PanGIA-Docker error about pangia HOT 8 CLOSED

Do you have minimap2's index (.mmi) files in the database directory?

from pangia.

Today I installed PanGIA as outlined on the GitHub page. I ran PanGAI with the following command:

./pangia.py -i /home/dnd/data/MinION/HybridAssembly/Ft_Lux_clones/Guppy_hac_calls/Demux/1st_Run/barcode05.fastq -db ./PanGIA/NCBI_genomes_refseq89_BAV.fa ./PanGIA/NCBI_genomes_refseq89_adds.fa -t 24 --keepTemp -np -o /home/dnd/data/MinION/HybridAssembly/Ft_Lux_clones/Analysis/ -p FtLux_BC05.

This is nanopore sequence data and the error (as seen in the attached screenshot) seems to be from minimap2. I do not get this error when using short read data. Any suggestions to resolve the minimap2/nanopore issue would be appreciated.
Thanks,
Scott

from pangia.

Hi Scott,

I presumed it's due to the absence of minimap2 index file. I will upload these files to our downloading site today. Sorry for the inconvenience!

Thanks,
Paul

from pangia.

I do not have the index files in the database directory. How do I generate the index files for the databases I downloaded? For example NCBI_genome_refseq89_BAV and NCBI_genome_refseq89_adds.

from pangia.

Thank you.

from pangia.

If you prefer to create the index yourself, the original FASTA files can be downloaded from here:
https://edge-dl.lanl.gov/PanGIA/database/FASTA/

You can download these *.fa files, create minimap2 index and dump them to *.fa.mmi.

from pangia.

from pangia.

You're welcome. Glad to hear that Scott! I'm still uploading...

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