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segmentation fault at gvcf2bed #154
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Using fasta file from alternative sources will help you get rid of this. |
I am also getting this error. But what is it about the fasta file thats causing this error? Any more information that can help debug this? Thanks. |
Did you figure this out @meredith705? Looks like we are doing something very similar. |
@KatharineME @YuanfengZhang I have tried using a different version of GRCh38 and have still gotten the same error. The other version is https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta.gz |
(1) Try GDC/BWA/GATK/GA4GH/other sources. |
Hi All, I got hap.py working without changing the reference genome. I did the following. I'm assuming that you are using rtg as the vcf comparison engine:
If this doesn't work for you, I recommend trying to run the examples from the readme in the docker container. |
I had the same issue. Decompressing the reference fastq.gz and reindexing it with samtools faidx solved it for me. My other steps are here. |
Hello,
I'm running the hap.py v0.3.12 docker using the Genome In A Bottle HG002 vs GRCh38 truth set using the files below and getting a segmentation fault error in the gvcf2bed program.
The GIAB bottle truth set is here https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/AshkenazimTrio/HG002_NA24385_son/NISTv4.2.1/GRCh38/
The vcf I'm using as truth is:
HG002_GRCh38_1_22_v4.2.1_benchmark_phased_MHCassembly_StrandSeqANDTrio.vcf
from their supplementary files hereHigh confidence bed file:
HG002_GRCh38_1_22_v4.2.1_benchmark_noinconsistent.bed
file from the same directory as aboveThe GRCh38 reference is:
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GCA_000001405.15_GRCh38_no_alt_analysis_set_maskedGRC_exclusions_v2.fasta.gz
The query vcf I'm using is created by running dipcall on two haploid assemblies of chr11 ( a small test assembly ) using the same GRCh38 assembly as a reference:
paternal.dip.vcf.gz
Here is my command:
I get a segmentation fault error after about 2 minutes of run time.
I really appreciate your help figuring out this issue, please let me know what other information I can provide.
Thank you in advance,
Melissa
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