PoN creation error

sas

I'm trying to create a PoN but keep getting the following error in the merge_pons stage:

message: Workflow failed
causedBy:
message: Call input and runtime attributes evaluation failed for merge_pons
causedBy:
message: Invalid parameters for engine function sub: (Failure(java.util.NoSuchElementException: key not found: totSizeFloat),Success(WomString(..*)),Success(WomString())).
message: key not found: stringDiskSizeGB
message: Can't index Success(WomInteger(7)) with index Success(WomInteger(0))
message: key not found: sizeOfPonFile

https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis/monitor/93db83d4-6b54-456a-9f12-ccc91da67f51/f207c7bd-bf88-4e0f-b095-9fdacd6dcae7

Do you know what might be causing this?

Thanks

Chip

Firecloud tells me workspace https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis/ doesn't exist -or that I don't have access. I do have access to
broad-firecloud-wuclonal/Checkmate010_WES_SandBox_Analysis, which has a failed esalinas/token_pon_size_update job circa a couple of days ago. The version of the failed workflow is Snapshot ID:13. The version that I've used is Snapshot ID:10, which has fewer parameters and runs without failing. A suggestion would be to try Snapshot ID:10. I don't know the story behind Snapshot ID:13; perhaps it was not tested and has a syntax issue.

sas

Thanks Chip, Snapshot ID:10 ran through successfully!

For the Firecloud dev team: I have noticed a curious idiosyncrasy in Firecloud

https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis/

gives a "Page not found" error but

https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis

works fine.

sas

I'm trying to create a PoN but keep getting the following error in the merge_pons stage:

message: Workflow failed
causedBy:
message: Call input and runtime attributes evaluation failed for merge_pons
causedBy:
message: Invalid parameters for engine function sub: (Failure(java.util.NoSuchElementException: key not found: totSizeFloat),Success(WomString(..*)),Success(WomString())).
message: key not found: stringDiskSizeGB
message: Can't index Success(WomInteger(7)) with index Success(WomInteger(0))
message: key not found: sizeOfPonFile

https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis/monitor/93db83d4-6b54-456a-9f12-ccc91da67f51/f207c7bd-bf88-4e0f-b095-9fdacd6dcae7

Do you know what might be causing this?

Thanks

EADG

Hi @sas,

Call input and runtime attributes evaluation failed for merge_pons
message: key not found: stringDiskSizeGB
...

it seems that you forget to add several values to your input.json (Method Configuration in firecloud). Can you specify which script you use for the PON creation?

Greetings,
EADG

sas

Hi EADG,

This method (esalinas/token_pon_size_update) was suggested by Chet Birger; I will ask him to reply to this post.

Thanks

Chip

Firecloud tells me workspace https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis/ doesn't exist -or that I don't have access. I do have access to
broad-firecloud-wuclonal/Checkmate010_WES_SandBox_Analysis, which has a failed esalinas/token_pon_size_update job circa a couple of days ago. The version of the failed workflow is Snapshot ID:13. The version that I've used is Snapshot ID:10, which has fewer parameters and runs without failing. A suggestion would be to try Snapshot ID:10. I don't know the story behind Snapshot ID:13; perhaps it was not tested and has a syntax issue.

sas

Thanks Chip, Snapshot ID:10 ran through successfully!

For the Firecloud dev team: I have noticed a curious idiosyncrasy in Firecloud

https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis/

gives a "Page not found" error but

https://portal.firecloud.org/#workspaces/broad-firecloud-wuclonal/SandBox_Analysis

works fine.

KateN

Hm. Thank you for that report, I will pass it on to our developers.