wdecoster/nanostat

TypeError: get_input() got an unexpected keyword argument 'barcoded'

Closed this issue · 12 comments

mw55309 commented

Any idea what's going on here?

$ NanoStat --fastq MinION_chicken_ceca/MinION_chicken_ceca.fastq --outdir test
Traceback (most recent call last):
  File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/nanopack/bin/NanoStat", line 6, in <module>
    sys.exit(nanostat.NanoStat.main())
  File "/exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/nanopack/lib/python3.5/site-packages/nanostat/NanoStat.py", line 73, in main
    barcoded=args.barcoded)
TypeError: get_input() got an unexpected keyword argument 'barcoded'

??

The run isn't barcoded

wdecoster commented

Could you please check if you have the latest version of NanoStat and nanoget?

mw55309 commented

So I just installed using conda (pip install failed).

Running a conda env with python=3.5

wdecoster commented

I'm on teambuildingsweekend with colleagues so will help you later.

Can you give me the output of

python -c "import nanoget ; print(nanoget.version)"

wdecoster commented

Should have been __version__

mw55309 commented

0.15.0

mw55309 commented

OK, but I guess this is the version installed when I installed nanostat....

wdecoster commented

Possible, will check it later, but now you could already conda upgrade nanoget which I believe is going to solve the problem

mw55309 commented

Hmm, I am less convinced this is the problem

$ conda upgrade nanoget
Fetching package metadata .......................
Solving package specifications: .

# All requested packages already installed.
# packages in environment at /exports/cmvm/eddie/eb/groups/watson_grp/software/mickpython/nanopack:
#
nanoget                   1.5.0                    py35_0    bioconda
(nanopack) [mwatson9@login04(eddie) ~]$  python -c "import nanoget ; print(nanoget.__version__)"
0.15.0
wdecoster commented

This suggest that you already have another nanoget installation, which is earlier in sys.path.

Can you check

python -c "import nanoget ; print(nanoget.__file__)" which should reveal the path to the installation directory, maybe from pip?

mw55309 commented

You're right, it was from an old version of NanoFilt

Does the conda recipe need updating to specify a version of nanoget?

wdecoster commented

Yes, it does. I'll go over the recipes and update the minimally required version. Thanks