Error running prepResult

[priscalim00]

Hi there,

Thank you for your work in developing this tool. I have two separate but somewhat related issues that I'm hoping you can help out with.

1. I'm running into an error when I run the prepResult command:

#my command:
prepResult --binned data/assembly/binning/concoct/stool_01/bins/ --output data/assembly/binning/graphbin2/stool_01/ --prefix stool_01_bins

#the error:
Formatting initial binning results
Traceback (most recent call last):
  File "/users/p/r/prisca/miniconda3/envs/graphbin2/bin/prepResult", line 10, in <module>
    sys.exit(main())
  File "/users/p/r/prisca/miniconda3/envs/graphbin2/lib/python3.9/site-packages/graphbin2/support/prepResult.py", line 165, in main
    for label, seq in MinimalFastaParser(contigs_file):
NameError: name 'contigs_file' is not defined

The same error occurs regardless of binning algorithm.

2. I'm wondering if GraphBin2 can take bins that were consolidated by DAS_Tool as the initial binning output? Essentially, I assembled my reads using SPAdes, then ran three binning algorithms (Maxbin2, Metabat2 and CONCOCT), then consolidated all the bins using DAS_Tool. I would like to use the consolidated bins as "initial bins", but when I attempted to do so, I encountered an error because the bin names were not integers:

ERROR - Unexpected invalid literal for int() with base 10: 'concoct.52'
ERROR - Please make sure that you have provided the correct assembler type and the correct path to the binning result file in the correct format.

I could potentially rename all the bins to have unique integer names, but I'm not confident and don't want to introduce errors accidentally!

I appreciate any input you may have, thanks so much!

Best,
Prisca

Edit to add the graphbin2.log file:
graphbin2.log