To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

SVPreprocess Mismatch found between genome mask and reference


I'm trying to execute the SVPreprocess step on 48 samples I have.
I've gotten the program to run but two of the SVPreprocesss*.out files contain errors/run failures.

In one: SVPreprocess-5.out we are running:

Program Name:
Program Args: -O /home/dfermin/genomeStrip.gf48/metadata/genome_sizes.txt -R /home/dfermin/conf/hs37d5.fa -genomeMaskFile /home/dfermin/apps/masks/Homo_sapiens_assembly19.mask.101.fasta

The error message is:

Exception in thread "main" Mismatch found between genome mask and reference sequence:  Interval hs37d5:1-35477943 not found in genome mask

I'm guessing the issue is either:
1) A discrepancy between the header line of the FASTA file used from chromosome one for the initial BWA alignment (/home/dfermin/conf/hs37d5.fa) and the header line of the FASTA file in /home/dfermin/apps/masks/Homo_sapiens_assembly19.mask.101.fasta


2) A discrepancy in the size of chromosome 1 in these two files.


The second error is in SVPreprocess-6.out:

Program Name:
Program Args: -O /home/dfermin/genomeStrip.gf48/metadata/gcprofile/ -R /home/dfermin/conf/hs37d5.fa -md /home/dfermin/genomeStrip.gf48/metadata -writeReferenceProfile true -genomeMaskFile /home/dfermin/apps/masks/Homo_sapiens_assembly19.mask.101.fasta -configFile /home/dfermin/apps/genomeSTRIP/conf/genstrip_parameters.txt

The error here is:

Exception in thread "main" java.lang.RuntimeException: Invalid sequence position: hs37d5:201

This one I have no idea what's causing it.

Both errors look to be issues with the FASTA files involved but I can't figure out a correction.
Any suggestions?


Best Answer


Sign In or Register to comment.