Could not find reaper

[held...@gmail.com]

Hello,

I am attempting to run the test data set (MacOS High Sierra) and keep running into the error below. This is close to some of the other questions on here--though not identical-- and I could use some help!

#Running sample 'C1JB3ACXX_1_5':

#Running Module1 >>Quality Control<< ... (Date: '17-07-18' Time: '17h:26m:33s EDT')

real 0m18.054s

user 0m17.547s

sys 0m0.969s

real 0m18.055s

user 0m17.753s

sys 0m0.955s

 #Error# Pipeline exited with error code 141. 

---------------------------

Then when I check the output_kraken_stage_reaper.log:

####### Beginning step: REAPER #######

----------------------

Running a system check:

Sequence Imp - Copyright (C) 2011 2012 2013 EMBL - European Bioinformatics Institute 

This program is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.

This program is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.

Please contact us at: kra...@ebi.ac.uk

For more info (including full manual) see: http://www.ebi.ac.uk/enright/kraken/

Could not find reaper. To install reaper and for associated documentation please visit http://www.ebi.ac.uk/~stijn/reaper/. You will need to ensure the programme is installed in the file path

System check failed: Closing pipeline.

Please initiate pipeline with --system-check to identify missing software.

---------------------------------------

I am able to find reaper in kraken_tools_binaries. Is there a possible explanation for why the software is not able to be found?

Thanks!

Helen

[metatr...@gmail.com]

Hi Helen,

"Reaper" is a tool provided as a third-party tool but is bundled within MetaTrans. To ensure
everything is working fine, please download and test the samples dataset.

Follow the instructions of the README file:
http://metatrans.org/data/documents/README.txt

And download and install these files in this order as indicated in the README file:
http://metatrans.org/data/documents/1-Scripts.tar.gz
http://metatrans.org/data/documents/2-ThirdpartyTools.tar.gz
http://metatrans.org/data/documents/Databases-Test.tar.gz
http://metatrans.org/data/documents/Samples-Test.tar.gz

Hope this helps

[held...@gmail.com]

yes, I'm sorry I didn't make this clear before-- I followed all the instructions in the README.txt file, using the sample sequences. Unzipping and configuration went fine, but once I started the ./metatrans step, I got the error at module1 that I shared in the original post.

Thanks,

Helen

[metatr...@gmail.com]

Hi Helen,

If this is the case, please read the instructions pointed two thread before " error 141 ". That person had a similar problem to yours.
The suggestions mentioned in that thread are mainly thought for RedHat/CentOS, but according to the output you showed, the problem
seems similar if not equal. But, unfortunately, we cannot guarantee that the solution proposed for RedHat/CentOS is going to work out in your case

We are sorry, but we cannot provide further assistance right now for another environment like, in your case, Mac OS. We hope these suggestions
can help you out to overcome the issue.

Best