I'm trying to run SCOUT on a single sample I have from a 10X genomics run.
I have run the BAM file through the GATK recalibration steps and try to use SCOUT to call genotypes.
The program runs for a bit and then I get this error:
Fri Mar 4 15:18:01 2022: The first Annotation finished!
Fri Mar 4 15:18:01 2022: The second Annotation finished!
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/home/dfermin/.conda/envs/scout/lib/python3.10/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/nfs/scratch/projects/dfermin.scRNAseq_genotyping/bin/../SCOUT.git/bin/SCOUT.py", line 30, in WorkPip
PipEST.MakeCandidateDf(chrom, Start, End)
File "/nfs/scratch/projects/dfermin.scRNAseq_genotyping/SCOUT.git/source/Calculate/Candidate.py", line 296, in MakeCandidateDf
self.GetCutoffSimple()
File "/nfs/scratch/projects/dfermin.scRNAseq_genotyping/SCOUT.git/source/Calculate/Candidate.py", line 316, in GetCutoffSimple
estimator.fit(pd.DataFrame(MixDf['RawRate']))
File "/home/dfermin/.conda/envs/scout/lib/python3.10/site-packages/sklearn/cluster/_agglomerative.py", line 917, in fit
X = self._validate_data(X, ensure_min_samples=2, estimator=self)
File "/home/dfermin/.conda/envs/scout/lib/python3.10/site-packages/sklearn/base.py", line 566, in _validate_data
X = check_array(X, **check_params)
File "/home/dfermin/.conda/envs/scout/lib/python3.10/site-packages/sklearn/utils/validation.py", line 805, in check_array
raise ValueError(
ValueError: Found array with 1 sample(s) (shape=(1, 1)) while a minimum of 2 is required by AgglomerativeClustering.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/nfs/scratch/projects/dfermin.scRNAseq_genotyping/bin/../SCOUT.git/bin/SCOUT.py", line 169, in <module>
main(sys.argv[1:])
File "/nfs/scratch/projects/dfermin.scRNAseq_genotyping/bin/../SCOUT.git/bin/SCOUT.py", line 147, in main
res = ResultPool[k].get()
File "/home/dfermin/.conda/envs/scout/lib/python3.10/multiprocessing/pool.py", line 771, in get
raise self._value
ValueError: Found array with 1 sample(s) (shape=(1, 1)) while a minimum of 2 is required by AgglomerativeClustering.
This happens with both SCOUT scripts.
Any suggestion on how to fix it?
Hello,
I've tried to run SCOUT on single-cell WGS or bulk WGS data, and the pipline is OK.
Would you mind to provide one of your bam file for me to reproduce this error ?
Hello.
I'm trying to run SCOUT on a single sample I have from a 10X genomics run. I have run the BAM file through the GATK recalibration steps and try to use SCOUT to call genotypes.
This is the command I use:
The program runs for a bit and then I get this error:
This happens with both SCOUT scripts. Any suggestion on how to fix it?
Thanks