munmap_chunk(): invalid pointer

[krejciadam]

Hi!
In very rare cases, I get this error:

munmap_chunk(): invalid pointer
Aborted (core dumped)

Unfortunately, I can't share the fastq where this happens yet, because it is very large and I didn't manage to get a small portion that would demonstrate this behavior so far.

This happens for both the 0.3.0 release and the current source code (which I guess is 0.4.0)

Any help appretiated. Thank you!

[rfm-targa]

Hello,

I think I am running into a similar issue with a pair of FASTQ files I want to compress with repaq. Trying to compress both files into a single archive with repaq -c -i 109_R1.fastq.gz -I 109_R2.fastq.gz -o 109.rfq.xz outputs Segmentation fault. It still creates a file but repaq --compare returns the following:

{
	"result":"failed",
	"msg":"The RFQ file and FASTQ file have different sequence in the 606096 pair. ACCTATTGTTGTAACCAAAAGCTAAANATTAAAAAGCTGAAAACAAACGCCAAAAACCCCTTTAAAGCATCACATAAACCAACTAAGAAGCCTATTTTCAAACCAAAAACACGGATTGAGTTAGAGAGCAGATCGGAAGAGCACACGTCTG | ACCTATTGTTGTAACCAAAAGCTAAAGATTAAAAAGCTGAAAACAAACGCCAAAAACCCCTTTAAAGCATCACATAAACCAACTAAGAAGCCTATTTTCAAACCAAAAACACGGATTGAGTTAGAGAGCAGATCGGAAGAGCACACGTCTG",
	"fastq_reads":1212193,
	"rfq_reads":1212193,
	"fastq_bases":183041143,
	"rfq_bases":183041143
}

The sequences differ in a single position, with one sequence having a G and the other having an N. Here are the sequences with the different base highlighted with *:

ACCTATTGTTGTAACCAAAAGCTAAA*N*ATTAAAAAGCTGAAAACAAACGCCAAAAACCCCTTTAAAGCATCACATAAACCAACTAAGAAGCCTATTTTCAAACCAAAAACACGGATTGAGTTAGAGAGCAGATCGGAAGAGCACACGTCTG

ACCTATTGTTGTAACCAAAAGCTAAA*G*ATTAAAAAGCTGAAAACAAACGCCAAAAACCCCTTTAAAGCATCACATAAACCAACTAAGAAGCCTATTTTCAAACCAAAAACACGGATTGAGTTAGAGAGCAGATCGGAAGAGCACACGTCTG

If I try to compress the files separately it returns different errors for each file:

R1

repaq -c -i 109_R1.fastq.gz -o 109_R1.rfq.xz
Segmentation fault

R2

repaq -c -i 109_R2.fastq.gz -o 109_R2.rfq.xz
munmap_chunk(): invalid pointer
Aborted

Any idea about what may be the issue?
Thank you in advance.

Rafael