I am running GATK HAPLOTYPECALLER both with snakemake and as a command line on my Ubuntu 16.04 version, gatk-4.1.9.0 version:
Tools/gatk/gatk --java-options "-Xmx16g -XX:ParallelGCThreads=10"
HaplotypeCaller -R ref.fasta -I recal.bam -O outfile.vcf
--min-base-quality-score 20 --minimum-mapping-quality 20 -pairHMM AVX_LOGLESS_CACHING_OMP
This continues giving me the following error and I cannot find a solution for some days now...Any ideas how to solve this?
A USER ERROR has occurred: Machine does not support OpenMP AVX
PairHMM.
*********************************************************************** org.broadinstitute.hellbender.exceptions.UserException$HardwareFeatureException:
Machine does not support OpenMP AVX PairHMM.
at org.broadinstitute.hellbender.utils.pairhmm.VectorLoglessPairHMM.(VectorLoglessPairHMM.java:77)
at org.broadinstitute.hellbender.utils.pairhmm.PairHMM$Implementation.lambda$static$4(PairHMM.java:63)
at org.broadinstitute.hellbender.utils.pairhmm.PairHMM$Implementation.makeNewHMM(PairHMM.java:119)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.(PairHMMLikelihoodCalculationEngine.java:152)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyBasedCallerUtils.createLikelihoodCalculationEngine(AssemblyBasedCallerUtils.java:204)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.initialize(HaplotypeCallerEngine.java:243)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.(HaplotypeCallerEngine.java:186)
at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.onTraversalStart(HaplotypeCaller.java:259)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1055)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
at org.broadinstitute.hellbender.Main.main(Main.java:289)
EDIT: On both other PC's that have UBUNTU v.18.04 this is working, is this something correlated to ubuntu version?
EDIT: I cannot install anything on that PC as I do not have root permission. But I can install using conda.
Related
I'm trying to install Gtk2 from CPAN on my Mac (Big Sur), but it requires Glib, and Glib install is failing. The tail of the installer output is here:
echo Generating POD...
Generating POD...
"/usr/bin/perl" -I blib/lib -I blib/arch -MGlib::GenPod -MGlib \
-e "add_types (qq(doctypes)); Glib::GenPod::set_copyright(qq/Copyright (C) 2003-2011 by the gtk2-perl team.\n\nThis software is licensed under the LGPL. See L<Glib> for a full notice.\n/); Glib::GenPod::set_main_mod(qq(Glib)); xsdoc2pod(q(build/doc.pl), q(blib/lib), q(build/podindex));"
Can't load 'blib/arch/auto/Glib/Glib.bundle' for module Glib: dlopen(blib/arch/auto/Glib/Glib.bundle, 0x0001): open("", O_RDONLY) failed with errno=2 at /System/Library/Perl/5.30/darwin-thread-multi-2level/DynaLoader.pm line 197.
at blib/lib/Glib/GenPod.pm line 21.
Compilation failed in require at blib/lib/Glib/GenPod.pm line 21.
BEGIN failed--compilation aborted at blib/lib/Glib/GenPod.pm line 21.
Compilation failed in require.
BEGIN failed--compilation aborted.
make: *** [build/podindex] Error 2
FAIL
! Installing Glib failed. See /Users/principal/.cpanm/work/1626461722.68580/build.log for details. Retry with --force to force install it.
Retry with --force gives the same results. The specified build.log file gives less detail than the console output above.
If I understand what it's telling me, it is that the GenPod.m module fails at the point where it is trying to "use Glib;". But when I look at the specified search point (blib/arch/auto/Glib/Glib.bundle) there is such a file there.
I'm using the Mac-installed Perl (5.30) and have had no other issues installing via CPAN. Any help would be appreciated. I would even welcome knowing how to bypass the "GenPod" step, as having working code is better than having documentation. The latest post I could find on the topic of Glib failing to install on Mac was four years ago in the El Capitan days, and the OP there was having an entirely different problem.
I am trying to install the ScaLAPACK with the help of Python-based installer available at http://www.netlib.org/scalapack/scalapack_installer.tgz on CentOS 7(64bit). It is installing successfully but failing in test routines step and showing the error. how to fix it?
The command used for the compilation is as follows:
./setup.py --prefix=/home/tools/scalapack --blaslib="-L/usr/lib64 -lblas" --lapacklib="-L/usr/lib64 -llapack -lblas" --mpiincdir=/opt/apps/mpich32/include --fcflags="-fbounds-check" --mpirun=mpirun --mpicc=mpicc --mpif90=mpif90
The process description is as follows
Installing scalapack-2.0.2 ...
Writing SLmake.inc... done.
Compiling BLACS, PBLAS and ScaLAPACK... done
Getting ScaLAPACK version number... 2.0.1
Installation of ScaLAPACK successful.
(log is in /home/tools/scalapack_installer/build/log/scalog )
Compiling test routines... done
Running BLACS test routines... done
Running PBLAS test routines...
PBLAS: error running PBLAS test routines xcpblas2tst
PBLAS: Command mpirun -np 4 ./xcpblas2tst
stderr:
****************************************
At line 1 of file ctzpad.f
Fortran runtime error: Actual string length is shorter than the declared one for dummy argument 'herm' (-960965440/1)
I am using ptxdist to create kernel and rootfs images for a Linux embedded system, running on an ARM Cortex A8 CPU.
I was trying to use a newer compiler (GCC 5+) and so was forced to upgrade several external packages that would not compile under the new GCC.
