error In MosaikAligner "buffer overflow detected when creating the packed cigar string"

GoogleCodeExporter commented 8 years ago

What steps will reproduce the problem?
1. the first 4 steps from the "QuickStart" guide completed successfully
2. run the last (MosaikAligner -in read.mkb -out read.mka -ia ref.dat -j ref_15 
-annpe pe.ann -annse se.ann) command
3. after the message "Aligning read library (193668059)" i get the error 
message "buffer overflow detected when creating the packed cigar string" and 
this happens all the time, no matter which parameters I use

I use the latest version of the product, my OS is Linux 

I would be extremely grateful if someone could suggest some solution here! =)

Original issue reported on code.google.com by 19RuBisC...@gmail.com on 18 Sep 2014 at 12:30

Attachments:

[Screen Shot 2014-09-18 at 02.10.56 am.png](https://storage.googleapis.com/google-code-attachments/mosaik-aligner/issue-133/comment-0/Screen Shot 2014-09-18 at 02.10.56 am.png)

GoogleCodeExporter commented 8 years ago

I get the same error when running the demo.

Original comment by poga...@gmail.com on 28 Oct 2014 at 3:42

GoogleCodeExporter commented 8 years ago

[deleted comment]

GoogleCodeExporter commented 8 years ago

I get the same error when using the jump database option. If I exclude the jump 
database option it passes that step but instead I'm getting "9962 Segmentation 
fault (core dumped)" after loading the reference sequence when it's supposed to 
start align the reads!

Original comment by elfa2...@gmail.com on 11 Nov 2014 at 10:32

GoogleCodeExporter commented 8 years ago

I got the same error with 2.2.30. But when I replaced the aligner's binary file 
with 2.1.73 version the error is gone. I guess 2.2.30 need more memory. I have 
20G RAM, which might be small to the the jump positions database.

Original comment by janhui.w...@gmail.com on 17 Dec 2014 at 4:19

duncanca / mosaik-aligner

error In MosaikAligner "buffer overflow detected when creating the packed cigar string" #133