run bgc error in docker

[lidanqi1990]

Dear Martin:
I used the docker to run the bgc:
./bgc -a ~/test_file/YJS_newhybrids_chr10_filter_p0in.txt -b ~/test_file/YJS_newhybrids_chr10_filter_p1in.txt -h ~/test_file/YJS_newhybrids_chr10_filter_admixedin.txt -M ~/test_file/YJS_newhybrids_chr10_filter_map.txt -O 0 -x 50000 -n 25000 -p 1 -q 1 -N 1 -m 1 -D 0.5 -t 5 -E 0.0001 -d 1 -s 1 -I 0 -u 0.04

but it have something wrong like:

Reading input files
Number of loci: 1090786
Number of admixed populations: 1
Number of individuals: 6
Using the linkage model for locus effects
Allowing for uncertainty in allele counts
Allocating memory
gsl: init_source.c:40: ERROR: failed to allocate space for block data
Default GSL error handler invoked.
Aborted (core dumped)

I don't know how to deal with it, any guidance would be fantastic. Thank you!

[tkchafin]

What are the correct numbers of loci and individuals? My guess without seeing the files would be to check that your files have Unix line endings.

[lidanqi1990]

Hi Martin, thanks for your reply. here is my data with the chromosome10 generated by vcf2bgc.py, can you see if the file is correct? or can you run my data in your docker?       ------------------ Original ------------------ From: ***@***.***>; Date:  Tue, Mar 28, 2023 08:35 PM To: ***@***.***>; Cc: ***@***.***>; ***@***.***>; Subject:  Re: [btmartin721/ClineHelpR] run bgc error in docker (Issue #26)   What are the correct numbers of loci and individuals? My guess without seeing the files would be to check that your files have Unix line endings. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you authored the thread.Message ID: ***@***.***> 从腾讯企业邮箱发来的超大附件 YJS_chr10_admixedin.txt (57.56M, 2023年04月27日 20:43 到期)进入下载页面：https://exmail.qq.com/cgi-bin/ftnExs_download?key=ea3e536e380de9ea6ec68270d3bbd0b44d77eab3&from=wedrive&t=exs_ftn_download&fid=*0*E3WHiMKEP31vwfIo1Jdz7m4rWwcWK/5N2+MEMYXyGC61fl0KaDG2kAD9qjL4aHvvNPJK/eOD9wApxf2ZPLyCJtXIvLmTpgBSA+y+VcQOxMroDsPgnYxONascBQ6cb12qIQcAtYWuQ5Vg2BIplYr5uQ== YJS_chr10_p1in.txt (69.94M, 2023年04月27日 20:43 到期)进入下载页面：https://exmail.qq.com/cgi-bin/ftnExs_download?key=d64e7d6419253cc06267d51bd13409ef59336132&from=wedrive&t=exs_ftn_download&fid=*0*s4UCFE1C7Neo4Kvk7U3HnvKMX7LKpPXRFzHrcTIhrWhTaO6lp60I1gYSSSx3NWfb70MG9Y0HsKW5kDLR22j/ljTuASKioaOrxN01qwpCeUJuO9ClAbcR5IivwzjKUl8RJo1lEq03gJcal64ZVHVvGQ== YJS_chr10_p0in.txt (63.97M, 2023年04月27日 20:42 到期)进入下载页面：https://exmail.qq.com/cgi-bin/ftnExs_download?key=8249abc0ab39e339e50a94c8326ad11e00a45eac&from=wedrive&t=exs_ftn_download&fid=*0*68D7EHJSeaaKpZ6nb+jGq0GzTnkEE9KpooOFzRAmQDeHRTI9Jki8gBoszMw9f+2pK5+NwtodbzQdElgfcYMAae8rt5Tb3Ey0PpTLu4dYK7RvcGs2iD3Mh78rE0ZPY8jo8hk98p2qMhscIyI/RecV1w== YJS_chr10_map.txt (39.51M, 2023年04月27日 20:42 到期)进入下载页面：https://exmail.qq.com/cgi-bin/ftnExs_download?key=ae556147798ef3299df6013ef0d5ccf323f7f04d&from=wedrive&t=exs_ftn_download&fid=*0*Fy6XdyT5ulAfHSGUGFw+v4npQvrBHGOCZkIytTt7X6zNqnAe5o6enM13JB7QYta3NPUhqAyOguMvEqEFFLs2zZ7Da4Li+D9gSHrCO804dUSbJ5Ga9HEJsQih+Mu3p0ruhEX53NvFcA4R1BmZxvjvJw== YJS_chr10_loci.txt (18.42M, 2023年04月27日 20:41 到期)进入下载页面：https://exmail.qq.com/cgi-bin/ftnExs_download?key=e8c05bf40bed1817a25e454657306989e7630dea&from=wedrive&t=exs_ftn_download&fid=*0*idk+Y1Nv4LOB4xIK4zJ5mKROx9eAivFfD3Udb/L54d6BYYRd7ivyDGlqQNpDpOqTJsNaDWW4o9Hjtk9sjPdGBfXf6eTNlrHT94Le51PerCKNxtmi0gomsheIsQ3bwabSyIoRl+K0jy4rCY8qx1jDdw==

[lidanqi1990]

hi again. I can now run the program run_bgc.sh normally, and I am only using SNPs from one chromosome, approximately 1000000 of them, but it keeps stopping at "mcmc iteration: 0 ........ LnL: -9.80037e+06". Is this normal? Is there any way to make it faster?