I seek help understanding these 2 flags for BBDUK of BBMAP = 'tossbrokenreads' and 'nullifybrokenquality'
I see these flags mentioned in the STDERR of my bbduk.sh step using BBMap version 38-60 while decontaminating Illumina SE 100nt raw reads via "Adapter and Quality Trimming" - please see a relevant block of the STDERR copy-pasted below
[E::bgzf_read] Read block operation failed with error 2 after 58624 of 65536 bytes Error 3 in block starting at offset 1321362048(4EC26280) java.lang.Exception: Mismatch between length of bases and qualities for read 17377414 (id=HWI-ST797:117:D091UACXX:4:1303:5955:45869 1:). # qualities=27, # bases=101 CCCFFFFFHHHHHJJIIJJJIJIEIHJ TTCCCGATCATCCCGAGAAGGAACGTCTGCCATAATCTTCTCCTGACCGCGCCAAAGAATTTTGTCAATGACCCCAAATTCCTTAGCCAATAATGCGTCCA This can be bypassed with the flag 'tossbrokenreads' or 'nullifybrokenquality' at shared.KillSwitch.kill(KillSwitch.java:96) at stream.Read.validateQualityLength(Read.java:214) at stream.Read.validate(Read.java:104) at jgi.BBDuk$ProcessThread.run(BBDuk.java:2418)
However, the bbduk.sh help menu does not have these exact flags (too long to fully copy / paste here), the closest flag I see is
tossjunk=f . Therefore, I'm
A. confused about these messages,
B. curious when and why I would call these flags, and
C. why I receive these error messages - do they imply corrupted reads in my FASTQ input?
Could forum members please help? Thanks!