1 year ago
#77573
Rhea Bedi
how to convert imputed dosage files to plink format files
I am trying to convert imputed dosage file from michigan imputation server to plink files. For this purpuse I am using a tool called dosageconvertor. I tried to install it using the commands:
> git clone https://github.com/Santy-8128/DosageConvertor cd
> DosageConverter pip install cget --user module load
> cmake-3.8.1-gcc-4.8.5-zz55m7x ./install.sh
But I am getting error:
-- Build files have been written to: /home/scratch/TWAS/data_download/new_rna-seq/quality_Control/qc_vcf_impute/DosageConvertor/release-build Building ... make: Warning: File 'Makefile' has modification time 3675 s in the future make[1]: Warning: File 'CMakeFiles/Makefile2' has modification time 3675 s in the future make[2]: Warning: File 'CMakeFiles/DosageConvertor.dir/flags.make' has modification time 3675 s in the future Scanning dependencies of target DosageConvertor make[2]: warning: Clock skew detected. Your build may be incomplete. make[2]: Warning: File 'CMakeFiles/DosageConvertor.dir/flags.make' has modification time 3675 s in the future [ 33%] Building CXX object CMakeFiles/DosageConvertor.dir/src/HaplotypeSet.cpp.o [ 66%] Building CXX object CMakeFiles/DosageConvertor.dir/src/Main.cpp.o [100%] Linking CXX executable DosageConvertor /home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/miniconda3/envs/train/lib/libz.so: undefined reference to
memcpy@GLIBC_2.14' /home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/miniconda3/envs/train/lib/libstdc++.so: undefined reference to
aligned_alloc@GLIBC_2.16' /home/miniconda3/envs/train/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: /home/miniconda3/envs/train/lib/libstdc++.so: undefined reference to `clock_gettime@GLIBC_2.17' collect2: error: ld returned 1 exit status make[2]: *** [CMakeFiles/DosageConvertor.dir/build.make:101: DosageConvertor] Error 1 make[1]: *** [CMakeFiles/Makefile2:73: CMakeFiles/DosageConvertor.dir/all] Error 2 make: *** [Makefile:130: all] Error 2
Can anyone help me out with this? My main purpose is to convert the dose.vcf.gz file to vcf format or plink format files.
linux
installation
bioinformatics
genetics
vcf-variant-call-format
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