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nmdp-bioinformatics / gfe-db

Graph database representing IPD-IMGT/HLA sequence data as GFE
https://gfe-db.readthedocs.io
GNU General Public License v3.0
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Build process completes with no output for version 3350 #74

Closed chrisammon3000 closed 4 months ago

chrisammon3000 commented 1 year ago

Description

The build process for IMGT version 3350 does not create or copy the CSV file output to S3.

(Build logs can be fetch by running make get.logs)

Example logs for functioning build process (for 3510):

2023-02-14 14:58:30 - root - INFO - ****** Building graph for IMGTHLA version 3.51.0 ******
2023-02-14 14:58:30 - root - INFO - Parsing DAT file...
2023-02-14 14:58:49 - root - INFO - Getting GFE data for allele HLA00001.1...
2023-02-14 14:58:54 - Logger.seqann.gfe - INFO - GFE = HLA-Aw99-8-363-912-830-2901-128-581-151-324-198-9-316-80-508-43-30
2023-02-14 14:58:54 - root - INFO - Getting GFE data for allele HLA02169.1...
2023-02-14 14:58:54 - Logger.seqann.gfe - INFO - GFE = HLA-Aw100-8-363-912-831-2901-128-581-151-324-198-9-316-80-508-43-29
2023-02-14 14:58:54 - root - INFO - Getting GFE data for allele HLA14798.1...
2023-02-14 14:58:54 - Logger.seqann.gfe - INFO - GFE = HLA-Aw99-8-364-912-830-2901-128-581-151-324-198-9-316-80-508-43-30
...
2023-02-14 14:59:29 - root - INFO - Finished build for version 3.51.0
2023-02-14 14:59:29 - root - INFO - ****** Build finished in 58.61 seconds ******

Logs for version 3350 show that the script is not fetching GFE data:

2023-02-14 15:11:26 - root - INFO - ****** Building graph for IMGTHLA version 3.35.0 ******
2023-02-14 15:11:26 - root - INFO - Parsing DAT file...
2023-02-14 15:11:44 - root - INFO - Finished build for version 3.35.0
2023-02-14 15:11:44 - root - INFO - ****** Build finished in 18.14 seconds ******