[galaxy-user] bowtie stuck for past day

2012-04-27 Thread Eirini Trompouki
Hi, I started a series of bowtie runs yesterday but nothing has happened. i tried rerunning them but still nothing. is anyone else having this problem? et -- Eirini Trompouki,Ph.D. Karp Family Research Labs (Karp 7)RB07005F Zon lab 1 Blackfan Circle Boston MA 02115 USA

[galaxy-user] Chicken reference genome

2012-04-27 Thread Nicholas Beckloff
Dear Galaxy, I noticed upon uploading a FASTQ file that the ICGSC version of the 2011 November Chicken genome is available. Why is this not available for use with the tools? Also, is this available for download? -- Nicholas Beckloff, PhD Genomics Core Laboratory Director Department of Genetics

[galaxy-user] Cufflinks jobs in queue

2012-04-27 Thread Scroggins, Sheena
Hi, My cufflinks jobs sat in the queued state for 12+ hours so I restarted them this morning. They've been in the queued state now for about 2-3 hours. Any idea why? Here's a link to my history: https://main.g2.bx.psu.edu/u/sheenams/h/clone-of-s1jaf13mir-active-items-only Thanks Sheena

[galaxy-user] Jobs in queue

2012-04-27 Thread 杨继文
I have similar problems. My tophat job was sent 6 hours ago. Now the job is still waiting to be run. Jiwen Hi, My cufflinks jobs sat in the queued state for 12+ hours so I restarted them this morning. They've been in the queued state now for about 2-3 hours. Any idea why? Here's a link to

Re: [galaxy-user] long time waiting to run tophat jobs

2012-04-27 Thread Jennifer Jackson
Hello Matthew, Your job were in the queue - it is important to not stop and restart - hopefully they have completed by now? Galaxy has been under a very high NGS tool load for about a week, and even though we have substantial resources dedicated to supporting analysis on the public server,

Re: [galaxy-user] bowtie stuck for past day

2012-04-27 Thread Jennifer Jackson
Hello ET, Started job will be in the queue - it is important to not stop and restart. You want to leave them in the grey state while they wait their turn to run. Galaxy has been under a very high NGS tool load for about a week, and even though we have substantial resources dedicated to

Re: [galaxy-user] Chicken reference genome

2012-04-27 Thread Jennifer Jackson
Hello, This genome 'Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) (galGal4)' is currently in the genome builds list as a database assignment choice, but the actual genome data is not incorporated into Galaxy (yet). This allows data to be labeled and displayed at the UCSC Genome

Re: [galaxy-user] Cufflinks jobs in queue

2012-04-27 Thread Jennifer Jackson
Hello Sheena, Started jobs will be in the queue - it is important to not stop and restart. You want to leave them in the grey state while they wait their turn to run. Galaxy has been under a very high NGS tool load for about a week, and even though we have substantial resources dedicated to

[galaxy-user] bwa/bowtie not running

2012-04-27 Thread Furey, Terry
Hi- I'm having trouble getting bwa to run on the main server. It seems stuck in the waiting to run state. I have tried changing the assembly to align to, and have tried re-running a previous workflow that ran fine a couple weeks ago. I even tried running bowtie, and that seems stuck. Is

Re: [galaxy-user] bwa/bowtie not running

2012-04-27 Thread Jennifer Jackson
Hi Terry, Started jobs will be in the queue - it is important to not stop and restart. You want to leave them in the grey state while they wait their turn to run. Restarting will only cause then to move to the back of the queue again. Galaxy has been under a very high NGS tool load for