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Cutadapt not working

posted May 28, 2013, 9:47 AM by Kathryn Johnson

I am trying to remove sequencing adaptors with Cutadapt, but I keep getting the following error:

error
An error occurred with this dataset:/galaxy/PRODUCTION/database/pbs/galaxy_177075.sh: line 13: cutadapt: command not found

Is this tool no longer available?  If so, what tool should I use instead?

long delays to run short jobs

posted May 21, 2013, 1:10 PM by Kathryn Johnson

I have several jobs (cutadapt, fastq quality trimmer) that have been waiting to run for several hours even though they are acting only on small datasets (10,000 lines).  All say "job is waiting to run".  This is not the first time I have run into long delays to run simple processes, but it does not happen all the time.  Is there any way to avoid these delays?

Problem with FastqMcf

posted May 17, 2013, 5:32 PM by David Roe

I get this error when trying to run FastqMcf:

/galaxy/PRODUCTION/database/pbs/galaxy_173983.sh: line 13: fastq-mcf: command not found

100 RNA-seq data sets

posted Jan 17, 2013, 3:12 PM by Paul Walker

Hello,
I have a bit of a problem. I have 100 RNA-seq, paired end, 50 cycle, ~10 million read fastq data files that I would like to
run in Tophat, Genedata Refiner Genome and then make several statistical group comparisons using Genedata Analyst.
Should I try to work through UM Galaxy in smaller batches, say 20 samples/ history ( I would run my fastq pairings in Tophat after using Fastq groomer to set the appropriate file type)? Or, would it be better to try to get help writing a script to process all the files together before moving the Tophat bam files to Genedata Refiner genome?
Previously, I have done small workflows in Galaxy and GDE of about 10 samples per history or run.
Thanks.


Untitled Post

posted May 3, 2012, 5:10 PM by Tim Starr

Trying to upload file from my computer and the task just sits there saying "Job is waiting to run".  Will it no longer upload when I'm at home?  Do I need to be at the UM campus?

Trinity

posted Feb 28, 2012, 12:11 PM by Jerry Johnson

I am having a problem with Trinity, I think I am doing everything right.
I have a single end read RNA seq library in FASTQ format, which I ran through the FASTQ groomer.
When I try to run Trinity on the groomed data set, I get the following in the log:

Error, cannot find meryl at /soft/trinityrnaseq/20110820/bin/trinity-plugins/kmer/meryl/meryl at /soft/trinityrnaseq/20110820/bin/Trinity.pl line 194.


And there is no data in the Assembled transcript.
It looks to me like the program can't find the place it needs to run, but I could also be missing a setting.


Thanks for any help,

Jerry

Settings:
Data is single end,
Strand specific library is F or none (neither work)
No additional parameters

Here are the first few lines of the groomed FASTQ file:

@HWI-EAS432:5:1:1:264#0/1 TGACGGAGTTGACTNCCGGGGTATCTAATCCAGTTTGCGACCTACTCTCTCATCCCTCAGTGTCATATTATCGTA +HWI-EAS432:5:1:1:264#0/1 A=@CC>?B<@ABB:%<C@>9@13=CBBBBCBBB7BB2@;>ABA;>BBBBABBBBBB?=%3476??>???=?=399 @HWI-EAS432:5:1:1:769#0/1 TCTCCTCTCTTTCACGTTTCCGATTCGGCCGATCAATGGACGGCTTCACAGATCGGAAGAGAGGGTCAGGAGGAA +HWI-EAS432:5:1:1:769#0/1 ?;?@9?>BBBBBBB@6>BB<@1=AA?<>A@?;674?:729;;=<=='3;;7:1359/5/9/(67(0'0*%-/5,4 @HWI-EAS432:5:1:1:42#0/1 TCTCTCGGGAGCTCTTCGTCGAGGTGGAGTGGTAGACATGTACGGCTTCTTCCCCCCCCCCAAACCGGAGCCAAC +HWI-EAS432:5:1:1:42#0/1 ?B@B<B79@?<B6AA:A<<>1>??1=-:91777<7:B?8.9=;'5>7:769/9:*;='7&83;;((-0..,1-*( @HWI-EAS432:5:1:1:1924#0/1 CTGGATTCTGAAACATTTCTCTCATTTGGGTATTTGATTCCATCATGTTACGTACATTCGGGTTCATGTTGAGCA .
.
.


Galaxy Queues

posted Sep 6, 2011, 11:35 AM by James Johnson   [ updated Sep 6, 2011, 1:32 PM ]

Galaxy is currently unable to queue jobs to the compute cluster.  
Jobs are showing the Error message:  "Unable to queue job for execution."
We are investigating the problem.  
Back in production at 3:30 PM

Galaxy - unscheduled update

posted Jul 29, 2011, 5:27 AM by Anne-Francoise Lamblin

07/29/2011  7:30AM

Galaxy may be unreachable at this time.  We are experiencing a database connection problem and in the process of correcting the problem.

.

Increase walltime limit for Galaxy jobs

posted May 3, 2011, 2:52 PM by John Garbe   [ updated May 3, 2011, 3:05 PM ]

I've run into the 24 hour time limit on Galaxy jobs while running cufflinks on ~10Gb of sequence.  Running the same job in the "lab" PBS queue using 12 processors took about 48 hours of walltime to  finish. Could you bump up the time limit on Galaxy jobs so I can run these jobs from within Galaxy  instead of downloading all the files and running the job on a different computer?
=>> PBS: job killed: walltime 86421 exceeded limit 86400

Mothur version 1.18

posted Apr 18, 2011, 7:45 AM by James Johnson   [ updated May 5, 2011, 9:27 AM ]

Mothur version 1.18 was released on April 13.   A significant change was implemented eliminating the read.dist, read.otu, and read.tree commands.  I will be updating the Galaxy wrappers to be compataible with version 1.18.   From a galaxy users perspective, the tool wrappers probably won't need to change much, since the wrappers took care of the read commands internally.  However, there will be many changes required in the internal workings of the galaxy tool wrappers to match the new required parameters of many of the Mothur commands.  

This would also be a good time to make usability changes to the Galaxy wrappers.  If you have suggestions on what would make the Galaxy implementation of Mothur more useful to you, I'd like to hear your suggestions.  

Commands get.otulist and get.sharedseqs will be added to this release.

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