Shuai Wang comments

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                                            Shuai Wang

No module named `sklearn.neighbours.kde`

`pip install scikit-learn==0.22.1` solved my problem.

Connection Error, RemoteDisconnected

I met the same bug, and I am looking forward to your solution. ERROR: Download from NCBI failed: ConnectionError(ProtocolError('Connection aborted.', RemoteDisconnected('Remote end closed connection without response',)),)

error message could be improved when eigen isn't available

could I ask how to solve the problem? I met the same error ``` ./configure: line 26353: syntax error near unexpected token `EIGEN3,' ./configure: line 26353: ` PKG_CHECK_MODULES(EIGEN3, eigen3 >=...

C compiler does not work

I met a similar bug in https://github.com/bioconda/bioconda-recipes/issues/47103

Incorporate GTDB Taxonomy v214 into curatedMetagenomicData

I am also wondering if there is a way to convert the MetaPhlAn3 taxonomy to the GTDB taxonomy.

Question about minimap2 parameters in long_read_typing.py

Hi, Thank you for the patient effort. For long-read data only, `long_read_typing.py` should be used instead of `SpecHLA.sh`. For long-read-only typing, we put effort into binning reads instead of the...

Question about minimap2 parameters in long_read_typing.py

Hi, I guess two possible reasons: - Is the input data short reads or long reads? If they are short reads, it might be caused by PCR duplicates which can...

Question about minimap2 parameters in long_read_typing.py

Hi, SpecHLA indeed bins the long reads as well. Please look at the file `${sample}.db.sam` in the output folder, which records what alleles each read can map to. Best, shuai

Question about minimap2 parameters in long_read_typing.py

Hi, I found that the reads from the bacterial artificial chromosome (BAC) are wrongly assigned to DPB1. It would be a good idea to map the long reads to the...

Question about minimap2 parameters in long_read_typing.py

I also guess the BAC sequences are contamination introduced in sequencing; they might be used for sequencing accuracy assessment or human DNA amplification. However, further surveys are needed to confirm...