Bowtie2 - segmentation fault due to --sam-RG

[memento]

Hi,
Just tried to move my stuff to a new machine with Ubuntu 11.10 (not sure if that is the problem here) with no donut. I cannot add any --sam-RG since it causes "seg fault". Anyone had similar problem ?

issue #2, tried to run it without any RG header and got this:

Only read 402653184 bytes (out of 715335926) from reference index file hg19.4.bt2
Error: Encountered internal Bowtie 2 exception (#1)


truncated index ?

Its being run on i7 machine with 6gb (4+2). Bowtie1 works just fine.

I hope that someone can help....

[nchernia]

See this:

http://sourceforge.net/projects/bowtie-bio/forums/forum/856737/topic/4882702

[memento]

Thanks a lot! So basically, bowtie2 is not usable if one wants to use it with picard/GATK down the line....

[gringer]

So basically, bowtie2 is not usable if one wants to use it with picard/GATK down the line....

If you don't want to wait for the next beta, you can always download the trunk / development version, or modify the SAM headers using a few different tools (presumably including Picard), or use a script and/or text editor to edit the SAM headers in a more direct fashion.

Yay for FOSS and plain-text file formats.