SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
AB SOLiD Bioscope rdeborja Bioinformatics 35 09-27-2011 05:41 PM
Bioscope clip vs mismatch dsidote Bioinformatics 0 01-18-2011 12:59 PM
Bioscope - Format mapping jorjial SOLiD 6 11-15-2010 07:05 AM
BioScope Mapping Multiple csfasta-Files DNAjunk SOLiD 5 06-21-2010 10:50 PM
BioScope Mapping Rounds DNAjunk SOLiD 1 06-08-2010 01:57 AM

Reply
 
Thread Tools
Old 07-29-2011, 10:07 AM   #1
cjose
Member
 
Location: Dallas

Join Date: Jul 2011
Posts: 14
Default bioscope mapping issue

Hello all,

So I ran the demo paired-end pairing run and it worked fine. When I run my data, the mapping process doesn't seem to work. It gets hung up on this line for hours:
"Waiting for events on selector '62bd6599-6a93-4aa0-b37c-1575198a9529'"
The ini files/parameters are all the same, for the read.length which I changed from 25 to 35. Has anyone else had this same/similar issue?

Thanks in advance!
cjose is offline   Reply With Quote
Old 07-31-2011, 06:21 PM   #2
rdeborja
Member
 
Location: Toronto

Join Date: Aug 2008
Posts: 42
Default

Can you post your ini file for mapping?
rdeborja is offline   Reply With Quote
Old 08-05-2011, 08:00 AM   #3
cjose
Member
 
Location: Dallas

Join Date: Jul 2011
Posts: 14
Default

##################################
##################################
##
## global settings for the pipeline run
##
import ../globals/global.ini
reference = ${reference.dir}/ch11_12_validated.fasta
read.length = 50


##################################
##################################
##
## mapping pipeline
##
mapping.run = 1
mapping.tagfiles.dir =${base.dir}/reads
mapping.output.dir = ${output.dir}/s_mapping


##################################
##################################
##
## temp files and folders keep
## # don't keep for clean run ... make it =1, if you want them not to be deleted.
#pipeline.cleanup.middle.files = 0
#job.cleanup.temp.files = 0
cjose 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 07:47 PM.


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