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MosaikAligner - when using -om, getting "the reference index is out of the range when saving alignments" #120

Open GoogleCodeExporter opened 8 years ago

GoogleCodeExporter commented 8 years ago 
A) Using version 2.1.32

B) Steps to reproduce the problem:

1. Aligning to a transcriptome, with 25000 "chromosomes" in the reference.   I 
tried multiple hash sizes (fastest performance with a hs of 13, since most of 
the time is spent loading sets of 20 or so chromosomes into ram, and little 
time is spent aligning).  I also tried using a different tmp dir, etc.   
Machine has 20 gb ram and 16 cores.  

2. It seems the "-om" parameter doesn't always work.   It may be particular 
kinds of alignments (IE: aligning to the last base of the last chromosome, 
etc), that aren't seen in DNA alignment - but are common, and desired, in 
ampli-seq and rna-seq.

3. MosaikAligner -ia s1/combined_geneinfo.rsem.idx.fa.mosaik -in test.mosain 
-out test.foo.bam -j s1/combined_geneinfo.rsem.idx.fa.mosaik -annpe 
/opt/lib/Mosaik/2.1.26.pe.100.0065.ann -annse 
/opt/lib/Mosaik/2.1.26.se.100.005.ann -quiet -p 4 -lm -ls 200 -om

C) Ideas:

1. Simply modifying the source code to ignore the error, spit out a warning, 
and move on to the next index might fix it more easily than debugging the whole 
process...

C) Output:

Aligning chromosome 20-38 (of 28060):
- loading jump key database into memory... finished.
- loading jump positions database into memory... finished.
- loading reference sequence... finished.
Aligning read library (500000):

Aligning chromosome 39-56 (of 28060):
- loading jump key database into memory... finished.
- loading jump positions database into memory... finished.
- loading reference sequence... finished.
Aligning read library (500000):
ERROR: The reference index is out the range when saving alignments.

Original issue reported on code.google.com by earone...@gmail.com on 29 Aug 2012 at 2:49

GoogleCodeExporter commented 8 years ago 
Modified source with this.  Works OK, but I have to go through the output and 
"re-find" the mate-pairs and interleave them properly, since they don't match 
up.  IE:  I may get 7 alignments, because of the "junk" effect.

Original comment by earone...@gmail.com on 29 Aug 2012 at 3:22

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