SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SOAPec Segmentation Fault BugSeq Bioinformatics 1 11-11-2014 01:54 AM
Blast2 - Segmentation Fault bfantinatti Bioinformatics 4 05-13-2014 11:11 PM
gffread segmentation fault gokhulkrishnakilaru Bioinformatics 10 01-28-2013 10:28 AM
Segmentation fault in sift4.03 nkwuji Bioinformatics 2 12-20-2011 10:35 PM
cufflinks segmentation fault help please seq_newbie Bioinformatics 1 06-29-2011 11:52 AM

Reply
 
Thread Tools
Old 05-22-2018, 08:46 AM   #1
scamiolo
Junior Member
 
Location: UK

Join Date: May 2018
Posts: 3
Default Trinity segmentation fault

Hi there,

I would like to use the transcript assembler Trinity to assemble RNAseq data while using a reference genome as a guide. I aligned my reads on the reference genome with Tophat, sorted the obtained bam file and then used the following command:

Code:
~/Software/Trinityrnaseq-v2.6.6/Trinity --genome_guided_bam accepted_hits_sorted.bam --genome_guided_max_intron 32000 --max_memory 10G --CPU 10 &
The command returns a Segmentation fault error without any further details
Can someone help me with this please?
thanks!
scamiolo is offline   Reply With Quote
Old 05-22-2018, 09:24 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,747
Default

That 10G is a guide (I assume you took that from the example command line). What size is your BAM file? You may need to assign more RAM for this job.
GenoMax is offline   Reply With Quote
Old 05-22-2018, 11:25 AM   #3
scamiolo
Junior Member
 
Location: UK

Join Date: May 2018
Posts: 3
Default

Quote:
Originally Posted by GenoMax View Post
That 10G is a guide (I assume you took that from the example command line). What size is your BAM file? You may need to assign more RAM for this job.
Hi there,

thanks for your e-mail. I do not think it is a matter of amount of memory. The bam file is under 100 Mb, very small actually. Also Trinity version I am using is the latest. I really can not understand what is going on. Any ideas?
thanks a lot
scamiolo is offline   Reply With Quote
Old 05-22-2018, 01:58 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,747
Default

Have you run trinity with other data successfully? if not test it with something else. Did you compile the program yourself?
GenoMax is offline   Reply With Quote
Old 05-23-2018, 12:20 AM   #5
scamiolo
Junior Member
 
Location: UK

Join Date: May 2018
Posts: 3
Default

Yes it returns a segmentation fault also with other paired end data. I compiled directly with the make command as stated in the manual. It fails also if I provide only arguments --left and --right.
Actually I just checked the installation with make test_trinity and this failed with the following message

Code:
#######################################################
##  Run Trinity to Generate Transcriptome Assemblies ##
#######################################################

../../Trinity --seqType fq --max_memory 2G \
              --left reads.left.fq.gz \
              --right reads.right.fq.gz \
              --SS_lib_type RF \
              --CPU 4 
./runMe.sh: line 11: 42124 Segmentation fault      ../../Trinity --seqType fq --max_memory 2G --left reads.left.fq.gz --right reads.right.fq.gz --SS_lib_type RF --CPU 4
make[1]: *** [test] Error 139
make[1]: Leaving directory 
make: *** [test_trinity] Error 2

thanks
scamiolo is offline   Reply With Quote
Old 05-23-2018, 03:02 AM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,747
Default

Ok. So it is your compiler that may be the problem. What version of GCC did you use to compile this? You may need to use a newer version.
GenoMax 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 08:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO