Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
tophat taking too long to run fahim RNA Sequencing 7 05-14-2014 07:59 AM
STAR multi-mapping id0 Bioinformatics 1 03-28-2014 07:41 AM
STAR-alignment/confusion with mismatches & multi-mapping parameter babi2305 Bioinformatics 9 05-07-2013 12:45 PM
bowtie 80 mer-long mapping kenosaki Bioinformatics 5 07-03-2011 02:24 AM
PubMed: Comprehensive mapping of long-range interactions reveals folding principles o Newsbot! Literature Watch 0 10-10-2009 02:09 AM

Thread Tools
Old 05-02-2014, 03:56 AM   #1
Location: germany

Join Date: Feb 2014
Posts: 20
Default STAR Mapping taking too long


I am using Star v 2.3.0 for mapping.
I have 6 samples, all paired-end.
The genome generation step went without any problem.
But the mapping is taking too long: it has been running since last evening and is stuck at the following:
May 01 19:21:13 ..... Started STAR run
May 01 19:21:19 ..... Started mapping
The sam file size is increasing, but very incrementally. Similarly for the corresponding logout file.

Any ideas why this might be happening??

mtiwaridros is offline   Reply With Quote
Old 05-02-2014, 08:26 AM   #2
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Run top and check the CPU utilization; there could be a problem. Also, how many cores are you running it on, how much memory is available, what is the size of the input, and what is the size of the reference? And, of course, what was your command line?
Brian Bushnell is offline   Reply With Quote

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 05:21 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO