Error

[chandni sidhu]

Hi,

I am getting the following error message every time I run ./config in Metatrans Pipeline.

#Error# The source shell file "./0-Software/pipelinescripts/pipeline.source" did not have "<INSTALLSHELLPATH>" tag.

I have tried using "export PATH" but it did not work. Please advise. 

Also, pipeline.source file in not present. I renamed pipeline.sh to pipeline.source, but again it did not work.

Seeking urgent help.

Best regards,

Dr. Chandni Sidhu

MPI for Marine Microbiology

[metatr...@gmail.com]

Hi Dr. Chandni,

We have downloaded, decompressed, and run the sample test published in the website and works fine.

Could you please try to test the sample dataset following step by step the installation instructions described in

the README file (http://metatrans.org/data/documents/README.txt)?

It should work with no problems, if not, please  describe your environment (OS flavour, python version, ...). MetaTrans

was tested under Ubuntu 12.04/14.04. Unfortunately, so far, we can not provide further support for newer releases.

Find here a description of the environment in which it was tested: http://metatrans.org/#requirements

The error you get about "<INSTALLSHELLPATH>" is normally caused because you run "./config" more than once.

"./config" should be run only once. The first time is run it translates "<INSTALLSHELLPATH>" for the appropriate shell path

in your environment in the main scripts. Therefore, a second run will show up the error you describe.

Hope this helps,

Greetings

[Giovanna Ventola]

Hi, I'm Giovanna and I have this error, when I run the test:

./metatrans

#Checking pipeline files' integrity (Date: '06-10-20' Time: '09h:42m:45s CEST')... 

#Checking sequence files' integrity (Date: '06-10-20' Time: '09h:42m:45s CEST')... 

  File "./0-Software/scripts/getMeta.py", line 190

    print len(mydata[0])

          ^

SyntaxError: invalid syntax

  File "./0-Software/scripts/getMeta.py", line 190

    print len(mydata[0])

          ^

SyntaxError: invalid syntax

 #Error# Sequence './0-Sequences/' file not found. 

 #Error# Pipeline exited with error code 1. 

 #HELP# An error may lead files in an intermediate state. To re-run the pipeline some folder might be deleted. 

My system is CentOS 8. Is this a problem?

Can you help me?

Thanks 

Giovanna