load-vcf error

[Neeba Dijo]

Hi

I created project using the following command

./pseq /users/nsebastian/Data/CGI/test/test-project new-project --vcf /users/nsebastian/Data/CGI/zipped/*.vcf.gz --resources /users/nsebastian/Data/CGI/test/hg19/ --scratch /users/nsebastian/Data/CGI/test/scratch/

  and started loading  vcf file with the  test-project load-vcf


but after loading some file the process stops

loading : /users/nsebastian/Data/CGI/zipped/vcfBeta-NA06985-200-37-ASM.vcf.gz ( 1 individuals )
parsed 9690000 rows
loading : /users/nsebastian/Data/CGI/zipped/vcfBeta-NA06994-200-37-ASM.vcf.gz ( 1 individuals )
Killed 1441000 rows

Can you please help me to overcome this error and for  loading  file


Thanks
Neeba

[Neeba Dijo]

Hi

And I am trying to load again the files showing the following error message


pseq error : database (/store/cgi/project/cgi-project_out/vardb) error (11) database disk image is malformed


Please explain what is this error?

[Davis McCarthy]

I am also getting this error. The same commands applied to a different VCF file work fine, so I suspect it is some problem with that specific VCF. 

Any help from a guru on this would be welcomed by me too.

Best wishes

Davis

[Priya Bhatt]

I'm getting a similar error as well!  Can someone help?

 pseq testproject new-project --resources hg19
 pseq /path/to/project/testproject load-vcf --vcf /path/to/TestVCFs/*.vcf

 pseq error : database (/path/to/project/testproject_out/vardb) error (5) database is locked