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Default limit on file input to read_lines is too small
See original GitHub issueCurrently, this is set to default to 128000. This is too small for most practical use, especially given that gs URLs can get quite long. Can the new limit be much higher? We’ll need 5GB (no joke!) for some our larger analyses. Or at least a workflow option to temporarily override?
Otherwise, we get an error such as:
"Workflow has invalid declarations: Could not evaluate workflow declarations:\nSingleSampleGenotyping.gvcfs_list:\n\tUse of WdlSingleFile(gs://broad-dsde-methods/gauthier/Finnish_FE_WGS.1000samples.gvcf_list) failed because the file was too big (174730 bytes when only files of up to 128000 bytes are permissible"
Issue Analytics
- State:
- Created 6 years ago
- Reactions:2
- Comments:11 (7 by maintainers)
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You want
java -Dsystem.input-read-limits.lines=500000 -jar /cromwell-34.jarFor reference you are setting this: https://github.com/broadinstitute/cromwell/blob/0ad9cb61f90276e3576f6ba135cab65c02f09a9e/core/src/main/resources/reference.conf#L157
@LeeTL1220 since its possible to configure this limit as needed, I’m hoping you’ve got what you needed. Feel free to reopen if I missed something.