SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat: segment-based junction search failed with err =-11 jdanderson Bioinformatics 15 10-14-2017 06:47 AM
Tophat Error: Error: segment-based junction search failed with err =-6 sjnewhouse RNA Sequencing 8 03-19-2013 04:14 AM
TopHat closure based search and coverage based search tasteandsee Bioinformatics 1 03-27-2012 01:47 AM
TopHat closure-search: what does it do? d f Bioinformatics 4 03-15-2012 12:28 PM
TopHat and Cufflinks; closure search poisson200 Bioinformatics 0 08-13-2010 07:13 AM

Reply
 
Thread Tools
Old 06-06-2011, 09:27 PM   #1
bambootear
Junior Member
 
Location: beijing,china

Join Date: Apr 2011
Posts: 1
Default tophat 1.3.0(Beta) closure search failed

I tried to run tophat 1.3.0(Beta) with 90*2 illumina RNA-seq

tophat -o tophat-output -F 0.1 -p 6 -r 10 --mate-std-dev 45 --solexa1.3-quals --library-type fr-firststrand -i 30 --min-closure-intron 30

--min-coverage-intron 30 --closure-search --coverage-search --segment-length 30 ref polyA.1.fq polyA.2.fq


The same data and parameters worked well with tophat 1.2.0


Quote:
[Tue Jun 7 01:43:17 2011] Beginning TopHat run (v1.3.0)
-----------------------------------------------
[Tue Jun 7 01:43:17 2011] Preparing output location tophat-output/
[Tue Jun 7 01:43:17 2011] Checking for Bowtie index files
[Tue Jun 7 01:43:17 2011] Checking for reference FASTA file
[Tue Jun 7 01:43:17 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Jun 7 01:43:17 2011] Checking for Samtools
Samtools Version: 0.1.12
[Tue Jun 7 01:43:17 2011] Generating SAM header for ref
[Tue Jun 7 01:43:17 2011] Preparing reads
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
Left reads: min. length=90, count=11331560
Right reads: min. length=90, count=11332998
[Tue Jun 7 01:59:21 2011] Mapping left_kept_reads against ref with Bowtie
[Tue Jun 7 02:08:18 2011] Processing bowtie hits
[Tue Jun 7 02:19:24 2011] Mapping left_kept_reads_seg1 against ref with Bowtie (1/3)
[Tue Jun 7 02:21:27 2011] Mapping left_kept_reads_seg2 against ref with Bowtie (2/3)
[Tue Jun 7 02:23:34 2011] Mapping left_kept_reads_seg3 against ref with Bowtie (3/3)
[Tue Jun 7 02:25:36 2011] Mapping right_kept_reads against ref with Bowtie
[Tue Jun 7 02:34:46 2011] Processing bowtie hits
[Tue Jun 7 02:45:21 2011] Mapping right_kept_reads_seg1 against ref with Bowtie (1/3)
[Tue Jun 7 02:47:13 2011] Mapping right_kept_reads_seg2 against ref with Bowtie (2/3)
[Tue Jun 7 02:49:07 2011] Mapping right_kept_reads_seg3 against ref with Bowtie (3/3)
[Tue Jun 7 02:51:00 2011] Searching for junctions via segment mapping
[Tue Jun 7 03:02:19 2011] Searching for junctions via mate-pair closures
[FAILED]
Error: closure-based junction search failed with err =-11
bambootear 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 02:02 PM.


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