error in running pipeline with singularity

[nilesh-tawari]

Hi, Thanks for the wonderful pipeline.
I am trying to run pipeline first time but i am getting error.
Below is my command to run pipeline:

nextflow run nf-core/rnaseq --reads '*6206911_{1,2}.fastq.gz' --genome CanFam3.1 --saveReference --saveAlignedIntermediates  -with-singularity 
/hpcn/users/nil/00_pipelines/nfcore-rnaseq-1.1.img

I am getting error as,

ERROR ~ Error executing process > 'fastqc (SRR)'

Caused by:
  Process `fastqc (SRR)` terminated with an error exit status (127)

Command executed:

  fastqc -q SRR6206911_1.fastq.gz SRR6206911_2.fastq.gz

Command exit status:
  127

Command output:
  (empty)

Command error:
  /bin/bash: line 0: cd: /hpcn/users/nil/test/RNAseq-nf/work/b1/39c36ab709e094aba99fff7bec1140: No such file or directory
  /bin/bash: .command.stub: No such file or directory

Work dir:
  /hpcn/users/nil/test/RNAseq-nf/work/b1/39c36ab709e094aba99fff7bec1140

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

 -- Check '.nextflow.log' file for details
[d8/2362b9] NOTE: Process `get_software_versions` terminated with an error exit status (127) -- Error is ignored
[nfcore/rnaseq] Pipeline Complete

Complete .nextflow.log file is attached herein.
.nextflow.log
Any suggestion what is going wrong? Please let me know if further information needed from my side.
Thanks,
-Nilesh

[ewels]

Duplicate of #113, fix in pull request #116

@nilesh-tawari - Thanks for reporting this. We'd seen the same error recently too and have hopefully just merged in a change to the pipeline that fixes the problem.

The fixed code is now available in the dev version of the pipeline and will be released soon. Until then, you can run the development version of the code by adding -r dev to your nextflow run command. Note that you will have to pull an updated singularity container too, with the dev tag: docker://nfcore/rnaseq:dev

I think we're overdue a new release for this pipeline, so an updated stable release should hopefully be ready soon.

Phil

[nilesh-tawari]

@ewels
Hi Phil thanks for the prompt reply. I tried the dev version, still I am getting same error. Below are the commands I used,

singularity pull docker://nfcore/rnaseq:dev

Run dev version

nextflow run nf-core/rnaseq --reads '*6206911_{1,2}.fastq.gz' --genome CanFam3.1 --saveReference --saveAlignedIntermediates -with-singularity rnaseq-dev.simg -profile standard,singularity -r dev

following version was used

Launching `nf-core/rnaseq` [adoring_lichterman] - revision: 90b42ca77e [dev]

I am missing something?
Thanks for the support.
-Nilesh

[ewels]

@nf-core/core - any ideas?

@nilesh-tawari we're really close to pushing the release, so maybe we can just wait for that and try again if that's ok.

Phil

[apeltzer]

How is your Singularity configured in general? Sounds a bit like the path is not accessible from inside the container, maybe a bind-path issue?

[nilesh-tawari]

How is your Singularity configured in general? Sounds a bit like the path is not accessible from inside the container, maybe a bind-path issue?

@apeltzer
Thanks, yes it seems the bind-path is issue. Singularity is installed system wide, I can use from as,

nil@aq-login-0001 $ singularity --version
2.5.2-dist

Can you suggest possible way to debug?
Thanks,
-Nilesh

[apeltzer]

You could edit the /etc/singularity.conf and try to add bind paths for your cluster system and/or auto-mounts.