I/O error when converting Plink files to Merlin format for imputation using MACH?
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2.7 years ago
anamaria ▴ 180

Hello,

as I understand in order to do imputation on MACH I have to convert my plink files to Merlin format.

I was using mega2 but I am getting this I/O error. I do have space on my disk and I do have write permissions so that should not be the problem. Errors I am seeing are these:

DB sqlite3_exec (file "dbmega2.db") failed: #10:disk I/O error

DB prep "INSERT INTO int_table(key, value) VALUES(?, ?);" (file "dbmega2.db") failed: #10:disk I/O error


and they are the same when I use .ped .map files or .bim, .fam, .bed files

I am wondering if I am entering some options in mega2 wrong. the only things I selected are these: Please enter file stem > outputZ12 --missing-phenotype -9

and my .fam file looks like this:

fam0110_G110 fam0110_G110 0 0 2 -9
fam0113_G113 fam0113_G113 0 0 2 -9
fam0114_G115 fam0114_G115 0 0 1 -9
...


It is important for me to use MACH for imputation because I have to replicate some old results.

Do you maybe know any other software for converting plink to merlin format?

mega2 imputation mach • 666 views