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NationalGenomicsInfrastructure / TACA

Tool for the Automation of Cleanup and Analyses: tools for projects and data management at NGI Stockholm
MIT License
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Enable TACA to retrieve error and warnings in demux logs #369

Closed chuan-wang closed 1 year ago

chuan-wang commented 1 year ago

Example output email generated with a test run:

The run 230621_VH00203_286_AACNL3GM5 has been demultiplexed with errors or warnings!

                    Sub-Demultiplexing in Demultiplexing_0 completed with 0 errors and 548 warnings:

2023-06-22 14:28:39 [7f764770a700] WARNING: Synchronized file '/srv/illumina/nextseq_data/230621_VH00203_286_AACNL3GM5/Data/Intensities/BaseCalls/L001/C42.1/L001_2.cbcl' truncated: bytes_read=0 bytes_expected=4:Success (0)

2023-06-22 14:28:39 [7f764770a700] WARNING: Error reading CBCL file header. All data for this cycle in unavailable and will be skipped.

2023-06-22 14:28:39 [7f764970e700] WARNING: Mismatching cluster count in BCL file: Cycle #42, Tile#2101: bytes_read=0 bytes_expected=900362

2023-06-22 14:28:39 [7f764bf13700] WARNING: Mismatching cluster count in BCL file: Cycle #26, Tile#2102: bytes_read=896846 bytes_expected=937776

2023-06-22 14:28:39 [7f764bf13700] WARNING: Mismatching cluster count in BCL file: Cycle #27, Tile#2102: bytes_read=896846 bytes_expected=937776

Subsequent error messages have been truncated. Only the first 5 lines are displayed.
chuan-wang commented 1 year ago

Another example output:

The run 230719_VH00203_301_AACMMTTM5 has been demultiplexed with errors or warnings!

                    Sub-Demultiplexing in Demultiplexing_0 completed with 0 errors and 1 warnings:

2023-07-19 21:40:02 [7fa3adbc67c0] WARNING: Option: '--minimum-trimmed-read-length' with value: 35 is being overwritten by the shortest non-index read length: 15
chuan-wang commented 1 year ago

Looks fine, if you could add that there was ERRORS/WARNING in subject field would be good. Thanks!

Fixed!