Liudmila Elagina
Posts
Recent activity by Liudmila Elagina
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Download sample set metadata and then cannot upload it again
Hello Terra Team, I am trying to slightly modify metadata for sample_set. However, after downloading it and trying to upload back sample_set_entity.tsv file (even if that file was unmodified). I ...
- 2 followers
- 9 comments
- 0 votes
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CGA pipeline scatter getting stuck at localization step for hours
Hello Terra Team, I am running the CGA pipeline (CGA_WES_Characterization_Pipeline_v0.2_Jun2019) over a few pairs (~15 pairs). For each pair workflow runs scatter for MuTect1 and MuTect2 tasks. W...
- 3 followers
- 11 comments
- 0 votes
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Strange error message when trying to re-launch failures
Hello Terra team, I got this error message when trying to relaunch failed workflows for the getzlab/CGA_WES_Characterization_Pipeline_v0.1_Dec2018/2 pipeline: Error rerunning failed workflowsEr...
- 3 followers
- 3 comments
- 0 votes
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Incorrect parsing of wdl
Hello Terra Team, I noticed strange behavior in the method configuration. It suddenly got populated with a large number of default parameters (see screenshot): However, those are not optional ...
- 3 followers
- 16 comments
- 0 votes
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Restarting failed workflows while other worflows are still running in that job submission
Hello, I started running the method on pair set and some pairs failed right away as I didn't have access to the BAMs. I got access to the BAMs and now would like to restart those failed workflows. ...
- 1 follower
- 0 comments
- 0 votes
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Peculiar feature when importing method configurations from another workspace
Hello, I encountered very peculiar behavior when importing method configurations through Terra using the "Copy to another workspace" button: The namespace of the method changes to the namespace of...
- 2 followers
- 3 comments
- 0 votes
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Error invalid input while launching workflow
Hello, I get this error when trying to resubmit failed workflows from the JOB HISTORY tab: Is it because Tool name contains a dot in its name? If so, why it doesn't complain about dot when I submit...
- Edited
- 3 followers
- 13 comments
- 0 votes
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Saving one workspace attribute takes more than half a minute?
After pushing button save for a workspace attribute it took about 35 seconds for it to be saved (replicated several times). Without the option of loading workspace attributes from file this very ti...
- 2 followers
- 2 comments
- 0 votes
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Workflow error message when required annotations are missing
When workflow is missing annotations in Data Model Firecloud would output message like that: where is in Terra it is not so clear why workflow failed as it doesn't output anything: and after clic...
- 2 followers
- 6 comments
- 0 votes
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Uploading Method Configuration from JSON file throws an error
Uploading method configuration from json file in Terra throughs an error: Configuration json file was downloaded first from Firecloud and then from Terra. In both cases, I get the same error. Ther...
- Edited
- 2 followers
- 3 comments
- 0 votes