SAMFormatException: Unrecognized tag type: ^@ #1657
Comments
Do you have a line with that? |
Will investigate. Odd that only one file of 455 from the same source pipeline would have that as a tag type. |
Can't find an occurrences of
Samtools itself doesn't seem to complain
and an excerpt to SAM format transformed ok
|
This might be a bad Hadoop-BAM split? @ryan-williams has been tracking these down... |
The error was reported more than once, on the same executor though, so I suppose it could be a bad split. I've asked the data producer to help us confirm the BAM hasn't been corrupted since it was created, and I'll try to do something with htsjdk directly next. |
If the file reads OK on a single node, it looks a lot like a bad split to me... |
I have a bunch of utilities for investigating the bad split possibility. lmk if I can be of assistance / would love to get a look at the BAM |
@heuermh ping to retest with latest Hadoop-BAM in ToT. |
Works for me with ADAM version 0.23.0. |
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