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openvax / neoantigen-vaccine-pipeline

Bioinformatics pipeline for selecting patient-specific cancer neoantigen vaccines
Apache License 2.0
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Error when running test samples #152

Closed staracode closed 1 year ago

staracode commented 1 year ago

Hi,

I get the following error when I run the docker image with test samples.

docker run -it -v $(realpath inputs):/inputs -v $(realpath outputs):/outputs -v $(realpath reference-genome):/reference-genome openvax/neoantigen-vaccine-pipeline:0.6.2 --configfile=/inputs/idh1_config.yaml

Here is the error I get. I am running this on an ubuntu ec2 instance with 500Gb of space, more than 32 Gb of memory, and more that 16 cores. I have googled the error and can't seem to figure out what the cause is exactly.

`Oct 16 21:13:08 ..... started STAR run Oct 16 21:13:08 ..... loading genome Oct 16 21:13:24 ..... started mapping Oct 16 21:13:27 ..... started sorting BAM

EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: 228 0 46

Oct 16 21:13:27 ...... FATAL ERROR, exiting

EXITING because of FATAL ERROR: number of bytes expected from the BAM bin does not agree with the actual size on disk: 918 0 48

Oct 16 21:13:27 ...... FATAL ERROR, exiting`