I compiled the following versions of Upstart and its immediate dependencies:
upstart: 1.13.2
libnih: 1.0.3
dbus: 1.11.2
json-c: 0.12.1
When I boot, I get the following message:
init: com.ubuntu.Upstart.c:3525: Assertion failed in control_emit_event_emitted: env != NULL
init: Caught abort, core dumped
Kernel panic - not syncing: Attempted to kill init! exitcode=0x00000600
Searching online did not yield useful hints - the only relevant issue I found is this, but it is relevant to an older version of Upstart, and my libnih is of the correct version already.
According to comment #8 in the bug report you linked, it is not enough to use version 1.0.3 of libnih -- you have to specifically use the Ubuntu version, as this seems to include dbus fixes which could solve the problem you are seeing. From the bug report:
David Ireland (e-david) wrote on 2013-04-22: #7
I've built libnih
1.0.3 from source and also made sure that upstart builds with that version of the nih-dbus-tool. I'm still having this problem.
James Hunt (jamesodhunt) wrote on 2013-04-22: #8
Which problem? The
crash? If so, you are still using the wrong version of libnih: you
should be using the Ubuntu version (specifically 1.0.3-4ubuntu16) from
here:
https://code.launchpad.net/~ubuntu-branches/ubuntu/raring/libnih/raring
You do not need the --session flag to run a "Session Init" (yes, this
is a little confusing but --session was added for testing a long time
ago and is still required for that). A "Session Init" only requires
"--user".
I need help compiling nginx with the perl_module on my Mac:
System Software Overview:
System Version: OS X 10.11.1 (15B42)
Kernel Version: Darwin 15.0.0
Boot Volume: Macintosh HD
Boot Mode: Normal
Computer Name: Philipp
User Name: XXXXXXX XXXXXXXX (philipp)
Secure Virtual Memory: Enabled
Time since boot: 4 days 22:46
I configure nginx to be compiled with PCRE and PERL, i.e.,:
./configure --with-pcre=/Users/philipp/downloads/pcre-8.38 --with-http_perl_module --prefix=/servers/nginx
The output of the configure states:
checking for perl
+ perl version: This is perl 5, version 18, subversion 2 (v5.18.2)
built for darwin-thread-multi-2level
+ perl interpreter multiplicity found
If I execute make I run into the following error:
ld: symbol(s) not found for architecture i386
clang: error: linker command failed with exit code 1 (use -v to see invocation)
I googled and found a hint to export KERNEL_BITS=64, which did not solve the problem. Any suggestions on how to compile nginx with perl. The compilation succeeds without the --with-http_perl_module option, but in that case I cannot use perl in the nginx.conf (of course :)).
UPDATE:
I was not able to compile nginx with perl. I ended up using a pre-compiled package, which is kind of unsatisfying, because now I have to deal with a lot of packages I don't like. Anyways, if someone has a solution I'd be more than happy to know.
I'm not sure if this is offtopic or not, but as it's about using perl within nginx (which I do, and is awesome).
I had a similar problem when trying to build this module. The root of it was that I hadn't got the right LD flags.
The easiest way of doing this - IMO - is install nginx from a package, run nginx -V and see what flags were used - copy them all, and include the extras. (And check it wasn't already build in your distribution - it was in mine, which I think was a Centos 7.2 package - I don't have it to hand, but I'm not sure it would necessarily help)
You may also need to install a new perl version, to go with it though.
--with-pcre=../modules/pcre-8.38
--with-openssl=../modules/openssl-1.0.2g
--prefix=/usr/local/nginx
--with-http_perl_module
--with-http_ssl_module
--with-http_addition_module
--with-http_sub_module
--with-http_realip_module
--with-http_stub_status_module
--with-cc-opt='-I /usr/local/include'
--with-ld-opt='-L /usr/local/lib -L/usr/local/opt/perl518/lib'
I got the same problem. after about 3 hours digging with this, finally solved. This is my configure file, i installed perl518 with brew located in /usr/local/opt/perl518/lib, and use the newest nginx source code of version nginx version: nginx/1.10.0.
Things seems happend as #Sobrique said, you need to give the right --with-ld-opt & --with-cc-opt.
important, after ./configure, DO NOT doing make immediately, vi ./objs/Makefile and modify openssl config from './config' to './Configure darwin-x86_64-cc' so that it can build openssl in x86_64 mod.
Hope it can help you!
When I install Wordnet::Similarity on mac, the following error occur:
usr/local/bin/perl "-Iblib/arch" "-Iblib/lib" build/Depthfiles.PL blib/lib/WordNet/synsetdepths.dat
Generating default depth files.
Can't load '/usr/local/lib/perl5/site_perl/5.8.8/darwin-2level/auto/Digest/SHA1/SHA1.bundle' for module Digest::SHA1: dlopen(/usr/local/lib/perl5/site_perl/5.8.8/darwin-2level/auto/Digest/SHA1/SHA1.bundle, 1): no suitable image found. Did find:
/usr/local/lib/perl5/site_perl/5.8.8/darwin-2level/auto/Digest/SHA1/SHA1.bundle: mach-o, but wrong architecture at /usr/local/lib/perl5/5.8.8/darwin-2level/DynaLoader.pm line 230.
at blib/lib/WordNet/Tools.pm line 76
Compilation failed in require at blib/lib/WordNet/Tools.pm line 76.
My attempt was to enter to the downloaded package directory from terminal and type:
perl Makefile.PL
make
make test
sudo make install
I made sure to have installed all prerequisite http://search.cpan.org/dist/WordNet-Similarity/doc/install.pod#Prerequisites. I suspect that this may be due to mac processor version with Perl interface. Any suggestion on how to fix this?
Install libdigest-sha-perl in Ubuntu 14.04 has solved this issue.
Download link:http://packages.ubuntu.com/trusty/amd64/perl/libdigest-sha-perl