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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: org.broadinstitute.sv.apps.ComputeGenomeSizes
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" org.broadinstitute.sv.commandline.ArgumentException: 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: org.broadinstitute.sv.apps.ComputeGCProfiles
Program Args: -O /home/dfermin/genomeStrip.gf48/metadata/gcprofile/reference.gcprof.zip -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


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