Error Metatrans urgently

[Giovanna Ventola]

Hi. I'm Giovanna, a bioinformatician. I'm using metatrans pipeline on my 12 samples. 

I followed all steps explained in the manual, and I'm running the test, but also with the test the software stopped, and I obtained this error:

./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.
 #HELP# Please, read the troubleshooting section of the manual for help. 

Please, I need to run metatrans, urgently, Can You Help me?

Thanks so much.

Giovanna

Dott.ssa Giovanna Maria Ventola, Bioinformatics PhD

Phd in Bioinformatics

Master’s Degree in Biology

Bioinformatician in Genomix4Life S.r.l.

Genomix4Life Srl

c/o Laboratorio di Medicina Molecolare e Genomica

Campus di Medicina e Chirurgia, Prefab. 2

Via S. Allende, 1 - 84081 Baronissi (SA) - Italy

Mobile: +39 320 9272 160

e-mail: giovanna...@genomix4life.com or giovannav...@gmail.com

[Nasir Abbasi]

Dear Giovanna,

You need to make sure you have all packages which are needed by metatrans. I have got this error and i am not sure how I solved it but It was related to different dependency which are needed to run Metatrans.

Best Regards,

Nasir Mahmood Abbasi

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[Giovanna Ventola]

Thanks Nasir Mahmood Abbasi, 

but I have all packages wich are needed to metatrans. 

I have CentOS 8. Could this be a problem?

[Niclas Nordholt]

Hi Giovanna,

from a quick look, it seems like it is using the wrong version of Python. If I understand correctly, MetaTrans requires Python 2.7. In Python 3 the print method requires parentheses to work print('something') whereas in Python 2.7 it works like print 'something'. If Python 3 is your default, it will not work and give a syntax error as in your example. So maybe try and set your default Python to Python 2.7 or run MetaTrans from a virtual environment with Python 2.7. Not an expert in this, but I've stumbled upon this problem earlier with different programs. Hope it's useful.

Cheers