"Underflow impossible to recover" error

[mbyrska]

I ran shapeit4 on WGS sequencing data with a family-based scaffold and when I run it with version 4.1.2 or 4.1.3 (assuming the latter is the newest version since in the log it says v4.1.2 - see Issue #22) I get the following error:

* HMM computations [52%]^M * HMM computations [53%]^M * HMM computations [54%]^M * HMM computations [55%]^M * HMM computations [56%]^M * HMM computations [57%]^M * HMM computations [58%]^M * HMM computations [59%]^M * HMM computations [60%]^M * HMM computations [61%] ESC[31mERROR: ESC[0mUnderflow impossible to recover

However, when I run it with version 4.0.0 with the same default parameters it finishes with no issues. Any ideas of what can be causing that? Thanks!

Command I'm using: shapeit4 \ --input ${vcf} \ --map ${genetic_map} \ --region ${chr} \ --scaffold ${scaffold_vcf} \ --thread 20 \ --log phased.log \ --output ${outdir}/${prefix}.vcf.gz

[odelaneau]

Hi, Can you send me the complete log file; it would help me to spot the problem. To get the email address, run shapeit4 --help. Thanks,