bbMAP repair.sh killed line #: random number
I am trying to repair a .fq file using bbMap repair.sh command and I am running into an error. My .fq file is pair-end but is not sorted or interleaved, hence, needing to repair it before moving on to my next analysis.
When I run repair.sh it starts and then always errors out at the same spot, Line 87: 23354 Killed
I have changed the amount of memory allocated (-Xmx) as I thought I might be running into memory issues but this is not fixing the problem.
I am not sure what this error is pertaining to. I looked at my .fq on line 87 and saw no errors. Pasted below is lines 85-88 from my .fq.
@38_1_1101_31566_1016/1 CTGCAGGATCCTTCTCTGGGTTTCCCACCCCGTCCTCCTGGAATTTCACCACTTTCCTCCTGCCCAGCTGATGAGCTGATCCCACAGCAGATTCGGGGCTCCCTGATCCTGGAATTTTCTCCTTGTTTTTCTCAGGTTTT + FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFF::FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFF,FFF,,FFFFFFFFFFFF
I do not see any errors with the file, so I am thinking this may be an error somewhere with how I am running the command.
Any help would be appreciated in figuring out what the error means and how I can get bbmap to repair this file.
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