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icbi-lab / nextNEOpi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction
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Singularity image pull: "FATAL: the requested image was not found" #78

Closed CSree closed 1 week ago

CSree commented 1 week ago
Screenshot 2024-07-09 at 8 51 01 AM

slurm-38619545.txt Hi, I ran the pipeline using -profile singularity , and got the following error:

Pulling Singularity image https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif [cache /gpfs/data/sequence/results/krogsgaardlab/2024-04-23/results_NeoagPipeline_2024/Sample18/work/singularity/apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif] Pulling Singularity image https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11 [cache /gpfs/data/sequence/results/krogsgaardlab/2024-04-23/results_NeoagPipeline_2024/Sample18/work/singularity/depot.galaxyproject.org-singularity-gatk-3.8--hdfd78af_11.img] INFO: Mutect1 not available, skipping.... Pulling Singularity image https://depot.galaxyproject.org/singularity/cnvkit:0.9.9--pyhdfd78af_0 [cache /gpfs/data/sequence/results/krogsgaardlab/2024-04-23/results_NeoagPipeline_2024/Sample18/work/singularity/depot.galaxyproject.org-singularity-cnvkit-0.9.9--pyhdfd78af_0.img] WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /gpfs/data/sequence/results/krogsgaardlab/2024-04-23/results_NeoagPipeline_2024/Sample18/work/singularity -- Use env variable NXF_SINGULARITY_CACHEDIR to specify a different location Error executing process > 'RegionsBedToIntervalList (RegionsBedToIntervalList)'

Caused by: Failed to pull singularity image command: singularity pull --name apps-01.i-med.ac.at-images-singularity-nextNEOpi_1.3.2_18734d43.sif.pulling.1719238039463 https://apps-01.i-med.ac.at/images/singularity/nextNEOpi_1.3.2_18734d43.sif > /dev/null status : 255 message: INFO: Downloading network image FATAL: the requested image was not found

The images stored in the temporary location are similar to those generated during previous successful runs of the pipeline. However this time, the images are not found. Thanks in advance for your help Chai

riederd commented 1 week ago

Hi, we (accidentally) removed images for the outdated version, I put them back on the server. I hope they are the correct ones.

However, we strongly suggest to use a more recent version of nextNEOpi (e.g. v1.4.1)

CSree commented 1 week ago

Many thanks for your prompt response! I will update with the latest, and run it again. Have a great day