problem after running rxstacks : munmap_chunk(): invalid pointer when running cstacks

[angeles...@gmail.com]

Hi there,

In order to correct my data (that came already mapped), I've run the scripts available here http://catchenlab.life.illinois.edu/stacks/manual/#phand without using the first part with GSnap. pstacks required more memory that I had, so I run each scaffold separately and then before running populations I merged all files using gunzip and cat sampleid_scaffold.matches.tsv >> sampleid.matches.tsv

and so on for snps, alleles and tags. I then used populations with my pop map file, and got a fasta and other files. 

As I had sites with very many alleles, I was running rxstacks as shown in here http://catchenlab.life.illinois.edu/stacks/manual/#corr starting from rxstacks.

As I was running cstacks

cstacks -b 1 -n 2  -o cor_stacks/ $samp

where samp = -s cor_stacks/04N4206 -s cor_stacks/04N4219 -s cor_stacks/11004 -s cor_stacks/11005 -s cor_stacks/12204 -s cor_stacks/12M158 -s cor_stacks/12M159

 it crashes on sample 6, like this:

Processing sample cor_stacks/12204 [6 of 7]

  Parsing cor_stacks/12M158.tags.tsv.gz

  Parsing cor_stacks/12M158.snps.tsv.gz

  Parsing cor_stacks/12M158.alleles.tsv.gz

Searching for sequence matches...

  Distance allowed between stacks: 2

  Using a k-mer length of 21

  Number of kmers per sequence: 44

  Minimum number of k-mers to define a match: 2

  70514 loci in the catalog, 1759123 kmers in the catalog hash.

Merging matches into catalog...

*** Error in `cstacks': munmap_chunk(): invalid pointer: 0x00000000023d26e0 ***

Aborted (core dumped)

Any idea what could be causing this issue?

All help will be greatly appreciated,

angeles