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epi2me-labs / wf-bacterial-genomes

Small variant calling for haploid samples
https://labs.epi2me.io/
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Failed to pull singularity iamge #33

Open adbeggs opened 6 months ago

adbeggs commented 6 months ago

Operating System

Other Linux (please specify below)

Other Linux

RedHat Enterprise 8.3

Workflow Version

Latest

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

No response

Workflow Execution - CLI Execution Profile

None

What happened?

ERROR ~ Error executing process > 'calling_pipeline:getParams'

Caused by: Failed to pull singularity image command: singularity pull --name ontresearch-wf-bacterial-genomes-shaa4cda1aeeda01242c54f4af03419e9623397dc0c.img.pulling.1714050463708 docker://ontresearch/wf-bacterial-genomes:shaa4cda1aeeda01242c54f4af03419e9623397dc0c > /dev/null status : 255 message: WARNING: SINGULARITY_CACHEDIR and APPTAINER_CACHEDIR have different values, using the latter INFO: Converting OCI blobs to SIF format INFO: Starting build... Getting image source signatures Copying blob sha256:f9432144bf11a2ae3ffb7360b4e32f7b18c75c7c8c125274ec3cf49d0de28e24 Copying blob sha256:edaedc954fb53f42a7754a6e2d1b57f091bc9b11063bc445c2e325ea448f8f68 Copying blob sha256:e8b63ef4ca0ca489bb848ecf9f4db232528d222a2c0bb2a599b312ce6b5b551a Copying blob sha256:88397e6fd840152eca6643094559385065a6ab98a1c3c7e75eb676b9d97aad97 Copying blob sha256:0456c71d8011447360dd461b49b6a1a4cb36edf8f7250817e99ceeb0d353f06b Copying blob sha256:38cad909cfed9fb07cc2c6612612435d52302b48ebcf94a2a4b77e02b8414142 Copying blob sha256:cd889bc730171a0013130be60f28f869d7e7cc4d923396628660de9b67f7eec8 Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 Copying blob sha256:2042b0824681af825bf6a3c7d48cf91a218427db24a26198aaa7a2e92145081d Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 Copying blob sha256:973691ee7cdac427dd9005f99675e8e77fb7feda0e94e11626a95e46e5d2973e Copying blob sha256:4a9d7e589e1778374b42cbdb32d978af00de957133897cdc1171659808fb6f7f Copying blob sha256:3fc3949421420f916ca77ede3295a7f762d493b84b0bc2e4a2212f8573b76e3c Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 Copying blob sha256:6de220563c5cae03fae0f6b66c78c7e1091b6d2a91b0d199ec712fd216399bc6 Copying blob sha256:7f4c1460c3a6a5c0a29dd740394343f9e4dc867062c299febc85015eb3cf8606 Copying blob sha256:8e13bd657a727a4c167b0e27b05aa3ee5dab63fda01f8b2643400f4c10053dd8 Copying blob sha256:d8af254b567f3b0a15ba645cf6dee25e3223b4a610fe237a3ad31a4dedf679fc Copying blob sha256:786231868c62c95197f37ffa3046b4f0ccffc11bd49a4f206a032c700eb18ef6 Copying blob sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 Copying config sha256:755ac014996a07c3bf534514c4b2e0f7c0b97a0985a8be3111b8d76f22d8c30c Writing manifest to image destination FATAL: While making image from oci registry: error fetching image to cache: while building SIF from layers: conveyor failed to get: while getting config: no descriptor found for reference "0afe778952f0d96b21c5b5e679d0e4e7fa471a27de53375f550c47e3cfc5996f"

Relevant log output

As above

Application activity log entry

No response

Were you able to successfully run the latest version of the workflow with the demo data?

no

Other demo data information

No response

SamStudio8 commented 6 months ago

Hi @adbeggs, Nextflow may attempt to pull multiple images at once with Singularity which can occasionally lead to a race condition with simultaneous writes to the Singularity cache. You may find that running the workflow again may simply avoid the race condition and the image downloads will proceed without trouble.

Failing that, you may wish to try:

For Singularity this can be achieved by setting the environment variable SINGULARITY_DISABLE_CACHE=True.

You can run the indicated Singularity command yourself (removing the .pulling.NNNN extension), in the directory where you keep your images (usually set with NXF_SINGULARITY_CACHEDIR). Note that if you are not already setting NXF_SINGULARITY_CACHEDIR, I would strongly advise you to do so, to avoid downloading images for each workflow.

command: singularity pull --name ontresearch-wf-bacterial-genomes-shaa4cda1aeeda01242c54f4af03419e9623397dc0c.img docker://ontresearch/wf-bacterial-genomes:shaa4cda1aeeda01242c54f4af03419e9623397dc0c > /dev/null