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nf-core / cageseq

CAGE-sequencing analysis pipeline with trimming, alignment and counting of CAGE tags.
https://nf-co.re/cageseq
MIT License
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error: make_ctss.sh: line 18: Read-only file system Read-only file system #63

Open aboyd003 opened 2 years ago

aboyd003 commented 2 years ago

Hi,

I don't know if this technically qualifies as a bug but I am having issue using the pipeline on a hpcc. I don't have sudo privileges and am using singularity. I receive the error below when running with the test file (nextflow run nf-core/cageseq -r 1.0.2 -dsl1 -profile test,singularity).

make_ctss.sh: line 18: /tmp/make_ctss.sh.17128.txt: Read-only file system

My attempts at fixes that haven't worked

I have tried inserting a binding line into the Dockerfile at line 11 after the ENV PATH line. This seemed the most logical to me. I tried "exec --bind /scratch:/tmp" and "export SINGULARITY_BINDPATH=/scratch:/tmp" at this position. When this failed, I tried inserting the lines into line 12 of main.nf. I honestly did not expect this to work but figured I would try. I also tried inserting in the singularity block of nextflow.config at line 111.

mashehu commented 2 years ago

Hi,

Can you try to run it with singularity.runOptions = '-B $TMPDIR' in your nextflow.config. Otherwise, you can try to run the dev version (with -r dev), which is the dsl2 port and should have less of these kind of problems (and is just before being released 🤞🏻 ).