Singularity Error in rnaseq_pipeline_workflow.createSE

Operend / bulk-rna-seq-pipeline

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Singularity Error in rnaseq_pipeline_workflow.createSE #1

Open ghdulrich opened 3 months ago

ghdulrich commented 3 months ago

Getting the following error from rnaseq_pipeline_workflow.createSE: WARNING: 'nodev' mount option set on /restricted/projectnb, it could be a source of failure during build process INFO: Starting build... INFO: Fetching OCI image... FATAL: Unable to handle docker://docker.io/htanpipelines/aggregation@sha256:f9b6a2baeb8fcd425a1c0c30f0a79a497ed1baa465bfc0ee90b14747c229e781 uri: while building SIF from layers: conveyor failed to get: error writing layer: stream error: stream ID 45; INTERNAL_ERROR; received from peer

ghdulrich commented 3 months ago

BTW: Singularity's tmpdir is being set in multi_samples.qsub: export SINGULARITY_TMPDIR=/rprojectnb/cbmhive/daupipe/singtmp

ghdulrich commented 3 months ago

Getting a slightly different error from rnaseq_pipeline_workflow.HaplotypeCaller:0:1 however its using a different container registry: FATAL: Unable to handle docker://broadinstitute/gatk@sha256:29721056dd3ba120bfd19e1fe9766f64600e5f8a2802b11755066496a1d0a31b uri: while building SIF from layers: conveyor failed to get: unexpected end of JSON input

Its interesting that this was only one of 6 shards and the others succeeded

pshaughn commented 2 months ago

Hypothesis: possibly flock relies on certain file operations being atomic, but the way SCC has them set up might break that atomicity guarantee. If true, this might or might not relate to that "nodev" mount.