Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: MACS galaxy error
0
gravatar for schelarina
3.8 years ago by
schelarina • 0
schelarina • 0 wrote:
I am using MACS on Galaxy and I get this error. cant understand why.
I already lowered MFOLD parameter but still get this error!
INFO  @ Mon, 02 Feb 2015 09:51:28: 
# ARGUMENTS LIST:
# name = MACS_in_Galaxy
# format = BED
# ChIP-seq file = /galaxy-repl/main/files/010/312/dataset_10312081.dat
# control file = None
# effective genome size = 2.70e+09
# tag size = 25
# band width = 300
# model fold = 1
# pvalue cutoff = 1.00e-05
# Ranges for calculating regional lambda are : peak_region,1000,5000,10000 
INFO  @ Mon, 02 Feb 2015 09:51:28: #1 read tag files... 
INFO  @ Mon, 02 Feb 2015 09:51:28: #1 read treatment tags... 
WARNING @ Mon, 02 Feb 2015 09:51:29: NO records for chromosome cv11, minus strand! 
INFO  @ Mon, 02 Feb 2015 09:51:29: #1  Background Redundant rate: 0.04 
INFO  @ Mon, 02 Feb 2015 09:51:29: #1 finished! 
INFO  @ Mon, 02 Feb 2015 09:51:29: #2 Build Peak Model... 
INFO  @ Mon, 02 Feb 2015 09:51:29: #2 number of paired peaks: 0 
WARNING @ Mon, 02 Feb 2015 09:51:29: Too few paired peaks (0) so I can not build the model! Lower your MFOLD parameter may erase this error. 
WARNING @ Mon, 02 Feb 2015 09:51:29: Process is terminated!
mfold software error galaxy datatype macs • 1.2k views
ADD COMMENT • link •
modified 3.8 years ago by Jennifer Hillman Jackson ♦ 25k • written 3.8 years ago by schelarina • 0
0
gravatar for Jennifer Hillman Jackson
3.8 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Double check that the other input parameters are a fit for your data. The first options to check are the tag size and genome size. Click on the MACS documentation link on the tool form for the complete details for these options (and others).

In some cases, this error can also result from poor mapping in prior steps. Review the success rate. If low, there can be many reasons, but a common one is that the input sequence data had an incorrect datatype assigned (one that did not match the quality score scaling of the data). You can double check sequence datatype/quality scores - help for how to do that is here: 
http://wiki.galaxyproject.org/Support#FASTQ_Datatype_QA

Best, Jen, Galaxy team
ADD COMMENT • link written 3.8 years ago by Jennifer Hillman Jackson ♦ 25k
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 180 users visited in the last hour