Segmentation fault

[MichelNivard]

Hi I installed, and reinstalled, PAINTOR V3.0 executing it results in a segmentation fault

exact message:

"Segmentation fault (core dumped)"

exact command executed: ./PAINTOR -input ld_out.SZ.processed -Gname SZ Lname BSZ -out paintor_output/ -in SZ_Data/ -Zhead Zscore -LDname ld_out.SZ.ld

Any suggestions of how to proceed?

Best, Michel Nivard

[MichelNivard]

Some additional info, the example data does run, and the data I provide to PAINTOR is processed withthe python tool which computes the LD matrix

[ghost]

@MichelNivard you lack a hyphen before -Lname, which causes C to improperly parse arguments, resulting in a segmentation fault

viz. ./PAINTOR -input input.files -Zhead ZSCORE.P1 -LDname LD1 -in RunDirectory/ -out OutDirectory/ -annotations A5,A20,A93 -Gname Enrich.Final -Lname BF.Final
from https://github.com/gkichaev/PAINTOR_V3.0/wiki/3.-Running-Software-and-Suggested-Pipeline

[MichelNivard]

Thanks for the quick reply!

Unfortunately this doesn't seem to be the (only) issue. I Tried many configurations landing on:

./PAINTOR -input input.files -in SZ_EA_Data/ -out paintor_out/ -LDname ld -Zhead Zscore

This and all other attempts except for the demo code fail with a segmentation fault...

[ghost]

Unfortunately its going to be pretty difficult for anyone but you to trouble shoot a problem like this. From afar, all I can do is make suggestions, for instance, "have you double checked all the file paths" or "are you positive the column headings in each input file are correct?"

I hope the prior comment gives you some insight, though, into the meaning of the error itself..

[MichelNivard]

Thanks, I solved it,tyhe error was indeed caused by a misspecified path.

[ghost]

@MichelNivard great! unless you or Gleb needs to weigh in I would recommend closing the issue.

[gkichaev]

Many thanks for the helping debug the problem @vlaufer. I thought I added a check to ensure that all the input files were correctly specified. Will look into this to make sure.