AttributeError: 'pysam.csamtools.Fastafile' object has no attribute 'references'

[Vipul Jain]

Hi,

I have installed CAVA on my system and tried to used it but not getting desired result. Find below command I used and its output.

vipul@vipul-Linux:/media/

vipul/DATA/databases/CAVA/cava-v1.1.1$ python cava.py -c config.txt -i DGL_162_15120182_TSVC_variants.vcf -o output
-----------------------------------------------------------------------
CAVA (Clinical Annotation of VAriants) v1.1.1 is now running.
Started:  2016-01-11 10:50:06.475001

Configuration file:  config.txt
Input file (VCF):    DGL_162_15120182_TSVC_variants.vcf
Output file (VCF):   output.vcf
Log file:            output.log

Input file contains 1977 records to annotate.

Annotating variants ... 0.0%Process SingleJob-1:
Traceback (most recent call last):
  File "/usr/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "cava.py", line 245, in run
    record.annotate(self.ensembl,self.dbsnp,self.reference,self.impactdir)
  File "/media/vipul/DATA/databases/CAVA/cava-v1.1.1/basics.py", line 255, in annotate
    variant.annotate(ensembl,dbsnp,reference,impactdir)
  File "/media/vipul/DATA/databases/CAVA/cava-v1.1.1/basics.py", line 88, in annotate
    if not ensembl is None: self=ensembl.annotate(self,reference,impactdir)
  File "/media/vipul/DATA/databases/CAVA/cava-v1.1.1/data.py", line 292, in annotate
    protein,exonseqs=transcript.getProteinSequence(reference,None,None)
  File "/media/vipul/DATA/databases/CAVA/cava-v1.1.1/basics.py", line 459, in getProteinSequence
    codingsequence,exonseqa=self.getCodingSequence(reference,variant,exonseqs)
  File "/media/vipul/DATA/databases/CAVA/cava-v1.1.1/basics.py", line 436, in getCodingSequence
    exonseq=reference.getReference(self.chrom,exon.start+1,exon.end)
  File "/media/vipul/DATA/databases/CAVA/cava-v1.1.1/data.py", line 501, in getReference
    if not goodchrom in self.fastafile.references:
AttributeError: 'pysam.csamtools.Fastafile' object has no attribute 'references'

(Size of output file: 12.3 Kbyte)

CAVA (Clinical Annotation of VAriants) successfully finished.
Ended:  2016-01-11 10:50:06.494502
-----------------------------------------------------------------------

[Márton Münz]

Hi Vipul,

Looking at this error, my first guess is that you might use an old Pysam package not supported by CAVA.

Could you please check which version of Pysam do you have installed in your system?

Thanks!

Márton

[Márton Münz]

Hi,

As we have now also discussed in email, the minimal requirement for CAVA is Pysam version 0.7.7, so you need to update the 0.7.5 Pysam installation you are using. 

Best,

Marton