I am continuously getting an error with Platypus, the SNP and variant caller. The install and build appear to have worked properly and I receive no error messages when passing those commands. 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.
Which python version? Does the test data work?