Question: Platypus variantcaller.c:16971 errpr
0
gravatar for nuketbilgen
6 months ago by
nuketbilgen30
United Kingdom
nuketbilgen30 wrote:

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
ADD COMMENTlink modified 6 months ago by ATpoint21k • written 6 months ago by nuketbilgen30
1

Did you try to install it via conda?

ADD REPLYlink written 6 months ago by ATpoint21k

I installed it via conda now. But I don't know how to run it cause I can not locate Platypus.py file.

ADD REPLYlink written 6 months ago by nuketbilgen30

Just look around in the $HOME/anaconda3/bin folder like ls *platyp* *Platyp*. The binary should not be too difficult to find and will also be in PATH by default.

ADD REPLYlink written 6 months ago by ATpoint21k

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?

ADD REPLYlink written 6 months ago by nuketbilgen30

No, I think not. Just activate that envir and you should be good to go.

ADD REPLYlink modified 6 months ago • written 6 months ago by ATpoint21k

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

ADD REPLYlink written 6 months ago by nuketbilgen30
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