[Seqan-dev] razers3 "failed for left reads in thread"

[Nomi Meixner <nomi.meixner@student.uni-tuebingen.de>]

Dear all,

I've installed the latest svn version of SeqAn on Scientific Linux. I 
tried several compilers. Latest try were Intel 12.0 and Gnu 4.4.

Running the following command failed on all versions (though mentioned 
files were present):
razers3 -tc 4 -o reference.sam mass_timo_ccug_45783.1.genes.fasta 
GS120675_03_CGATGT_L001_R1_001.fastq GS120675_03_CGATGT_L001_R2_001.fastq

However a colleague was able to run razers3 on those files on his Ubuntu 
machine a while ago, probably not with the latest version!

The error looks the following on the gnu-compiled version:
ERROR: windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread 1230



ERROR: windowFindBegin() failed for right reads in thread 2
ERROR: windowFindBegin() failed for right reads in thread 3
ERROR: windowFindBegin() failed for right reads in thread 1
ERROR: windowFindBegin() failed for right reads in thread 0
ERROR: windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread 0
321ERROR: windowFindBegin() failed for right reads in thread 0

ERROR: windowFindBegin() failed for right reads in thread 1


ERROR: windowFindBegin() failed for right reads in thread 3
ERROR: windowFindBegin() failed for right reads in thread 2
ERROR: windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread 0132
ERROR: windowFindBegin() failed for right reads in thread 0

ERROR: windowFindBegin() failed for right reads in thread 1

ERROR: windowFindBegin() failed for right reads in thread 2

ERROR: windowFindBegin() failed for right reads in thread 3
ERROR: windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread ERROR: 
windowFindBegin() failed for left reads in thread 01
ERROR: windowFindBegin() failed for right reads in thread 1



It continues like this and terminated with a segmentation fault. The 
messages on the intel-compiled version look pretty much the same.

Except for the SeqAn source code I couldn't find anything about this 
issue on the web. To get clues from the source code, my knowledge about 
SeqAn is far too superficial.

I would be glad if someone could tell me what is going wrong here and 
how to tackle this issue.

Thank you very much in advance!
All the best,
Nomi