Yes. They are UKBiobank files.
Chrs 1 (@ SNP rs560419601) & 3 (@ SNP rs60180210) bombed out. Running it on PROCARDIS server on 4 cores. Chrs 2, 4, 5 & 6 are ongoing at the moment.
Thanks.
Anuj.
-----Original Message-----
From: Oxford Statistical Genetics Software [mailto:[log in to unmask]] On Behalf Of Gavin Band
Sent: 24 February 2016 12:11
To: [log in to unmask]
Subject: Re: [OXSTATGEN] QCTool issue
Thanks, are these the UK biobank release bgen files, if so which chromosome did you see the error for?
Best,
g.
> On 24 Feb 2016, at 12:05, Anuj Goel <[log in to unmask]> wrote:
>
> Dear Gavin,
> Thanks for getting back.
> The command line is :
> qctool -filetype bgen -g ../chr$i\impv1.bgen -s ../impv1.sample
> -snp-stats chr$i.qctool.txt
>
> Best,
> Anuj.
>
>
> From: Oxford Statistical Genetics Software
> [mailto:[log in to unmask]] On Behalf Of Gavin Band
> Sent: 24 February 2016 12:01
> To: [log in to unmask]
> Subject: Re: [OXSTATGEN] QCTool issue
>
> Thanks Anuj, can you send me the command line you are running?
> Best,
> g.
>
> --------------------------------------------------------------
>
> Dr. Gavin Band
>
> Wellcome Trust Centre for Human Genetics University of Oxford
>
> +44 1865 287532
> [log in to unmask]
>
> --------------------------------------------------------------
>
> On 23 Feb 2016, at 13:01, Anuj Goel <[log in to unmask]> wrote:
>
> Hi,
> I am using your QCTOOL (qctool_v1.4-scientific-linux-x86_64.tgz on a Centos 5 unix server) to analyse the UK Biobank imputed genotype probabilities and I am running into unexpected error which is causing the program to abort. The software works for a bit (in the example below, it processes ~2.4M rows) and then falls over.
>
> The tail of the error log looks like:
> Sample filter: (none).
> SNP filter: (none).
>
> # of samples in input files: 152249.
> # of samples after filtering: 152249 (0 filtered out).
>
> ======================================================================
> ==
>
> Processing SNPs : [************* ] (2403502/5192419,306086.2s,7.9/s)qctool: ../genfile/include/genfile/bgen.hpp:307: void genfile::bgen::impl::read_compressed_snp_probability_data(std::istream&, genfile::bgen::impl::uint32_t, genfile::bgen::impl::uint32_t, GenotypeProbabilitySetter) [with GenotypeProbabilitySetter = genfile::GenotypeSetter<std::vector<double, std::allocator<double> > >]: Assertion `result == 0' failed.
> ./qctool.bash: line 4: 442 Aborted
>
> Any idea how to resolve this. I wonder if –force will proceed or fail too?
> Could it be an issue with any library (to do with scientific linux)? Probably it is.
> Initially, I installed this as the static build didn’t work on Centos 5 server.
>
> Many thanks.
> Kind regards,
> Anuj.
> PS: I also tried downloading the source code and compiling it. The “configure” worked but compilation failed. Log below:
>
> Yum install zlib gives the following message “Package
> zlib-1.2.3-7.el5.x86_64 already installed and latest version”
>
> [root@proce64 gavinband-qctool-c09253b994fb]# ./waf-1.5.18 configure
> Setting blddir to : /data/temp/qctool/gavinband-qctool-c09253b994fb/build
> Using prefix : /usr/local
> Checking for program g++ or c++ : /usr/bin/g++
> Checking for program cpp : /usr/bin/cpp
> Checking for program ar : /usr/bin/ar
> Checking for program ranlib : /usr/bin/ranlib
> Checking for g++ : ok
> Checking for program gcc or cc : /usr/bin/gcc
> Checking for gcc : ok
> Checking for library blas : no
> Checking for library lapack : not found
> Checking for header sys/time.h : yes
> Checking for static library z : yes
> Checking for library dl : yes
> Checking for library rt : yes
> Checking for library m : yes
> Checking for library bz2 : not found
> Checking for library mgl : not found
> Checking for library cairo : yes
> Checking for library pthread : yes
> Checking for library readline : not found
> 'configure' finished successfully (3.262s)
>
> [root@proce64 gavinband-qctool-c09253b994fb]# ./waf-1.5.18
> Waf: Entering directory `/data/temp/qctool/gavinband-qctool-c09253b994fb/build'
> [ 1/810] qctool_version_autogenerated: ->
> build/default/qctool_version_autogenerated.hpp
> /bin/sh: line 6: hg: command not found [ 2/810]
> qctool_version_autogenerated: ->
> build/release/qctool_version_autogenerated.hpp
> /bin/sh: line 6: hg: command not found [ 3/810] cc:
> 3rd_party/sqlite3/sqlite3/shell.c ->
> build/default/3rd_party/sqlite3/sqlite3/shell_3.o
> [ 4/810] cc: 3rd_party/sqlite3/sqlite3/sqlite3.c ->
> build/default/3rd_party/sqlite3/sqlite3/sqlite3_3.o
> [ 5/810] cc: 3rd_party/sqlite3/extensions/extension-functions.c ->
> build/default/3rd_party/sqlite3/extensions/extension-functions_3.o
> [ 6/810] cc: 3rd_party/sqlite3/sqlite3/sqlite3.c ->
> build/default/3rd_party/sqlite3/sqlite3/sqlite3_4.o
> [ 7/810] cc: 3rd_party/sqlite3/sqlite3/shell.c ->
> build/release/3rd_party/sqlite3/sqlite3/shell_3.o
> [ 8/810] cc: 3rd_party/sqlite3/sqlite3/sqlite3.c ->
> build/release/3rd_party/sqlite3/sqlite3/sqlite3_3.o
> [ 9/810] cc: 3rd_party/sqlite3/extensions/extension-functions.c ->
> build/release/3rd_party/sqlite3/extensions/extension-functions_3.o
> [ 10/810] cc: 3rd_party/sqlite3/sqlite3/sqlite3.c ->
> build/release/3rd_party/sqlite3/sqlite3/sqlite3_4.o
> [ 11/810] cxx: genfile/src/PennCNVSNPDataSink.cpp ->
> build/default/genfile/src/PennCNVSNPDataSink_1.o
> cc1plus: error: unrecognized command line option "-Wno-redeclared-class-member"
> cc1plus: error: unrecognized command line option "-Wno-unused-local-typedef"
> Waf: Leaving directory `/data/temp/qctool/gavinband-qctool-c09253b994fb/build'
> Build failed: -> task failed (err #1):
> {task: cxx PennCNVSNPDataSink.cpp -> PennCNVSNPDataSink_1.o}
>
>
> ---
> Bioinformatician
> PROCARDIS Group
> Cardiovascular Medicine, University of Oxford Wellcome Trust Centre
> for Human Genetics Roosevelt Drive, Oxford
> OX3 7BN
> Tel: +44-(0)-1865-287679
> http://www.well.ox.ac.uk/anuj-goel
>
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