phase_common_static：ERROR: Opening [1Z.vcf]: unknown error

[yangwukaidi]

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)

• Author : Olivier DELANEAU, University of Lausanne
• Contact : olivier.delaneau@gmail.com
• Version : 5.1.0 / commit = 492781e / release = 2023-04-13
• Run date : 15/05/2023 - 14:17:53 Files:
• Input : [1Z.vcf]
• Output : [shapeitphase_1Z.vcf]
• Output format : [bcf] Parameters:
• Seed : 15052011
• Threads : 6 threads
• MCMC : 15 iterations [5b + 1p + 1b + 1p + 1b + 1p + 5m]
• PBWT : [window = 4cM / depth = auto / modulo = auto / mac = 5 / missing = 0.1]
• HMM : [window = 4cM / Ne = 15000 / Constant recombination rate of 1cM per Mb] Reading genotype data: [E::hts_open_format] Failed to open file "1Z.vcf" : No such file or directory ERROR: Opening [1Z.vcf]: unknown error

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!

[odelaneau]

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.

[selasphoruskershaw]

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.

[odelaneau]

By default, containers cannot see the file system of their host.

Please read about docker or use static binaries.