Adding cM coordinates with --cm-map never seems to end

[Enrique Mondragon Estrada]

Hi Chris,

I'm trying adding cM coordinates to the 1000 GP data filtered with only samples with my population of interest and variants present in the HapMap3 SNP list using this genetic map with the following command:

plink --file plink/chr${i}_SAS --cm-map genetic_map_hg38_withX.txt --recode --make-bed --out plink/chr${i}_SAS_genmap

Most of the chromosomes finish successfully in a couple of seconds. However,  chromosomes 4, 14, and 15 have been running for ~12 hours. I haven't found anything particular in those files. Any recommendations or insights would be appreciate it. Happy to share the data too.

Thank you,

Enrique

[Chris Chang]

I'm unable to replicate this stall, so yes, if you could share a dataset that produces this behavior on your end, that would be helpful.

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[Enrique Mondragon Estrada]

Thank you for your quick response. Sure, I have temporarily uploaded ZIP files corresponding to chr4, chr14 and chr15 here. I also included chr22 as an example of files that work as expected.
 

[Chris Chang]

Thanks, that was sufficient to produce an error on my end; will try to post a bugfix later today.

On Sun, Jun 15, 2025 at 9:39 AM Enrique Mondragon Estrada <emon...@gmail.com> wrote:

Thank you for your quick response. Sure, I have temporarily uploaded ZIP files corresponding to chr4, chr14 and chr15 here. I also included chr22 as an example of files that work as expected.
 

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[Enrique Mondragon Estrada]

Thank you for your time. Please let me know if you need anything else from my end.

[Chris Chang]

Bugfix is posted; let me know if you still have any problems with the new build.

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[Enrique Mondragon Estrada]

Works perfectly fine, thank you so much!