gaow / SEQPower

Power Analysis and Sample Size Estimation Software for Sequence Based Association Studies
GNU General Public License v2.0
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Issues in running on MacOS [HDF5]: Reopening the issue #10

Open kvshams opened 6 years ago

kvshams commented 6 years ago

I have installed the spower and working fine with sfs file and generating simulations. But when I download the .gdat file from http://bioinformatics.org/spower/download/data/SRV/, I am getting a 5DF5 error.


 spower -h
usage: spower [-h] [--version]
              {simulate,LOGIT,PAR,BLNR,LNR,ELNR,show,execute} ...

SEQPower, Power Analysis and Sample Size Estimation Software for Sequence
Based Association Studies

positional arguments:
  {simulate,LOGIT,PAR,BLNR,LNR,ELNR,show,execute}
    simulate            Simulate DNA sequences
    LOGIT               Case control data, penetrance model
    PAR                 Case control data, population attributable risk model
    BLNR                Case control data, quantitative trait loci model
    LNR                 Quantitative trait data
    ELNR                Extreme quantitative trait data
    show                Display various information
    execute             Execute a parameter configuration file

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

Copyright (c) 2013 Gao Wang <gaow@bcm.edu> under GNU General Public License |
http://bioinformatics.org/spower

Seems the docker is working fine. But when running an actual command, I am getting the same error as above

``INFO: Loading data from [Kryukov2009European1800Rep500.gdat] ... ERROR: HDF5 error back trace

File "H5F.c", line 586, in H5Fopen unable to open file File "H5Fint.c", line 1384, in H5F_open unable to read superblock File "H5Fsuper.c", line 360, in H5F__super_read file signature not found

End of HDF5 error backtrace

Unable to open/create file 'Kryukov2009European1800Rep500.gdat'

spower LOGIT KIT.gdat -a 1.5 --sample_size 2000 --alpha 0.05 -v2 -o K1AP --method CFisher Calpha --permutations 1000 BurdenBt KBAC --permutations 1000 WSSRankTest --permutations 1000 VTtest --permutations 1000 -r 100 -j8 INFO: Loading data from [KIT.gdat] ... ERROR: HDF5 error back trace

File "H5F.c", line 586, in H5Fopen unable to open file File "H5Fint.c", line 1384, in H5F_open unable to read superblock File "H5Fsuper.c", line 360, in H5F__super_read file signature not found

End of HDF5 error back trace

Unable to open/create file 'KIT.gdat'