Michigan Imputation server failed job

Question

[Najla]

This is the first time I use Michigan Imputation Server. My imputation worked as it should on all chromosomes (1 to 22) apart from chromosome 9, where the job starts and then it fails and I don't know why and how to fix this issue. Here are some details of my job to give you an idea of the situation.

Input Validation

1 valid VCF file(s) found.

Samples: 795
Chromosomes: 9
SNPs: 2997
Chunks: 7
Datatype: unphased
Build: hg19
Reference Panel: apps@1000g-phase-3-v5 (hg19)
Population: mixed
Phasing: eagle
Mode: imputation
Rsq filter: 0.3

Quality Control

Skip allele frequency check.

Calculating QC Statistics

Statistics:
Alternative allele frequency > 0.5 sites: 0
Reference Overlap: 99.97 %
Match: 2,127
Allele switch: 860
Strand flip: 0
Strand flip and allele switch: 0
A/T, C/G genotypes: 0
Filtered sites:
Filter flag set: 0
Invalid alleles: 0
Multiallelic sites: 0
Duplicated sites: 0
NonSNP sites: 0
Monomorphic sites: 0
Allele mismatch: 9
SNPs call rate < 90%: 2,502

Excluded sites in total: 2,511
Remaining sites in total: 485
See snps-excluded.txt for details
Typed only sites: 1
See typed-only.txt for details

Warning: 1 Chunk(s) excluded: < 3 SNPs (see chunks-excluded.txt for details).
Remaining chunk(s): 7

Pre-phasing and Imputation

Chr 9

Imputation on chromosome 9 failed. Imputation was stopped.

Any idea on why to fix this issue?

Thanks

Answer 1

[Najla]

I believe this is a recurrent error that happens on human chromosome 9 with Michigan Imputation Server. I couldn't find a solution for that so I had to use another imputation server