SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat for finding long ncRNA with short reads? KevinLam Bioinformatics 3 02-24-2017 10:11 AM
Tophat Run time bassu Bioinformatics 11 09-17-2013 10:59 PM
How long should paired-end alignment run? agc Bioinformatics 11 09-07-2011 01:31 AM
How to run Tophat with annotation file masylichu Bioinformatics 2 09-06-2011 08:25 PM
Tophat bug -- excessively long match ebartom Bioinformatics 3 02-28-2011 01:39 PM

Reply
 
Thread Tools
Old 07-20-2011, 05:53 AM   #1
seq_newbie
Member
 
Location: Ireland

Join Date: Jun 2011
Posts: 14
Default Very long tophat run

Hi,

I have submitted a job to the queue on my cluster with 7 successive tophat jobs in the file. It has been 2 days and only the directory for the first job has been created and there is still no accepted_hits.bam file

(only left_kept_reads.info logs right_kept_reads.info tmp)

There are no error files generated and the job is still on the queue. Does anyone know what might be going on and if I should kill the job and start again? I don't want to kill it if there's a chance it's normal for such a long run.

Thanks,

K.
seq_newbie is offline   Reply With Quote
Old 07-20-2011, 08:54 AM   #2
dariober
Senior Member
 
Location: Cambridge, UK

Join Date: May 2010
Posts: 311
Default

Hi,
It might be normal if you have lots of reads (can't tell how many, but I guess hundreds of millions would take days on a single thread/processor).

Also, could it be that you submitted the job two days ago but stayed in the queue waiting to start for several hours?

If you post more details (number of reads, log files etc...) someone in SEQanswers might give some insights...

Dario
dariober is offline   Reply With Quote
Old 07-20-2011, 09:11 AM   #3
seq_newbie
Member
 
Location: Ireland

Join Date: Jun 2011
Posts: 14
Default

Hi Dariober,

Thanks for your reply. I'm pretty sure the job started running straight away. I'm not sure of the number of reads but I reckon it would be in the millions. I tried uploading log files but I get invalid file message. I'll just wait and see I suppose.

K.
seq_newbie is offline   Reply With Quote
Old 04-15-2014, 08:02 AM   #4
jeales
Member
 
Location: UK

Join Date: Oct 2012
Posts: 13
Default

You can do "wc -l my_reads.fastq" on one of the fastq files then divide by 4 and that is the number of reads in the file
jeales is offline   Reply With Quote
Reply

Tags
tophat

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:54 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO