SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Cufflinks gets stuck at chrUm fron (rat) rn4 mapping Jluis Bioinformatics 2 01-01-2013 11:29 PM
3730XL stuck on yellow? pmiguel Sanger/Dye Terminator 0 12-21-2011 12:20 PM
solid reads stuck at searching juntions in TopHat zorph Bioinformatics 8 12-13-2010 04:50 PM
Newbie stuck with Galaxy filter kcarss Bioinformatics 2 07-23-2010 12:28 AM

Reply
 
Thread Tools
Old 10-05-2012, 09:51 AM   #1
EGrassi
Member
 
Location: Turin, Italy

Join Date: Oct 2010
Posts: 66
Default Tophat 2.0.0 is stuck

Hello, I have a tophat process that seems stuck:

Code:
[2012-10-03 14:47:19] Beginning TopHat run (v2.0.0)
-----------------------------------------------
[2012-10-03 14:47:19] Checking for Bowtie
                  Bowtie version:        2.0.0.6
[2012-10-03 14:47:19] Checking for Samtools
                Samtools version:        0.1.18.0
[2012-10-03 14:47:19] Checking for Bowtie index files
[2012-10-03 14:47:19] Checking for Bowtie index files
[2012-10-03 14:47:19] Checking for reference FASTA file
[2012-10-03 14:47:19] Generating SAM header for ../alignment/expanded_genome2
        format:          fastq
        quality scale:   phred33 (default)
[2012-10-03 14:47:56] Reading known junctions from GTF file
[2012-10-03 14:48:01] Preparing reads
         left reads: min. length=50, count=29715271
        right reads: min. length=50, count=29535618
[2012-10-03 15:02:14] Using pre-built transcriptome index..
[2012-10-03 15:02:18] Mapping left_kept_reads against transcriptome genes with Bowtie2
[2012-10-03 15:18:27] Mapping right_kept_reads against transcriptome genes with Bowtie2
[2012-10-03 15:34:00] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-10-03 15:40:53] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
[2012-10-03 15:47:50] Resuming TopHat pipeline with unmapped reads
[2012-10-03 15:48:14] Mapping left_kept_reads.m2g_um against expanded_genome2 with Bowtie2
[2012-10-03 15:57:12] Mapping left_kept_reads.m2g_um_seg1 against expanded_genome2 with Bowtie2 (1/2)
[2012-10-03 16:00:07] Mapping left_kept_reads.m2g_um_seg2 against expanded_genome2 with Bowtie2 (2/2)
[2012-10-03 16:03:12] Mapping right_kept_reads.m2g_um against expanded_genome2 with Bowtie2
[2012-10-03 16:12:05] Mapping right_kept_reads.m2g_um_seg1 against expanded_genome2 with Bowtie2 (1/2)
[2012-10-03 16:15:47] Mapping right_kept_reads.m2g_um_seg2 against expanded_genome2 with Bowtie2 (2/2)
[2012-10-03 16:19:25] Searching for junctions via segment mapping
[2012-10-03 21:18:12] Retrieving sequences for splices
[2012-10-03 21:20:47] Indexing splices
[2012-10-03 21:33:14] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie2 (1/2)
...since this step never took so long I'm beginning to wonder if maybe it is really stuck there...maybe there is a problem in the multicore approach. I see the process listed as running and using CPU but strace does not report any syscall and the virtual memory used is fixed...I am checking /proc/PID data but I am not sure which is the correct file to
understand this kind of problems (maybe stack?).
Anyone experienced this kind of problems? I don't see it listed as a solved issue in successive version so I am not sure if it's time-wise to stop it and try with a newer version.

Thank you very much,
E.G.
EGrassi is offline   Reply With Quote
Old 10-06-2012, 01:33 AM   #2
vplagnol
Member
 
Location: London, UK

Join Date: Sep 2008
Posts: 13
Default

+1 to this. I had similar issues (perhaps the same one) with the tophat 2.0.4 and multicore. I now (painfully) only use single core and it works fine, albeit very slowly.

Vincent
vplagnol is offline   Reply With Quote
Old 10-06-2012, 01:37 AM   #3
EGrassi
Member
 
Location: Turin, Italy

Join Date: Oct 2010
Posts: 66
Default

Ouch, sad. Thanks, I will try to launch it in sigle core mode and see if it works (assuming that it will end before my contract does that ).
EGrassi is offline   Reply With Quote
Old 10-06-2012, 10:58 AM   #4
billstevens
Senior Member
 
Location: Baltimore

Join Date: Mar 2012
Posts: 120
Default

Do you need to upgrade to Tophat 2? I got good alignment with Tophat 1.4 and Bowtie 1, and I'm wondering if I should upgrade. If it can only do one core at a time, I definitely won't.
billstevens is offline   Reply With Quote
Old 10-08-2012, 05:41 AM   #5
EGrassi
Member
 
Location: Turin, Italy

Join Date: Oct 2010
Posts: 66
Default

...no luck. Even the single core process got stuck at that point...I'm working on a public dataset (GSE27003). I've added the --no-novel-juncs option and it has finished. I really do not understand what's the problem.
EGrassi is offline   Reply With Quote
Old 10-08-2012, 07:22 AM   #6
turnersd
Senior Member
 
Location: Charlottesville, VA

Join Date: May 2011
Posts: 112
Default

I've had the same issues and my solution was to "upgrade" to Tophat 1.4.1.
turnersd is offline   Reply With Quote
Old 10-08-2012, 08:06 AM   #7
hbt
Member
 
Location: UK

Join Date: Jan 2011
Posts: 20
Default

We've also had problems running Tophat 2 on multiple cores, usually it would fail at the point where multiple BAM files are merged into 1.
However we found that running on 4 cores worked so have switched to that for now...
hbt is offline   Reply With Quote
Old 10-08-2012, 08:09 AM   #8
EGrassi
Member
 
Location: Turin, Italy

Join Date: Oct 2010
Posts: 66
Default

Tophat 2 on a different dataset worked for me with different number of cores, ranging from 2 to 6. I'm wondering what could be the problem, even if in this peculiar case the problem is still there with a single core.
EGrassi is offline   Reply With Quote
Old 10-24-2012, 03:08 AM   #9
alaincoletta
Junior Member
 
Location: Brussels

Join Date: Oct 2012
Posts: 3
Default

We're using TopHat2 on Ubuntu 12.0.4. Parts of the process take up the max number of threads (16 threads: -p 16). https://insilicodb.org
alaincoletta is offline   Reply With Quote
Reply

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 04:35 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO