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RabadanLab / TOBI

TOBI predicts somatic variants from .vcf or .bam input
MIT License
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Error running annotation step #2

Open qtrinh opened 8 years ago

qtrinh commented 8 years ago

Hi, I am trying out TOBI but get the following error on the annotation step. Could someone please tell me how to get around this error?

Thanks

TOBIvaf.py --inputdir input/vcf --output output --steps A --ref $REF --cluster hpc --snpeff $SNPEFF --dbnsfp $dbNSFP Exception in thread Thread-1: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(_self.args, *_self.__kwargs) File "/.mounts/labs/public/softwares/TOBI-master/TOBIvaf.py", line 195, in annotate args.annovcf = args.annovcf.replace("\n","") AttributeError: 'NoneType' object has no attribute 'replace'

Exception in thread Thread-2: Traceback (most recent call last): File "/usr/lib/python2.7/threading.py", line 810, in bootstrap_inner self.run() File "/usr/lib/python2.7/threading.py", line 763, in run self.__target(_self.args, *_self.__kwargs) File "/.mounts/labs/public/softwares/TOBI-master/TOBIvaf.py", line 195, in annotate args.annovcf = args.annovcf.replace("\n","") AttributeError: 'NoneType' object has no attribute 'replace'

cjmadubata commented 8 years ago

Hello, This error suggests that no annotating VCFs were supplied to TOBI in the config file. A set of annotating VCFs is required to run TOBI, as stated in the readme and demonstrated in the example config file.

Please try pulling the latest version of TOBI, then running it using annotating VCFs such as COSMIC's VCF Files for coding mutations (found at http://grch37-cancer.sanger.ac.uk/cosmic/download via SFTP Download: /files/grch37/cosmic/v77/VCF/CosmicCodingMuts.vcf.gz).

If you continue having errors, please include the error message, command, and config file in your message to us.