Segmentation fault during MosaikAligner

[GoogleCodeExporter]

What steps will reproduce the problem?
I'm trying to align ~20M reads to an assembly of ~44k contigs.  The reads
are in a fastq format like this: 
@HWI-EAS303:6:1:0:502#0/1
.TTCACCCTCAACACGGAGCCGGTGGAGGCTGTACT
+
DNTTTTTSTTTTTTTRTTRTURTSTRTRTTBBBBBB

The contigs are in a basic fasta format.
I've built them into binary files with these options:
MosaikBuild -fr contig.fasta -oa contig.dat -ds "description"
MosaikBuild -q reads1.fastq -q2 reads2.fastq -out reads.dat -ds
"description" -mfl 350

The options I used for the Jump database are:

MosaikJump -ia contig.dat -out contig_15 -hs 15

And finally I call the aligner:
MosaikAligner -in reads.dat -ia contig.dat -out aligned.dat -hs 15 -mm 4
-mhp 100 -act 20 -j contig_15 -p 4 -rur unused.fasta -bw 13

I've run a very similar set on the windows distribution successfully
(albeit with not entirely satisfactory results).  I wanted to try the
latest build so I moved to linux.

What is the expected output? What do you see instead?
A segmentation fault occurs once the program hits the "Aligning read
library" step. A 25 byte aligned.dat file is created and 0 byte
unused.fasta file is created.

What version of the product are you using? On what operating system?
I'm using the 64-bit version 1.0.1388 on 64 bit fedora 12.

Please provide any additional information below.

Original issue reported on code.google.com by Tzintz...@gmail.com on 5 Feb 2010 at 7:28

[GoogleCodeExporter]

I encountered the peoblem too, and it is followed by a Error mention :
Error:
ap_mosaik.sh: line 10:  2803 Segmentation fault    ./MosaikAligner -in 
myreads.dat -
out myreads_aligned.dat -ia humanChr.csfasta -ibs humanChr.dat -hs 15 -mm 4 
-mhp 
100 -act 20 -j humanChr_15 -p 8
------------------------------------------------------------------------------
MosaikSort 1.0.1388                                                 2010-02-01
Michael Stromberg                 Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- resolving the following types of read pairs: [unique orphans] [unique vs 
unique] 
[unique vs multiple] 
ERROR: The alignment archive header indicates that no reads are contained in
       this file. This might happen when the file was not closed properly -
       usually from a killed process or a crash. Your only recourse is to
       realign this data set.
       filename: [myreads_aligned.dat]
What's the problem??

Original comment by passiont...@gmail.com on 10 May 2010 at 1:08

[GoogleCodeExporter]

MosaikAligner -in SOLID_Sample001_F3_mosaik.dat \
-out SOLID_Sample001_F3_mosaikAligned.dat \
-ibs ../../mosaikrefs/human_g1k_v37_mosaik.dat \
-hs 15  -mm 4 -act 20 
-j ../../mosaikrefs/human_g1k_v37_hs15 \
-p 40 \
-ia ../../mosaikrefs/human_g1k_v37_mosaik_CS.dat 
------------------------------------------------------------------------------
MosaikAligner 1.1.0021                                              2010-11-10
Michael Stromberg & Wan-Ping Lee  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

- Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch threshold of 4
- Using a hash size of 15
- Aligning in colorspace (SOLiD)
- Using 40 processors
- Using an alignment candidate threshold of 20bp.
- Using a jump database for hashing. Storing keys & positions in memory.
- loading basespace reference sequences... finished.
- loading reference sequence... finished.
- loading jump key database into memory... finished.
- loading jump positions database into memory... finished.

Aligning read library (67156628):
 2% [                                             ]   1,264.0 reads/s  ETA  14:27:43 \Segmentation fault (core dumped)

 Filesystem    Type    Size  Used Avail Use% Mounted on
/data          ext4    1.9T  137G  1.7T   8%

I added /data with free 1.7T space as the tmp directory.
Getting same error and same 25kb output file.

Original comment by 2007...@gmail.com on 4 Apr 2011 at 2:00