MosaikBuild segmentation fault and MosaikAligner hashing reference sequence

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Dear Mosaik Developers,

we have used Mosaik with Human Microbiome Project reference data (you can 
download them from 

http://139.91.162.50/metagenome/all_seqs.fa.tar.gz

The file contains 105311927 lines and 188039 sequences. The MosaikBuild fails 
with a segmentation fault:

MosaikBuild 2.2.3 
- creating concatenated reference sequence:
12% [========>                                                                  
  ]                                     |./
mosaik_pavlos.sh: line 10: 10922 Segmentation fault      (core dumped) 
MosaikBuild -fr data/

When we get the first 70,000,000 lines (or less) of the reference fasta file 
(head -70000000 all_seqs.fa > sample_seqs.fa) then build is working OK. 

However then we got an execution halt of MosaikAligner 2.2.3

Hashing reference sequence:
21% [===============>                                                           
 ]    0.0000 ref bases/s       ETA  0 s

It has remained at this state for more than 12hours. 

We are using (lsb_release -a):
Distributor ID: Ubuntu
Description:    Ubuntu 12.04.5 LTS
Release:        12.04
Codename:       precise

and (uname -a)
Linux cerberus 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 
UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

Thanks a lot,
Pavlos

Original issue reported on code.google.com by pavlid...@gmail.com on 15 Dec 2014 at 9:38