What steps will reproduce the problem?
1. I use the linux version of MOSAIK.
I created the reference file : cluseq.fa.bin
and the read file : raeds.bin
Then, I launched Mosaik Aligner with this command :
pyrobayes/UnifiedRelease/bin/MosaikAligner
-in reads.bin -ia cluseq.fa.bin -out reads.bin.aligned -hs 15 -mm 4 -act
20 -mhp 100 -m all -a all
2.
3.
What is the expected output? What do you see instead?
I get this :
---------------------------------------------------------------------------
---
> MosaikAligner 0.9.0891
> 2009-01-31
> Michael Stromberg 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
> - Using an alignment candidate threshold of 20bp.
> - Setting hash position threshold to 100
> - Using a homo-polymer gap open penalty of 4
>
> Hashing reference sequence:
>
100%[==========================================================
==============================================================
==================================================]
> 2,426,161 ref bases/s in 18 s
>
> - loading reference sequence... finished.
>
> Aligning read library (11035):
> 0%
[
> ] |ERROR: Tried to read 3150435 bytes,
> but received only 1359822 bytes.
What version of the product are you using? On what operating system?
I use MosaikAligner 0.9.0891 on Linux
Please provide any additional information below.
How can I handle this ?
I thank you in advance for your kind help.
Regards
Original issue reported on code.google.com by nathalie...@yahoo.fr on 25 Feb 2010 at 7:43
Original issue reported on code.google.com by
nathalie...@yahoo.fron 25 Feb 2010 at 7:43