Problem with SHAPEIT

Question

[dongxinyu510]

My code is as follows,At the end it has an error and I don't know how to fix it:

shapeit \
  -M genetic_map_hg38_withX.txt \
  --input-bed chr22.bed chr22.bim chr22.fam \
  --input-ref RefPanel.hap.gz   RefPanel.legend.gz    sample.txt \
--exclude-snp chr22.alignments.snp.strand.exclude\
 -O chr22.phased

Segmented HAPlotype Estimation & Imputation Tool
  * Authors : Olivier Delaneau, Jared O'Connell, Jean-François Zagury, Jonathan Marchini
  * Contact : send an email to the OXSTATGEN mail list https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=OXSTATGEN
  * Webpage : https://mathgen.stats.ox.ac.uk/shapeit
  * Version : v2.r904
  * Date    : 03/08/2022 17:23:38
  * LOGfile : [shapeit_03082022_17h23m38s_89c6ccf7-de3b-47ca-a258-5cda5331d54b.log]

MODE -phase : PHASING GENOTYPE DATA
  * Autosome (chr1 ... chr22)
  * Window-based model (SHAPEIT v2)
  * Reference panel of haplotypes used
  * MCMC iteration

Parameters :
  * Seed : 1659518618
  * Parallelisation: 1 threads
  * Ref allele is NOT aligned on the reference genome
  * MCMC: 35 iterations [7 B + 1 runs of 8 P + 20 M]
  * Model: 100 states per window [100 H + 0 PM + 0 R + 0 COV ] / Windows of ~2.0 Mb / Ne = 15000

Reading SNPs to exclude from input file in [chr22.alignments.snp.strand.exclude]
  * 277 snps found in the exclude list

Reading site list in [chr22.bim]
  * 9486 sites included
  * 277 sites excluded

Reading sample list in [chr22.fam]
  * 306 samples included
  * 306 unrelateds / 0 duos / 0 trios in 306 different families

Reading genotypes in [chr22.bed]
  * Plink binary file SNP-major mode

Reading sample list [/gpfs/lab/liangmeng/members/dongxinyu/SHAPEIT/sample.txt]
  * 5094 reference haplotypes included

Reading SNPs in [/gpfs/lab/liangmeng/members/dongxinyu/SHAPEIT/RefPanel.legend.gz]
  * 9486 reference panel sites included
  * 1049593 reference panel sites excluded

Reading reference haplotypes in [/gpfs/lab/liangmeng/members/dongxinyu/SHAPEIT/RefPanel.hap.gz]

ERROR: Line=9799 found=5096 fields, expected=5094

[4galaxy77]

Your reference file seems to be truncated somehow but it's impossible to know how unless we can see those lines of a file. Is there any reason you are using a piece of software that is many versions out of date? You should strongly consider using a more recent version here. It'll also mean you won't have to work with antiquated file formats like .hap.

[dongxinyu510]

Your mean is that the version of SHAPEIT2 is too old ?

[4galaxy77]

It's very old compared to the new version - shapeit4 is much, much faster (saving lots of energy in the process!) and more accurate and uses more standard file formats (vcf). I'm not related to shapeit at all, I just like to encourage people to use the most up to date software where they can. shapeit2 won't give you 'bad' results though.