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nf-core / scnanoseq

Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
https://nf-co.re/scnanoseq/
MIT License
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Failed to pull singularity image #33

Closed sme229 closed 1 month ago

sme229 commented 1 month ago

Description of the bug

I'm running the pipeline and getting this error:

ERROR ~ Error executing process > 'NFCORE_SCNANOSEQ:SCNANOSEQ:UCSC_GTFTOGENEPRED'

Caused by: Failed to pull singularity image command: singularity pull --name depot.galaxyproject.org-singularity-ucsc-gtftogenepred-447--h954228d_0.img.pulling.1727829650369 https://depot.galaxyproject.org/singularity/ucsc-gtftogenepred:447--h954228d_0 > /dev/null status : 255 hint : Try and increase singularity.pullTimeout in the config (current is "20m") message: FATAL: Error making http request: Head "https://depot.galaxyproject.org/singularity/ucsc-gtftogenepred:447--h954228d_0": dial tcp 128.118.250.14:443: connect: connection refused

Command used and terminal output

nextflow run -r dev nf-core/scnanoseq --input './Elena-cDNA-2/20240624_1312_1D_PAW58377_76308a2c/fastq_pass/fastq_data.csv' --outdir scnanoseq_test --fasta '/datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/Rabbit_New/fasta/genome.fa' --gtf '/datasets/work/hb-rabbit-gbc/work/Maria_Jenkel_ONT_Data_04-07-2024/Rabbit_New/genes/genes.gtf' --barcode_format 10X_3v3 -profile singularity

Relevant files

slurm-64022331.txt

System information

nextflow version 24.04.2.5914 HPC slurm singularity Linux dev

lianov commented 1 month ago

Hi @sme229 :

Thanks for reporting - this is an issue that has been observed (sporadically) in other nf-core pipelines as well, so we will need to solve it on an individual basis (unlikely to be something within scnanoseq itself). See for example https://github.com/nf-core/rnaseq/issues/482 from the rnaseq pipeline.

Let's start with the following steps:

  1. Please ensure you set a singularity cache directory ($NXF_SINGULARITY_CACHEDIR). You can do so with something like export NXF_SINGULARITY_CACHEDIR=<path_in_your_system>, noting that the path_in_your_system should be location with sufficient storage (a bit on this is present at https://nf-co.re/docs/usage/getting_started/introduction/#tips-and-tricks.

  2. Please run the pipeline with the test profile first. This will allow you to a. ensure the pipeline is running properly with a downsample input b. along the way it will download the images, and if there are continued issues we will be able to test them quicker.

You can run the test (after completing step 1 above), with the following command: 

nextflow run nf-core/scnanoseq -r dev  -profile test,singularity --outdir ./scnanoseq_test_out

Let us know what happens with the above. Further, I saw your other comment on joining the nf-core slack community. Left you instructions there and indeed this would be a good case to also take it to slack since there are other comments in that location to aid in troubleshooting.

sme229 commented 1 month ago

Hi @lianov thanks so much for your help, it has now completed successfully.