search

snayfach / MIDAS

An integrated pipeline for estimating strain-level genomic variation from metagenomic data
http://dx.doi.org/10.1101/gr.201863.115
GNU General Public License v3.0
124 stars 52 forks source link

Building database error #119

Open JX-Zhong opened 3 years ago

JX-Zhong commented 3 years ago

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 commented 3 years ago

Finegoldia_magna_FDAARGOS_764.zip

JX-Zhong commented 3 years ago

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 commented 1 year ago

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