What Causes The Bwa Error: "Assertion `Re - Rb == Rlen' Failed."

Question

[Cacau]

Neither bwa 6.0.2 nor bwa 7.0.5 worked for my alignment. The size of my genome is about 1.5M and the number reads are 25000000.

However, when I tried to reduce the number of reads to 15000000 it worked with bwa 6.0.2 (not sure about bwa 7.0.5).

Would anyone please help me figure out what the problem is?

ERROR MESSAGE is as follows:

[bwa_sai2sam_pe_core] refine gapped alignments... bwa: bwase.c:182: bwa_refine_gapped_core: Assertion `re - rb == rlen' failed.

[Alastair Kerr]

At a guess it sounds like there is a malformed sequence in the input causing it to crash. Check if it is the number of sequences that are the problem or a specific one. Split the input set into many chunks, run each chunk and see if one is consistently responsible. Then subdivide it until you can track down the problem.

[Pierre Lindenbaum]

if that's a bug, you'd better ask the samtools-dev mailing list.

Answer 1

[Baoxu]

It seems that some of reads in fastq have some problem. I suspect the some of the reads may be too short ( < 30bp).