Closed yangwukaidi closed 1 year ago
Right-hand side of the GitHub page, there's the "release" panel. You'll find there precompiled static binaries. Try using them instead of the docker. That might be easier.
Hello,
I am getting the same error as the original poster. My unphased vcf is in the current directory, but shapeit is saying it's not there: ERROR: Opening [NC_053450.1.vcf.gz]: unknown error [E::hts_open_format] Failed to open file "NC_053450.1.vcf.gz" : No such file or directory
I am using the following command: docker run shapeit5_2023-05-05_d6ce1e2 phase_common_static --input NC_053450.1.vcf.gz --region NC_053450.1 -O NC_053450.1.phased
I have been unable to compile from source or to use the precompiled static binaries.
Please help, thank you.
By default, containers cannot see the file system of their host.
Please read about docker or use static binaries.
hi,dear Delaneau. Sorry to bother you, I have a problem with phase_common that bothers me. as follows:
[root@localhost LD-Decay]# docker run shapeit5_2023-03-23_a4a1818 phase_common_static -I 1Z.vcf -R 1 -O shapeitphase_1Z.vcf --thread 6 [SHAPEIT5] phase_common (jointly phase multiple common markers)
I'm pretty sure 1Z.vcf is in the current running directory. But these errors still occur. I still have this problem when I try to add absolute paths. How can I solve this problem? Looking forward to your reply!