SHAPEIT - getting 'Segmentation fault'
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Entering edit mode
2.1 years ago
Larson • 0

Hi there,

I am having difficulty running SHAPEIT for my specific case - I am getting Segmentation fault. Nothing that I managed to find online solved my problem.

In principle, I want to phase a subset of SNPs present in two, separated regions of the X chromosome, for a single sample. I am using a .vcf file as input.

The command I would typically run would be:

shapeit --input-vcf Mix0_1_S1/RD_RHDA_v1_1/data/full_variant_table.vcf \
-M genetic_map_chrX_nonPAR_combined_b37.txt \
--output-log Mix0_1_S1.chrX.log \
--output-max Mix0_1_S1.tab \
--chrX \
--input-ref 1000GP_Phase3_chrX_NONPAR.hap.gz 1000GP_Phase3_chrX_NONPAR.legend.gz 1000GP_Phase3.sample \

I also tried various other options (restricting to a smaller region, changing window size, not using reference etc) but no matter what I do I get the enigmatic Segmentation fault message just when reading the .vcf. I would appreciate any help.

PS. I am running v2.r904

phasing haplotype haplotyping SHAPEIT • 863 views
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Entering edit mode

The issue might reside in several causes, but I would favor lack of RAM or malformed input file.

Some suggestions requirements:

1) Can you post the exact error message? Maybe is the one listed in this post? SHAPEIT Segmentation Fault on Input Read-In

2) Have you tried running on a test data distributed with the software?

3) Have you tried running on a very reduced set of data?

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