about inStrain profile with KeyError: 'version'

[ZT-ls]

Hi, i'm encounting a issue when running inStrain profile, it raised the keyError:'version' which like this is there any ways to deal with it? thank you very much

[MrOlm]

Hi @ZT-ls - this seems to be a stange bug with the python package "pandas" that I've never seen before.

I would recommend re-installing inStrain in a new conda environment, which should give you a fresh installation of pandas.

Best, Matt

[ZT-ls]

hi Matt， thank you very much for your response, actually, i tried a new conda environment and the error still existed , then i re-installed the latest annaconda3, but the issue still happened. i agree with you on the pandas version issue, can you give me some matched conda version and pandas version that might work? i tried different version of python, and i found python that below or 3.10 might installed sucessfully but encounted the pandas issue,the python 3.11 might not be succesfully installed. can you please tell me the latest python version or pandas version that inStrain works? thank you very much Matt Best. ZT

[ZT-ls]

i mean, could you tell me one or two version compositions of python or conda and pandas that you used which succesfully worked, thank you very much

[MrOlm]

Hi @ZT-ls -

Here's the details of one of my current, working inStrain installations:

$ inStrain check_deps
$$$$$$$$$$ DEPENDENCY REPORT $$$$$$$$$$
PYTHON
Running python v3.9.12 (main, Jun  1 2022, 06:34:44)
[Clang 12.0.0 ]

PROGRAM DEPENDENCIES
samtools...................... ! NOT WORKING ! (version=na) (location = None)
coverm........................ all good   (version=coverm 0.6.0) (location = /Users/mattolm/.cargo/bin/coverm)

PYTHON DEPENDENCIES
numba......................... ! NOT WORKING ! Not needed, but installing will increase filter_reads runtime
matplotlib.................... all good   (version=3.7.2) (location = /Users/mattolm/mambaforge/envs/python3.9_instrain/lib/python3.9/site-packages/matplotlib/__init__.py)
seaborn....................... all good   (version=0.12.2) (location = /Users/mattolm/mambaforge/envs/python3.9_instrain/lib/python3.9/site-packages/seaborn/__init__.py)
numpy......................... all good   (version=1.25.1) (location = /Users/mattolm/mambaforge/envs/python3.9_instrain/lib/python3.9/site-packages/numpy/__init__.py)
Bio........................... all good   (version=1.74) (location = /Users/mattolm/mambaforge/envs/python3.9_instrain/lib/python3.9/site-packages/Bio/__init__.py)
pysam......................... all good   (version=0.21.0) (location = /Users/mattolm/mambaforge/envs/python3.9_instrain/lib/python3.9/site-packages/pysam/__init__.py)
pandas........................ all good   (version=2.0.3) (location = /Users/mattolm/mambaforge/envs/python3.9_instrain/lib/python3.9/site-packages/pandas/__init__.py)

Best, Matt

[ZT-ls]

there is note that it was not succefully installed for instrain by conda install, then i just selected different versions of python in conda environmant and installed instrain using pip, "conda install inStrain" did't return error but it took a long time to finish

[ZT-ls]

ok, thank you, Matt

[ZT-ls]

hi Matt, i tried same version of pandas but the error still existed, according to the Traceback, is there any possibility that version here is the inStrain version?
just like the figure posted where the code marked, i installed the latested vesion of inStrain, or maybe the script didnot catched the version info in SNVprofile.py, line 487, in _initialize_attributes?

[MrOlm]

Hi @ZT-ls - I see. What is the commend you're trying to run? It seems that you're passing inStrain what it thinks is an inStrain profile folder, but that folder doesn't have the necessary attributes file in the raw_data folder.

Best, Matt

[ZT-ls]

thanks Matt， this issue appeared when running inStrain profile, is it necessary for me to download some folder? this time i installed inStrain through mamba

[MrOlm]

To run inStrain profile you don't need to have a folder, but this error makes me think that the output folder you are telling inStrain to create already exists, and that is causing the problem.

Make sure that the output folder you specify does not already exist.

Best, Matt

[ZT-ls]

ok, thanks Matt, i found it was the reason, some xxx.IS was generated, after removing these it works, very apperciate it !