I am working with TCGA_READ_hg38_ControlledAccess data and running SigprofilerSBS workflow on it. I am getting this error:
Failed to evaluate 'SigprofilerSBS.diskGB' (reason 1 of 1): Evaluating ceil((size(maf, "GB") * 2) + 20) failed: java.lang.IllegalArgumentException: Could not build the path "438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz". It may refer to a filesystem not supported by this instance of Cromwell. Supported filesystems are: HTTP, Google Cloud Storage, DRS. Failures: HTTP: 438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz does not have an http or https scheme (IllegalArgumentException) Google Cloud Storage: Path "438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz" does not have a gcs scheme (IllegalArgumentException) DRS: 438904c4-5618-4159-a16c-8789f7209386/TCGA.READ.varscan.438904c4-5618-4159-a16c-8789f7209386.DR-10.0.protected.maf.gz does not have a drs scheme. (IllegalArgumentException) Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems
I think the error is saying that my file paths are not correct but I just imported the data from TCGA and have not tampered with it at all. A sample file path from my data looks like: c5ed2903-cbaf-446f-870d-167eed6e0bba/TCGA.READ.mutect.c5ed2903-cbaf-446f-870d-167eed6e0bba.DR-10.0.protected.maf.gz. I believe the file path should have a prefix like gs/ http etc. but I am not sure if I need to add that here as well.
Any help is greatly appreciated!
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