Interrupted bowtie2 mappping

[wjyzidane]

Hi all,

my bowtie mapping is somehow interrupted without any error message.

The standard out only print:
Time loading reference: 00:00:00
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:01

without anything else.
The output sam file include part of the reads(~60%) mapped (including the 0 time, 1 time and > 1 times) but not all. And repeated try stopped at the same reads position.

I am wondering what causes the interrupt and how to fix it. Thx!

Jingyi

[westerman]

Well, as a general troubleshooting idea, since the program stops at the same place then the problem is probably due to a specific read abnormality. Look at the reads close to that position and see if there is anything strange about them.

Other than that, without looking at the actual data, it will be hard for us on SeqAnswers to figure out what is wrong. Obviously bowtie should not just stop.