Building database error

[JX-Zhong]

Hi, When I want to build a 30 species pangenome database for snp calling, I meet some errors. fna and other files were downloaded from PATRIC database. I found that some of strain's fna files failed for building , but I have not found any difference between these files. Error is
`
Building pangenome database
Finegoldia_magna
catting genes
clustering genes
Traceback (most recent call last):
File "/home/zhongjiaxin/app/MIDAS/scripts/build_midas_db.py", line 74, in
build_db.run_pipeline(args)
File "/home/zhongjiaxin/app/MIDAS/midas/build/build_db.py", line 490, in run_pipeline
build_pangenome_db(args, species)
File "/home/zhongjiaxin/app/MIDAS/midas/build/build_db.py", line 323, in build_pangenome_db
p.cluster_genes(args['threads'], args['resume'])
File "/home/zhongjiaxin/app/MIDAS/midas/build/build_db.py", line 151, in cluster_genes
self.store_cluster_membership()
File "/home/zhongjiaxin/app/MIDAS/midas/build/build_db.py", line 170, in store_cluster_membership
gene.centroid_99 = gene.centroid_id[99]
KeyError: 99

`

[JX-Zhong]

Finegoldia_magna_FDAARGOS_764.zip

[JX-Zhong]

I meet another error when I try to use merge_midas.py , error output is
Traceback (most recent call last): File "/home/shileisheng/anaconda3/envs/py2.7/bin/merge_midas.py", line 441,
in run_program(program, args)
File "/home/shileisheng/anaconda3/envs/py2.7/bin/merge_midas.py", line 431, in run_program snps.run_pipeline(args) File "/home/zhongjiaxin/app/MIDAS/midas/merge/snps.py", line 499,
in run_pipeline parallel_build_sharded_tables(species, args)
File "/home/zhongjiaxin/app/MIDAS/midas/merge/snps.py", line 387,
in parallel_build_sharded_tables parallel(build_sharded_tables, argument_list, args['threads'])
File "/home/zhongjiaxin/app/MIDAS/midas/merge/snps.py", line 225, in parallel r.get() File "/home/shileisheng/anaconda3/envs/py2.7/lib/python2.7/multiprocessing/pool.py", line 572,
in get raise self._value
KeyError: 'end'
how to sovlve it ?

[Damianyangyang]

Hi~May I ask how you downloaded the reference genome, how did you download the .gene file and the .faa file?