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