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License: Other
PanGIA (Pan-Genomics for Infectious Agents)
License: Other
Hello,
I get the following error while running PanGIA.
Traceback (most recent call last):
File "./pangia.py", line 2278, in
genome_size, host_genome = getStrainSize( argvs.database )
File "./pangia.py", line 2055, in getStrainSize
import mappy
ModuleNotFoundError: No module named 'mappy'
The command used was as follows:
pangia.py -i /home/Desktop/guppy_basecalled/basecall_combined.fastq -d /home/data0/pangia_db/PanGIA/NCBI_genomes_refseq89_*.fa.mmi -t 70 --keepTemp -rm minimap2
Does pangia currently work with minimap2 or only bwa? Are bwa index files available or do they have to be generated from the 20180915_NCBI_genomes_refseq89*.fa.tar files? I have attached the log file if need.
basecall_combined.pangia.log
Thanks,
Scott
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