,single_sample > single_sample.config
nextflow -C single_sample.config run vib-singlecell-nf/vsn-pipelines -r -entry single_sample

This the config file that I use.
single_sample.config.txt

[cflerin]

Hi @Ijoanito ,

And you still get an error after running these commands, or not? It looks like there is a typo in your run command -- you haven't specified branch develop. It should be:

nextflow -C single_sample.config run vib-singlecell-nf/vsn-pipelines -r develop -entry single_sample

[Ijoanito]

Gezz, I didnt notice that. It is running perfectly now.
Thanks a lot @cflerin!

[cflerin]

@Ijoanito , glad to hear that it's working for you now!