v2.14.1 attributeError: 'Namespace' object has no attribute 'cdhit_max_memory'

[Coldheart79]

Updated ariba to version2.14.1 and started running in to problems, please advice, error occurs when running Task: prepareref and the same when running 'ariba test out'

Running ARIBA on test data...

|=============================================================================|
| Preparing input data |
|=============================================================================|

Made output directory out. Copying test data files into it:
copied ref_seqs.fa
copied metadata.tsv
copied reads_1.fq
copied reads_2.fq

|=============================================================================|
| Try running ariba prepareref |
|=============================================================================|

Running ariba prepareref with:
/usr/local/bin/ariba prepareref --verbose -f ref_seqs.fa -m metadata.tsv --threads 1 PREPAREREF

ARIBA version: 2.14.1

External dependencies:
bowtie2 2.3.4.1 /usr/bin/bowtie2
cdhit 4.7 /home/ant4317/Program/cd-hit-v4.6.8/cd-hit-est
nucmer 3.1 /usr/bin/nucmer

External dependencies OK: True

Python version:
3.6.8 (default, Jan 14 2019, 11:02:34)
[GCC 8.0.1 20180414 (experimental) [trunk revision 259383]]

Python packages:
ariba 2.14.1 /home/ant4317/.local/lib/python3.6/site-packages/ariba/init.py
bs4 4.7.1 /home/ant4317/.local/lib/python3.6/site-packages/bs4/init.py
dendropy 4.4.0 /home/ant4317/.local/lib/python3.6/site-packages/dendropy/init.py
pyfastaq 3.17.0 /home/ant4317/.local/lib/python3.6/site-packages/pyfastaq/init.py
pymummer 0.10.3 /home/ant4317/.local/lib/python3.6/site-packages/pymummer/init.py
pysam 0.15.2 /home/ant4317/.local/lib/python3.6/site-packages/pysam/init.py

Python packages OK: True

Everything looks OK: True
Traceback (most recent call last):
File "/usr/local/bin/ariba", line 298, in
args.func(args)
File "/home/ant4317/.local/lib/python3.6/site-packages/ariba/tasks/prepareref.py", line 24, in run
cdhit_max_memory=options.cdhit_max_memory,
AttributeError: 'Namespace' object has no attribute 'cdhit_max_memory'

Something went wrong. See above for error message(s). Return code was 1

[Coldheart79]

Do not know if this might be connected to the problem there is no ".local/lib/python3.6/site-packages/ariba/". Ariba is found under ".local/lib/python3.6/dist-packages/ariba/"

[kpepper]

How is your installation set up? What is getting installed here: /usr/local/bin/ariba (and which version)? Where is the new version of Ariba installed? Do you set the PYTHONPATH variable at all?

[kpepper]

Hi @Coldheart79. Did you manage to get your install working?

[Coldheart79]

Yes its fixed

[kpepper]

Great. I'll close the issue then.