[galaxy-user] Galaxy Error

2013-06-07 Thread Delong, Zhou
/knockdown Besides, is it possible to show the grade of progress of uploading? Thanks, Delong ZHOU ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please

[galaxy-user] FTP upload problem

2013-06-10 Thread Delong, Zhou
Hello, I was using the ftp uploading via filezilla. It worked perfectly this morning, but after a disconnection of the internet I can no longer upload any file. This is the message I got: 530 Sorry, the maximum number of clients (3) for this user are already connected I restarted my computer and

[galaxy-user] Cuffmerge error: duplicate GFF ID encountered

2013-07-04 Thread Delong, Zhou
Hello, I was doing a RNA analyse and I wished to compare the transcription and expression of two samples using a reference annotation, however this is the error message I got: =Quote= Error running cuffmerge. [Thu Jul 4 07:32:59 2013] Beginning transcriptome assembly merge

[galaxy-user] RE : Cuffmerge error: duplicate GFF ID encountered

2013-07-09 Thread Delong, Zhou
Thank you for the reply. I will try this annotation GIF when I get my local galaxy to function. Have a good day, Delong De : Jennifer Jackson [j...@bx.psu.edu] Envoyé : 9 juillet 2013 14:30 À : Delong, Zhou Cc : galaxy-u...@bx.psu.edu Objet : Re: [galaxy-user

[galaxy-user] Tophat Error: segment-based junction search failed with err

2013-08-27 Thread Delong, Zhou
Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get this error for all of them.. segment-based junction search failed with err = 1 or -9 Here is an example of full error report: Error in tophat: [2013-08-23 11:56:58] Beginning TopHat run (v2.0.6)

[galaxy-user] Tophat2 not working?

2013-08-29 Thread Delong, Zhou
Hello, I've been trying tophat 2 on the public server since last week but I don't get any results. I got one empty output for the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. one error with Unable to queue job for

[galaxy-user] Error out of memory when trying to retrieve output

2013-08-29 Thread Delong, Zhou
Hello, I wanted to download the accepted junction .bam file from tophat output of my local instance and I get an out of memory error. When I examine the server via command line, I found that a python process used by galaxy occupied more than 80% of total memory (on the virtual machine with 10G

[galaxy-user] RE : Error out of memory when trying to retrieve output

2013-08-30 Thread Delong, Zhou
Hello, This solved my problem. Thanks. Delong De : Dannon Baker [dannon.ba...@gmail.com] Envoyé : 29 août 2013 16:07 À : Delong, Zhou Cc : galaxy-u...@bx.psu.edu Objet : Re: [galaxy-user] Error out of memory when trying to retrieve output Do you have debug

[galaxy-user] Tophat Error: segment-based junction search failed with err

2013-10-02 Thread Delong, Zhou
but it changes nothing. Thanks. Delong De : Delong, Zhou Envoyé : 27 août 2013 9:36 À : galaxy-u...@bx.psu.edu Objet : Tophat Error: segment-based junction search failed with err Hello, I have run several analysis with Tophat 2 on my local instance of galaxy and I get