Entering edit mode
5.2 years ago
nuketbilgen
▴
40
Hi everyone. I am trying to use Platypus for variant calling. Even though I have tried everything I could to fix it (moved htslib to usr/local, exported paths to it) I always got the following error. I deleted and reinstalled platypus and htslib as well. Could you help me, please?
python Platypus.py callVariants --nCPU=3 --bamFiles=/home/nuketbilgen/kedigenom/fel9allignedminnos/minnos_felcat9aligned.bam --refFile=/home/nuketbilgen/feliscatus9/felCat9.fa output=/home/nuketbilgen/kedigenom/fel9allignedminnos/minnos9avariantcalls.vcf
Traceback (most recent call last):
File "Platypus.py", line 9, in <module>
import runner
File "/home/nuketbilgen/Platypus_0.8.1/runner.py", line 9, in <module>
import variantcaller
File "htslibWrapper.pxd", line 203, in init variantcaller (variantcaller.c:16971)
ImportError: libhts.so.2: cannot open shared object file: No such file or directory
Did you try to install it via conda?
I installed it via conda now. But I don't know how to run it cause I can not locate Platypus.py file.
Just look around in the
$HOME/anaconda3/binfolder likels *platyp* *Platyp*. The binary should not be too difficult to find and will also be inPATHby default.I can find it in /home/nuketbilgen/anaconda3/envs/my_env/bin/platypus as a link to program. Is it a problem that I have installed it into my_env?
No, I think not. Just activate that envir and you should be good to go.
As you have said, it is working. but now I get this error.
print "\n\n%s command is not yet implemented\n\n" %(x) ^ SyntaxError: invalid syntax
I have the same problem... where you able to solve?