Platypus installation difficulty

Question

[RCG]

I am trying to install Platypus (next-gen sequencing variant caller), and following the instructions on the website (http://www.well.ox.ac.uk/platypus). I get the following error messages. I'm sure this is basic but any help would be much appreciated. Thanks.

./buildPlatypus.sh
Building Platypus
running build
running build_py
copying pyvcf/__init__.py -> build/lib/pyvcf
copying pyvcf/axt2variants.py -> build/lib/pyvcf
copying pyvcf/bam-naive-caller.py -> build/lib/pyvcf
copying pyvcf/filez.py -> build/lib/pyvcf
copying pyvcf/vcf-add-ac.py -> build/lib/pyvcf
copying pyvcf/vcf-add-hr.py -> build/lib/pyvcf
copying pyvcf/vcf-add-labels.py -> build/lib/pyvcf
copying pyvcf/vcf-compare.py -> build/lib/pyvcf
copying pyvcf/vcf-concordance.py -> build/lib/pyvcf
copying pyvcf/vcf-diff.py -> build/lib/pyvcf
copying pyvcf/vcf-extract.py -> build/lib/pyvcf
copying pyvcf/vcf-indel-polarize.py -> build/lib/pyvcf
copying pyvcf/vcf-mendelian.py -> build/lib/pyvcf
copying pyvcf/vcf.py -> build/lib/pyvcf
running build
running build_py
copying extendedoptparse.py -> build/lib
running build
running build_py
copying window.py -> build/lib
running build
running build_py
copying variantutils.py -> build/lib
running build
running build_py
copying platypusexceptions.py -> build/lib
running build
running build_py
running build
running build_py
copying filez.py -> build/lib
running build
running build_py
copying runner.py -> build/lib
running build
running build_ext
building 'ctabix' extension
cc -fno-strict-aliasing -fno-common -dynamic -arch x86_64 -arch i386 -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -mno-fused-madd -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch x86_64 -arch i386 -pipe -Itabix -Ipysam -I/System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7 -c ctabix.c -o build/temp.macosx-10.9-intel-2.7/ctabix.o
clang: error: unknown argument: '-mno-fused-madd' [-Wunused-command-line-argument-hard-error-in-future]
clang: note: this will be a hard error (cannot be downgraded to a warning) in the future
error: command 'cc' failed with exit status 1


Finished building Platypus

python Platypus.py callVariants --help
Traceback (most recent call last):
  File "Platypus.py", line 7, in <module>
    import runner
  File "/Users/rgrant/Desktop/NGS_Tools/Platypus_0.7.2/runner.py", line 10, in <module>
    import variantcaller

[Phil S.]

check this out!

Answer 1

[tanya.copley]

I have the same problem, however the install and build appear to have worked properly. I get the error after trying to run callVariants:

python Platypus.py callVariants --bamFiles=/home/whatsaname/script_test/aligned/FC20111007_trimmed_RG_sorted.bam --refFile=/home/whatsaname/gbs/Gmax_ref_genome/Gma1.01.20140304.fasta --output=/home/whatsaname/script_test/Playtupus_test.vcf 2016-10-25 11:12:48,182 - INFO - Beginning variant calling 2016-10-25 11:12:48,183 - INFO - Output will go to /home/whatsaname/script_test/Playtupus_test.vcf 2016-10-25 11:12:48,256 - INFO - Processing region Gm01:0-100000. (Only printing this message every 10 regions of size 100000) Segmentation fault (core dumped)

Has anyone figured out how to fix this issue? I have spoken with a few colleagues who all get the same error.