Segmentation fault when using genetic map

[GenevieveKrause]

I am attempting to run phase_common_static from the docker image loaded from shapeit5_v5.1.1.docker.tar.gz on the All of Us research platform. I was able to successfully run the program using the following command:
phase_common_static --input E300-2024-06-05.vcf.gz --region chr20 --output E300-phase_common-map.bcf --thread 8 However, when I added the --map to the same dataset I got a seg fault. phase_common_static --input E300-2024-06-05.vcf.gz --region chr20 --map chr20.b38.gmap.gz --output E300-phase_common-map.bcf --thread 8 Here is what the output looks like: `[SHAPEIT5] phase_common (jointly phase multiple common markers)

• Author : Olivier DELANEAU, University of Lausanne
• Contact : olivier.delaneau@gmail.com
• Version : 5.1.1 / commit = 990ed0d / release = 2023-05-08
• Run date : 05/06/2024 - 20:43:41

Files:

• Input : [/mnt/data/mount/gs/fc-secure-60ad3bba-4af3-4245-b945-479d3e9eb953/microarry-vcfs/E300-2024-06-05.vcf.gz]
• Genetic Map : [/mnt/data/mount/gs/fc-secure-60ad3bba-4af3-4245-b945-479d3e9eb953/genetic_maps/chr20.b38.gmap.gz]
• Output : [/mnt/data/output/gs/fc-secure-60ad3bba-4af3-4245-b945-479d3e9eb953/shapeit/E300-phase_common-map.bcf]
• Output format : [bcf]

Parameters:

• Seed : 15052011
• Threads : 8 threads
• MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
• PBWT : [window = 4cM / depth = auto / modulo = auto / mac = 5 / missing = 0.1]
• HMM : [window = 4cM / Ne = 15000 / Recombination rates given by genetic map]

Reading genotype data:

• VCF/BCF scanning done (7.82s)
  • Variants [#sites=43173 / region=chr20]
  • Samples [#target=300 / #reference=0]
• VCF/BCF parsing done (7.37s)
  • Genotypes [0/0=74.701%, 0/1=13.389%, 1/1=7.347%, ./.=4.564%, 0|1=0.000%]

Setting up genetic map:

• GMAP parsing [n=0] (0.11s) /mnt/data/script/shapeit-e300: line 4: 7 Segmentation fault (core dumped) `

Unfortunately, because I am running this using data from the All of Us platform I am unable to share the files.

[dtaliun]

Hi @GenevieveKrause ,

GMAP parsing [n=0] (0.11s) indicates that it read 0 lines from your chr20.b38.gmap.gz file. Could it be that the file is empty, or something went wrong when mounting data to the image?

If there were 0 positions read from the genetic map file, then this line inside variant_map::interpolateCentiMorgan will result in segmentation fault because it assumes that the vector holding genetic map coordinates is never empty and accesses the first element using [] operator.

[GenevieveKrause]

Hello,

You were correct. The file got corrupted somewhere in the process. I got a clean copy of the file and it worked fine. Thank you.