Errors with__init__() got an unexpected keyword argument 'cachedir'

[echoduan]

I want to use LRBinner to perform metagenomics binning of the assembly contigs from Pacbio HiFi reads via the command:

LRBinner contigs -r ../${sample}_reads.fasta -c ${sample}.contigs.fasta -bc 10 -bs 32 -o ${outf} --resume --ae-dims 4 --ae-epochs 200 -t ${threads}

After finishing VAE training, it will report the error messages:

"Training VAE: 100%|██████████| 200/200 [1:06:03<00:00, 19.82s/it] 2022-12-17 08:11:02,102 - INFO - VAE training complete Traceback (most recent call last): File "/work/home/acq7wsloil/soft/LRBinner/LRBinner", line 197, in main() File "/work/home/acq7wsloil/soft/LRBinner/LRBinner", line 179, in main pipelines.run_contig_binning(args) File "/work/home/acq7wsloil/soft/LRBinner/mbcclr_utils/pipelines.py", line 243, in run_contig_binning output, fragment_parent, separate, contigs, threads) File "/work/home/acq7wsloil/soft/LRBinner/mbcclr_utils/cluster_utils.py", line 489, in perform_contig_binningHDBSCAN from hdbscan import HDBSCAN File "/public/home/acq7wsloil/anaconda3/envs/lrbinner/lib/python3.7/site-packages/hdbscan/init.py", line 1, in from .hdbscan import HDBSCAN, hdbscan File "/public/home/acq7wsloil/anaconda3/envs/lrbinner/lib/python3.7/site-packages/hdbscan/hdbscan_.py", line 509, in memory=Memory(cachedir=None, verbose=0), TypeError: init() got an unexpected keyword argument 'cachedir'"

Could you tell me how to fix it, please?

[anuradhawick]

Looks like a version mismatch. I’ll get back to you after holidays in January. I will update the functions to latest python and PyTorch versions.

Is this a public dataset, so I can test. If not I’ll try on my mock datasets.

Thanks.

On Tue, 20 Dec 2022 at 9:06 am, echoduan @.***> wrote:

I want to use LRBinner to perform metagenomics binning of the assembly contigs from Pacbio HiFi reads via the command:

LRBinner contigs -r ../${sample}_reads.fasta -c ${sample}.contigs.fasta -bc 10 -bs 32 -o ${outf} --resume --ae-dims 4 --ae-epochs 200 -t ${threads}

After finishing VAE training, it will report the error messages:

"Training VAE: 100%|██████████| 200/200 [1:06:03<00:00, 19.82s/it] 2022-12-17 08:11:02,102 - INFO - VAE training complete Traceback (most recent call last): File "/work/home/acq7wsloil/soft/LRBinner/LRBinner", line 197, in main() File "/work/home/acq7wsloil/soft/LRBinner/LRBinner", line 179, in main pipelines.run_contig_binning(args) File "/work/home/acq7wsloil/soft/LRBinner/mbcclr_utils/pipelines.py", line 243, in run_contig_binning output, fragment_parent, separate, contigs, threads) File "/work/home/acq7wsloil/soft/LRBinner/mbcclr_utils/cluster_utils.py", line 489, in perform_contig_binningHDBSCAN from hdbscan import HDBSCAN File "/public/home/acq7wsloil/anaconda3/envs/lrbinner/lib/python3.7/site-packages/hdbscan/ init.py", line 1, in from .hdbscan import HDBSCAN, hdbscan File "/public/home/acq7wsloil/anaconda3/envs/lrbinner/lib/python3.7/site-packages/hdbscan/hdbscan_.py", line 509, in memory=Memory(cachedir=None, verbose=0), TypeError: init() got an unexpected keyword argument 'cachedir'"

Could you tell me how to fix it, please?

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[echoduan]

Hi Wickramarachchi,

Thanks for your quick reply.

Sorry, this Pacbio HiFi data was recently generated by myself. I used the Hicanu program to de novo assemble it and then want to bin the assembly contig using LRBinner.

There was the error message after running 2-3 hours.

Best,

Shoufu

[anuradhawick]

Hi @echoduan,

I updated the codes and conda command to install the latest stuff. Now the error about cachedir should no come.

You need to re-create the conda env. Also now the command is lrbinner.py instead of LRBinner.

Let me know how it goes.

Cheers Anuradha