Hi,
As we all are aware there have been some upgrade issues, patches, and fixes on FC over the past weeks.
I had several runs (of sets) that failed (several times over) and generated a whole bunch of unusable intermediate sep file and folders that basically ate away all my GATK-FC free credit and my google cloud credits. With all the overage it basically disconnected the workspace from both my fccredits-terbium account and my google cloud account. The only way I can now access it is through my saved bookmark.
The failure obviously happened between FC and Google cloud storage (of the broad institute), since it is not able to read the reference files (see below, BTW all references are from 5$ germline method).
Q1. Is there a way to recover these credits and complete my run to actually get usable data?
Q2. Should this happen again, how do we avoid/clean-up the large "intermediate step data" dump?
Q3. Is it possible to get my workspace to be reconnected to my fccredits-terbium account
Q4. Is it possible to have some kind of support when such things happen (chat would be great) ? It is quite terrifying to see all reds alters <!> all over the account and not be able to see the workspace all of a sudden.
Any help is much appreciated.
Call #18:
Operation:
Status:
Failed
Cache Result:Miss
Started:August 4, 2018, 1:46 AM (3 days ago)
Ended:August 4, 2018, 1:46 AM (3 days ago)
Inputs:Show
Outputs:None
stdout:stdout
stderr:stderr
JES log:BaseRecalibrator-17.log
Failures:Show
"message: Either ["gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz","gs://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"] exists on a filesystem not supported by this instance of Cromwell, or a failure occurred while building an actionable path from it. Supported filesystems are: Google Cloud Storage. Failures: Google Cloud Storage: The specified GCS path '["gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz","gs://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz"]' does not parse as a URI. Illegal character in scheme name at index 0: %5B%22gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz%22,%22gs://broad-references/hg38/v0/Homo_sapiens_assembly38.known_indels.vcf.gz%22%5D Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems"