vcf2maf could not specify the output path
songeric1107 opened this issue · 1 comments
trying to run the script as follows by specifying the output path, however, get an error as follows.
perl /usr/local/packages/vcf2maf/vcf2maf.pl --input-vcf /local/devel/ysong/vcf2maf/mskcc-vcf2maf-754d68a/tests/test.vcf --output-maf /local/scratch/ysong/test.vep.maf --vep-path /usr/local/packages/miniconda3/envs/vep/bin
MSG: ERROR: Output file /local/devel/ysong/vcf2maf/mskcc-vcf2maf-754d68a/tests/test.vep.vcf already exists. Specify a different output file with --output_file or overwrite existing file with --force_overwrite
If I remove the pre-existing file and run the script again, the output is wroten to the following path, not the path that I specified.
STATUS: Running VEP and writing to: /local/devel/ysong/vcf2maf/mskcc-vcf2maf-754d68a/tests/test.vep.vcf
Is this issue resolved? I get the same error