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-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson Sent: 06 July 2011 16:23 To: A Bierzynska Cc: galaxy-u...@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 > bi...@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: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ -- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ___________________________________________________________ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender. Almac Group (UK) Limited, registered no. NI061368. Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited, registered no. NI046249. Almac Pharma Services Limited, registered no. NI045055. Almac Clinical Services Limited, registered no. NI041905. Almac Clinical Technologies Limited, registered no. NI061202. Almac Diagnostics Limited, registered no. NI043067. All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK. Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034. Almac Clinical Services LLC, Almac Clinical Technologies LLC and Almac Diagnostics LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: www.almacgroup.com ___________________________________________________________ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
