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nf-core / raredisease

Call and score variants from WGS/WES of rare disease patients.
https://nf-co.re/raredisease
MIT License
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Test+Docker profile fails: "The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine." #590

Open sitems opened 1 month ago

sitems commented 1 month ago

Description of the bug

ERROR ~ Error executing process > 'NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT ( earlycasualcaiman)'

Caused by:
Process NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT (earlycasualcaiman) term inated with an error exit status (134)

Command executed:

/opt/deepvariant/bin/run_deepvariant \
--ref=reference.fasta \
--reads=earlycasualcaiman_sorted_md.bam \
--output_vcf=earlycasualcaiman_deepvar.vcf.gz \
--output_gvcf=earlycasualcaiman_deepvar.g.vcf.gz \ --model_type=WGS \ \ --intermediate_results_dir=tmp \
--num_shards=2

cat <<-END_VERSIONS > versions.yml
"NFCORE_RAREDISEASE:RAREDISEASE:CALL_SNV:CALL_SNV_DEEPVARIANT:DEEPVARIANT": deepvariant: 1.6.1 END_VERSIONS

Command exit status: 134

Command output: (empty)

                                                                                              [100/1899]

Command error: The TensorFlow library was compiled to use AVX instructions, but these aren't available on your machine. /opt/deepvariant/bin/run_deepvariant: line 2: 34 Aborted (core dumped) python3 -u /opt/d eepvariant/bin/run_deepvariant.py "$@"

Work dir: shortened/work/30/b59653cd5fb9be91a8c525651d6d0e

Tip: you can replicate the issue by changing to the process work dir and entering the command bash .command. run

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

-- Check '.nextflow.log' file for details
-[nf-core/raredisease] Pipeline completed with errors-

Command used and terminal output

nextflow run nf-core/raredisease -revision dev -profile test,docker --outdir out

Relevant files

No response

System information

Nextflow version: 24.04.4.5917 Hardware: Desktop Executor: local Container engine: Docker OS: Ubuntu 22.04 Version of nf-core/raredisease: dev (on 2024-08-12)

ramprasadn commented 1 month ago

@sitems Are you able to run deepvariant outside of nf-core/raredisease?

sitems commented 1 month ago

No, the error is the same when I run 'docker run google/deepvariant:1.6.1 ...'

ramprasadn commented 1 month ago

hmm.. This could be because some libraries/tools are missing on your machine. Others have reported similar issues with deepvariant. Looks like there might be a workaround. Check https://github.com/google/deepvariant/issues/657

Oliversinn commented 14 hours ago

I'm facing the same issue here. The only difference is that I am using Linux Mint instead of Ubuntu.

sitems commented 6 hours ago

Based on what I've read so far, it looks that my processor is a bit outdated (since it doesn't support AVX instruction), so I decided to move the pipeline to another hardware (rather than doing some compilation hacks).