Merging large amounts of .ped files -- trouble.

[Kaden Winspear]

Hello! I am currently working on a project with 193 scaffolds scattered among 96 .ped files. I need to merge these files for my further analyses, but have run into difficulties when using plinks bmerge. I have already formatted the .map files for the respective scaffolds as 'contig_1".... and am using the --allow-extra-chr argument but for some odd reason after I successfully merge the first 26 .ped files my terminal just goes stagnant. After submitting jobs to merge a ped file (containing the first 26 ped files) to the rest of the ped files there is no progress shown in the .log file at all and the job never finishes. Is this a ram issue? I do not understand why I can easily merge the first 26 .peds, but have trouble adding on from there! Thank you. 

I know .log files are needed for help, but in this situation my log files spits nothing out. 

[Chris Chang]

Add —debug to your command-line to get a partial .log file.

On Tue, Jun 25, 2024 at 11:03 AM Kaden Winspear <kadenw...@gmail.com> wrote:

Hello! I am currently working on a project with 193 scaffolds scattered among 96 .ped files. I need to merge these files for my further analyses, but have run into difficulties when using plinks bmerge. I have already formatted the .map files for the respective scaffolds as 'contig_1".... and am using the --allow-extra-chr argument but for some odd reason after I successfully merge the first 26 .ped files my terminal just goes stagnant. After submitting jobs to merge a ped file (containing the first 26 ped files) to the rest of the ped files there is no progress shown in the .log file at all and the job never finishes. Is this a ram issue? I do not understand why I can easily merge the first 26 .peds, but have trouble adding on from there! Thank you. 

I know .log files are needed for help, but in this situation my log files spits nothing out. 

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