Cloufield
commented
1 year ago Hi, Sorry that I might need more information to pinpoint the error. Would you please provide some context (your script and sample data)? Thanks.
Open soumickmj opened 1 year ago
Cloufield
commented
1 year ago Hi, Sorry that I might need more information to pinpoint the error. Would you please provide some context (your script and sample data)? Thanks.
Hi @Cloufield I'm having a weird error while performing liftover that I cannot explain.
multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "src/liftover/chain_file.pyx", line 76, in liftover.chain_file.ChainFile.getitem KeyError: '12'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/gwaslab/fixdata.py", line 1163, in liftover_variant lifted = sumstats.loc[variants_on_chrom_to_convert,[pos,status]].apply(lambda x: liftover_snv(x[[pos,status]],chrom_to_convert,converter,to_build),axis=1) File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/pandas/core/frame.py", line 8848, in apply return op.apply().finalize(self, method="apply") File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/pandas/core/apply.py", line 733, in apply return self.apply_standard() File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/pandas/core/apply.py", line 857, in apply_standard results, res_index = self.apply_series_generator() File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/pandas/core/apply.py", line 873, in apply_series_generator results[i] = self.f(v) File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/gwaslab/fixdata.py", line 1163, in
lifted = sumstats.loc[variants_on_chrom_to_convert,[pos,status]].apply(lambda x: liftover_snv(x[[pos,status]],chrom_to_convert,converter,to_build),axis=1)
File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/gwaslab/fixdata.py", line 1141, in liftover_snv
results = converter[chrom][pos_0_based]
File "src/liftover/chain_file.pyx", line 78, in liftover.chain_file.ChainFile.getitem
KeyError: 'chr12'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/center/genomics/soumick/fede/manipulate_sumstats/manipulate_sumstats.py", line 92, in
manipulator.liftover(n_threads=args.n_threads)
File "/center/genomics/soumick/fede/manipulate_sumstats/manipulate_sumstats.py", line 46, in liftover
self.sumstats.liftover(n_cores=n_threads,
File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/gwaslab/Sumstats.py", line 379, in liftover
self.data = parallelizeliftovervariant(self.data,from_build=from_build, to_build=to_build, log=self.log,**args)
File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/site-packages/gwaslab/fixdata.py", line 1192, in parallelizeliftovervariant
sumstats.loc[:,[chrom,pos,status]] = pd.concat(pool.map(partial(func,chrom=chrom,pos=pos,from_build=from_build,to_build=to_build,status=status),df_split))
File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/multiprocessing/pool.py", line 367, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/scratch/soumick.chatterjee/conda_envs/BeegFSTorchHTBeta2/lib/python3.10/multiprocessing/pool.py", line 774, in get
raise self._value
KeyError: 'chr12'
Any idea?
Thanks :)