Question: Platypus callVariants error
gravatar for tanya.copley
3.2 years ago by
tanya.copley10 wrote:

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 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.

ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 3.2 years ago by tanya.copley10

Which python version? Does the test data work?

ADD REPLYlink written 3.2 years ago by WouterDeCoster42k
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