pathologically long line on .gen file (.imputed.gz)

[정여진]

Hi.

Nom i'm trying to convert imputed.gz file to plink binary files

all results on chromosomes except chr11 and chr15 were successful.

on chr11 line 355921, and chr15 line 31790, there's an error message "Line __ of .gen file is pathologically long". 

How can I fix this problem?

thanks. 

[Christopher Chang]

Can you post the full .log file from one of the failing runs?

[정여진]

Here is the full log of chr11 and chr15

And this is the failing line (355921th line of chr11.imputed) 

It seems like monoallelic...

 The other line (before the failing line) in chr11.imputed is just same as this.

 -

And this is sample of non-failing chromosome (chr22, 10th line)

2021년 2월 19일 금요일 오전 1시 43분 18초 UTC+9에 chrch...@gmail.com님이 작성:

[Christopher Chang]

If you run the same command (after replacing "--missing-genotype" with "--input-missing-genotype") in plink 2.0, do you still get this error?