humanpaingeneticslab
commented
2 years ago The "core dumped" was due to usage of data grabbed using: git clone https://github.com/comorment/containers.git
One has to enable this first, before the "git clone ...": git lfs install
Program seems to work, despite missing entries in the libbgmg.so file \o/
Hello,
trying to run mixer; I get a nice message :-(
Call: ./mixer.py fit1 \ --out SSGAC_EDU_2018_no23andMe_noMHC.fit.rep1 \ --lib /home/GENOME/mixer/src/build/lib/libbgmg.so \ --bim-file /scratch/GENOME/containers/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.bim \ --ld-file /scratch/GENOME/containers/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.@.run4.ld \ --trait1-file SSGAC_EDU_2018_no23andMe_noMHC.csv.gz \ --extract /scratch/GENOME/containers/reference/ldsc/1000G_EUR_Phase3_plink/1000G.EUR.QC.prune_maf0p05_rand2M_r2p8.rep1.snps ) INFO:root:init(lib_name=/home/GENOME/mixer/src/build/lib/libbgmg.so, context_id=0) terminate called after throwing an instance of 'std::invalid_argument' terminate called recursively Aborted (core dumped)
OK, what's inside that libbgmg.so file?
$ ldd /home/GENOME/mixer/src/build/lib/libbgmg.so linux-vdso.so.1 (0x00007ffe02f84000) libboost_filesystem.so.1.69.0 => /home/GENOME/boost_1_69_0/stage/lib/libboost_filesystem.so.1.69.0 (0x00007fc97688f000) libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00007fc976694000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007fc976545000) libgomp.so.1 => /lib/x86_64-linux-gnu/libgomp.so.1 (0x00007fc976503000) libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fc9764e8000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fc9764c3000) libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fc9762d1000) /lib64/ld-linux-x86-64.so.2 (0x00007fc9769fa000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fc9762cb000)
So, where are these files? They're not in libbgmg.so?? libboost_date_time.so libboost_system.so libboost_program_options.so
Any help appreciated!