duncanca / mosaik-aligner

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MosaikAligner #53

Open GoogleCodeExporter opened 9 years ago

GoogleCodeExporter commented 9 years ago
MosaikBuild:
 commond:./MosaikBuild -fr ../../mydata/F3_csfasta_a -
fq ../../mydata/F3_QV_qual_a -fr2 ../../mydata/R3_csfasta_a -
fq2 ../../mydata/R3_QV_qual_a -out myreads.dat -st solid
----------------------------------
 I use that to build the mate-pair reads,it seems that the output is 
reasonable.
but when i use the aligner, the mistake come out as follows:

             Aligning read library (92413079):
 0% 
[                                     ]                                  /-
--------------------
---------------------------------------------------------
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_d.dat]
------------------------------------------------------------
commond:
./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
-------------------------------------
who can help me?

Original issue reported on code.google.com by passiont...@gmail.com on 9 May 2010 at 7:38