Question: Macs Failed Because Of Lambdaset Options
0
gravatar for Philipe Moncuquet
5.9 years ago by
Australia
Philipe Moncuquet40 wrote:
Hi, I am trying to use MACS and I get the following error when the job fails : Usage: macs <-t tfile> [-n name] [-g genomesize] [options] Example: macs -t ChIP.bam -c Control.bam -f BAM -g h -n test -w --call-subpeaks macs: error: no such option: --lambdaset I am not really familiar to MACS so I checked the documentation and it seems Galaxy is rigth to complain because there is no such option as --lambdaset (http://liulab.dfci.harvard.edu/MACS/README.html). I went back to the xml wrapper and there is this ( <param name="lambdaset" type="text" ....)="" parameters="" that="" corresponds="" to="" the="" text="" box="" 3="" levels="" of="" regions="" around="" the="" peak="" region="" to="" calculate="" the="" maximum="" lambda="" as="" local="" lambda:="" does="" anyone="" face="" the="" same="" problem="" ?="" any="" clue="" on="" what="" i="" should="" try,="" should="" i="" modify="" the="" wrapper="" ?="" cheers,="" philippe<="" div="">
macs • 791 views
ADD COMMENTlink modified 5.9 years ago by Jennifer Hillman Jackson25k • written 5.9 years ago by Philipe Moncuquet40
0
gravatar for Jennifer Hillman Jackson
5.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Philipe, Is this problem occurring on the public Main Galaxy server at http://main.g2.bx.psu usegalaxy.org)? If so, please submit a bug report so that we can examine. http://wiki.g2.bx.psu.edu/Support#Support.Reporting_tool_errors If this is occurring on a local instance, it could be that there is a mismatch between the version of MACS supported by the Galaxy wrapper and the version of MACS installed. The current wrapper is for MACS v 1.3. http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies The final possibility is that this is on another public instance - if you need help finding out how to contact their support/administrator, or if your question has been misunderstood, please let us know. Best, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org
ADD COMMENTlink written 5.9 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 134 users visited in the last hour