I am trying to run my RNA-seq bams through "rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg" pipeline, but all of my tasks failed with the attached error. Do you know what is the problem and how can I fix it? Thanks!
Since the workspace cannot be shared, the rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg method is private, and the provided files don't state a clear message showing Firecloud as the problem my best advice is to contact the author of method to determine that the workflow is functional and the method configurations are set correctly.
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Thank you for reporting your issue here. Is this workspace the same one you have been working with @bshifaw on?
If not, and it isn't under an authorization domain, please share your workspace on FireCloud using the Share button with [email protected]. In this thread, please give us the name of your workspace as well as the submission ID where you encountered this error.
Looking at the files you attached, an error message isn't immediately obvious to me. If you're able to share the workspace, maybe there's an error message that isn't immediately evident. I'm looping in Beri to take a look tomorrow.
It's the same workspace. I am not sure why you guys don't have the access yet. I will remind my PI one more time to grant you the access. Thank you!
I can't see any obvious reasons for the errors from the posted files either.
Also the method you mentioned rnaseq_bam_star_rsem_rnaseqc_v1-1_BETA_cfg isn't one we posted, ours is normally under the gatk method namespace. You may want to contact the original author of method for guidance.