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cpreid2 / gdc-rnaseq-tool

Tool to download/merge RNASeq data from the GDC Portal in matrices identified by TCGA barcode
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KeyError when trying to upload a manifest #2

Closed gaheens closed 6 years ago

gaheens commented 6 years ago

Received a KeyError when trying to upload a manifest. Attached is the manifest and error message. key-error-rnaseq-tool gdc_manifest_20180214_175133.txt

The issue is that I had an extra file reference (VCF) in my manifest that was the wrong file type for this tool and it is also a controlled access file. May want to handle this error condition and display an error message vs. a KeyError.

cpreid2 commented 6 years ago

@gaheens I have updated the code to resolve this error just a few moments ago. The issue was that I didn't clean up the .gz files that were downloaded from a previous run of the tool. So the key error was from the code looking for files downloaded previously. You shouldn't see this error any longer.

gaheens commented 6 years ago

@cpreid2 I downloaded the new version of the code (dated today) but am still seeing this same error, even with the Test manifest.

cpreid2 commented 6 years ago

@gaheens If you delete the RNA-Seq and miRNASeq folders in the same directory as the manifest it should resolve the problem for you.

Though, I just updated the tool to move my fix to another part of the code so that this error shouldn't occur anymore and won't require you (or others ) to delete those folders so that it will work. Try it again with the new code and let me know if it works.

gaheens commented 6 years ago

@cpreid2 This worked. Thanks!