Errors got at callVariants step

[NGSA]

Dear All,

I am trying to use Platypus for my research purpose. I want to do variant call for my HLA data. Ones I used the command like

python Platypus.py callVariants --bamFiles=NVP000006abcr_S1_aligned_hla_gene.bam.sorted --refFile=hla_gen.fasta --output=NVP000006abcr_S1.vcf --logFileName=Platypus_log.txt

I got the following error:

2018-01-08 15:28:53,873 - INFO - Beginning variant calling
2018-01-08 15:28:53,873 - INFO - Output will go to NVP000006abcr_S1.vcf
Traceback (most recent call last):
  File "/data/ngs/programs/Platypus/bin/Platypus.py", line 46, in <module>
    possCommands[command](sys.argv[2:])
  File "/data/ngs/programs/Platypus/bin/runner.py", line 600, in callVariants
    runVariantCaller(options)
  File "/data/ngs/programs/Platypus/bin/runner.py", line 454, in runVariantCaller
    regions = sorted(platypusutils.getRegions(options), cmp=regionSort)
  File "cython/platypusutils.pyx", line 957, in platypusutils.getRegions (cython/platypusutils.c:14521)
  File "cython/platypusutils.pyx", line 88, in platypusutils.isIndexable (cython/platypusutils.c:2697)
AttributeError: 'NoneType' object has no attribute 'lower'


Could you please help me to solve the error, so that I could run Platypus successfully for my research purpose?

Thanking you in advance.

[Bobbie Shaban]

Hi, was there an answer found for this? I am having the same issue

[bobbieshaban@spartan-snowy032 test]$  python /data/cephfs/punim0256/progs/platypus/bin/Platypus.py callVariants --nCPU=32 --bamFiles=opossum.outputAligned.aligned.sorted --refFile=/data/cephfs/punim0256/irene/opossum/chim_ref/chimpanzee.fa_removec.txt_removed.fa --output=test.output.output.vcf

2018-12-05 13:10:28,775 - INFO - Beginning variant calling

2018-12-05 13:10:28,776 - INFO - Output will go to test.output.output.vcf

Traceback (most recent call last):

  File "/data/cephfs/punim0256/progs/platypus/bin/Platypus.py", line 46, in <module>

    possCommands[command](sys.argv[2:])

  File "/data/cephfs/punim0256/progs/platypus/bin/runner.py", line 600, in callVariants

    runVariantCaller(options)

  File "/data/cephfs/punim0256/progs/platypus/bin/runner.py", line 454, in runVariantCaller

    regions = sorted(platypusutils.getRegions(options), cmp=regionSort)

  File "cython/platypusutils.pyx", line 957, in platypusutils.getRegions

  File "cython/platypusutils.pyx", line 88, in platypusutils.isIndexable

AttributeError: 'NoneType' object has no attribute 'lower'