Jason Cerrato

1. Community
2. General Discussion
3. Interval problem with haplotypecaller-gvcf-gatk4 (suggested workflow

Hi Matthew, The hg38_wgs_scattered_calling_intervals.txt contains 50 lines. Each line points to a different intervals list - the contents of each are different. You will see that each gsutil bucket...

• View comment
• January 27, 2020 15:24
• 0 votes

1. Community
2. Completed Feature Requests
3. monitoring_script and monitoring_image options in Terra

Hi Kenny, The feature has not yet been built, but I would be happy to reach out and let you know if that changes. Kind regards, Jason

• View comment
• January 24, 2020 17:55
• 0 votes

1. Community
2. General Discussion
3. Interval problem with haplotypecaller-gvcf-gatk4 (suggested workflow

Hi Matthew, The variable scattered_calling_intervals_list in the workflow is expecting a file with a list of interval files that should be stored in Google buckets. Here is an example of...

• View comment
• January 24, 2020 15:28
• 0 votes

1. Community
2. General Discussion
3. New error (Validation errors: Extra inputs) running somatic calling pipeline: problem with Cromwell 48?

Hi Ick, Are the files unable to be shared due to an authorization domain? If so, even if the workspace is shared with the GROUP, only members who are part of the authorization domain will be able t...

• View comment
• January 23, 2020 20:40
• 0 votes

1. Community
2. General Discussion
3. Interval problem with haplotypecaller-gvcf-gatk4 (suggested workflow

Hi Matthew, Can you share your interval file and let us know how it was made? Can you confirm that it fits one of the mandatory formats listed in this document? https://gatk.broadinstitute.org/hc/e...

• View comment
• January 23, 2020 17:21
• 0 votes

1. Community
2. General Discussion
3. New error (Validation errors: Extra inputs) running somatic calling pipeline: problem with Cromwell 48?

Hi lck, Would you be willing to share the workspace where you are seeing this issue with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in either the icon of your workspace in t...

• View comment
• January 23, 2020 17:04
• 0 votes

1. Community
2. General Discussion
3. Failed to check notebook status: "Autosave Failed!"

Hi Stephen,   To clarify, is the terminal open in a separate tab when this notebook error occurs?   Kind regards, Jason

• View comment
• January 22, 2020 19:05
• 0 votes

1. Community
2. Known Issues
3. Hanging Localization Step

Hi Susan, We are currently collecting information to request reimbursement from Google for users affected by this error. Please email support@terra.bio with the following pieces of information: Pro...

• View comment
• January 22, 2020 16:10
• 0 votes

1. Community
2. General Discussion
3. Failed to check notebook status: "Autosave Failed!"

Hi Stephen,   We'll be happy to take a look! Can you provide the project name(s) and workspace(s) where you are seeing this happen? Is this happening on notebooks across different projects/workspac...

• View comment
• January 22, 2020 15:12
• 0 votes

1. Community
2. Known Issues
3. Hanging Localization Step

Hi Luda,   Our tests did indeed pass with the latest patch, but it is becoming clearer with each step that the underlying problem is quite complex. Each of the fixes thus far have resulted in some ...

• View comment
• January 21, 2020 20:56
• 0 votes