Looks like a bowtie error. The first chunk memory size can be increased on the command line with --chunkmbs=128 The default is 64. I don't know if this is possible in Galaxy though. -----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of Jennifer Jackson Sent: 06 July 2011 16:23 To: A Bierzynska Cc: galaxy-user@bx.psu.edu Subject: Re: [galaxy-user] Error aligning sequence Hello Agnieszka, To confirm, you are using the public Galaxy site? If so, would you be able to share a link to your history? Use "Options -> Share or Publish" then email me directly to keep your data private. Thanks! Jen Galaxy team On 7/6/11 3:25 AM, A Bierzynska wrote:

Hi,

I was wondering if you could help me to understand an error which I

get

when mapping using Galaxy:

An error occurred running this job: Error aligning sequence. Warning: Exhausted best-first chunk memory for read BIO-SEQUENCER1_0011:1:1:9519:2064#CGATGT/1 (patid 703); skipping read Warning: Exhausted best-first chunk memory for read BIO-SEQUENCER1_0011:1:1:1795:6806#CGATGT/1 (patid 4461);

If you know what's the error may mean, could you please let me know?

Best Wishes,

Agnieszka

---------------------- A Bierzynska Academic Renal Unit University of Bristol bizab@bristol.ac.uk ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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