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anuradhawick / LRBinner

LRBinner is a long-read binning tool published in WABI 2021 proceedings and AMB.
https://doi.org/10.4230/LIPIcs.WABI.2021.11
GNU General Public License v2.0
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error with separate_reads.py #13

Open thulasis opened 1 year ago

thulasis commented 1 year ago

Hi I used contigs mode o bin the metagenomes (long-reads). Then I am trying to run the separate_reads.py and I am getting the following error:

Traceback (most recent call last):
  File "separate_reads.py", line 21, in <module>
    bins = pickle.load(open(bins, "rb"))
_pickle.UnpicklingError: could not find MARK

I tried the option f.seek (0) before loading the pickle but I am getting Attribute Error. I am using conda pyhton 3.8. Is it a issue with python? I downgraded python to 3.6 and tried but no use. Please let me know how to process the LRBinner output to get specie/genus level bins separately.

Thanks, Tulasi

anuradhawick commented 1 year ago

Hi @thulasis,

separate reads cannot be used to separate the binned contigs. Would you like me to create a script for that? separation of reads was done for assembly, did not notice a use case having to separate contigs.

Cheers Anuradha

thulasis commented 1 year ago

Hi @anuradhawick,

Thank you for the reply. Is it possible for you to create the script for that, if yes I would like to use the script. I would like to bin the reads from the LRBinner output.

Thanks, Tulasi