Question: FastQ Groomer Problem - Syntax
gravatar for tony.shu
9 months ago by
tony.shu10 wrote:


I have searched all over and I cannot find a solution to this. When I run the FastQ groomer I have installed through the tool shed, I get this in the history:

File "/project/sysbio/shed_tools/", line 29

print "Groomed %i %s reads into %s reads." % ( read_count + 1, input_type, output_type )

SyntaxError: invalid syntax

I have python 2.7.8 and run galaxy locally. I have not included a: from __future__ import print_function anywhere. When running the FastQ Groomer tool, my inputs are:


Sanger & Illumina 1.8+


Any help will be appreciated, thanks.


fastq software error devteam • 247 views
ADD COMMENTlink modified 8 months ago by Jennifer Hillman Jackson24k • written 9 months ago by tony.shu10
gravatar for Jennifer Hillman Jackson
8 months ago by
United States
Jennifer Hillman Jackson24k wrote:


This appears to be a tool install problem. Make sure that you are using the latest version of Galaxy (17_05) and the most recent version of FastQC. Use the default conda dependency resolution for best results, unless you are configuring a specific system as an administrator and can troubleshoot locally.

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 8 months ago by Jennifer Hillman Jackson24k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 58 users visited in the last hour