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Troubleshooting

Common issues and solutions for gbcms.

Installation Issues

Rust Compilation Fails

Error: error: linker 'cc' not found

Solution: Install build tools: 

# macOS
xcode-select --install

# Ubuntu/Debian
apt-get install build-essential

# CentOS/RHEL
yum groupinstall "Development Tools"

htslib Linking Error

Error: cannot find -lhts

Solution: The Rust backend compiles htslib statically. Ensure you have: 

# Dependencies
apt-get install zlib1g-dev libbz2-dev liblzma-dev libcurl4-openssl-dev

Runtime Issues

BAI Not Found

Error: BAI index not found for sample.bam

Solution: Create or verify index: 

samtools index sample.bam

Chromosome Mismatch

Error: Chromosome X not found in reference

Solution: Ensure chromosome naming matches between VCF/MAF, BAM, and FASTA (e.g., chr1 vs 1).

Nextflow Issues

Container Not Found

Error: Unable to find image 'ghcr.io/msk-access/gbcms:X.Y.Z'

Solution: Pull manually: 

docker pull ghcr.io/msk-access/gbcms:X.Y.Z
# or
singularity pull docker://ghcr.io/msk-access/gbcms:X.Y.Z

Task Metrics Error

Error: Command 'ps' required by nextflow to collect task metrics

This occurs when running containers that lack procps. Use a newer image with procps installed.