how to identify the percentage of RNA contamination in DNA-Seq?

[jingydz]

when I set the contaminated (“positive”) and uncontamined (“negative”) groups (the first is my sample that may be contaminated, the second is public 1kgp sample)

$ cat positives.list
/xxx/bam_list/mysample.bam
$ cat negatives.list
/xxx/bam_list/NA12878.bam

and then run
rna_cd-train -c chrM -pl positives.list -nl negatives.list -j 3
--chunksize 100 -o model.json --plot-out pca.png

but I meet the error

Start time is 2023/10/19--11:05
[ 2023-10-19 03:05:59.771258 ] Calculating features for mysample.bam
[ 2023-10-19 03:05:59.771483 ] Calculating features for NA12878.bam
[ 2023-10-19 03:10:22.019794 ] Done calculating features for mysample.bam
[ 2023-10-19 03:12:44.830715 ] Done calculating features for NA12878.bam
[ 2023-10-19 03:12:45.702813 ] Setting up processing pipeline for SVM model
[ 2023-10-19 03:12:45.708970 ] Starting grid search for SVC model with 3 cross validations
Traceback (most recent call last):
File "/xxx/software/miniconda3/bin/rna_cd-train", line 8, in
sys.exit(train_cli())
File "/xxx/software/miniconda3/lib/python3.9/site-packages/click/core.py", line 1128, in call
return self.main(*args, **kwargs)
File "/xxx/software/miniconda3/lib/python3.9/site-packages/click/core.py", line 1053, in main
rv = self.invoke(ctx)
File "/xxx/software/miniconda3/lib/python3.9/site-packages/click/core.py", line 1395, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/xxx/software/miniconda3/lib/python3.9/site-packages/click/core.py", line 754, in invoke
return __callback(*args, **kwargs)
File "/xxx/software/miniconda3/lib/python3.9/site-packages/rna_cd/cli.py", line 138, in train_cli
model = train_svm_model(positives, negatives, chunksize=chunksize,
File "/xxx/software/miniconda3/lib/python3.9/site-packages/rna_cd/models.py", line 157, in train_svm_model
searcher.fit(arr_X, arr_Y)
File "/xxx/.local/lib/python3.9/site-packages/sklearn/model_selection/_search.py", line 875, in fit
self._run_search(evaluate_candidates)
File "/xxx/.local/lib/python3.9/site-packages/sklearn/model_selection/_search.py", line 1375, in _run_search
evaluate_candidates(ParameterGrid(self.param_grid))
File "/xxx/.local/lib/python3.9/site-packages/sklearn/model_selection/_search.py", line 125, in init
raise ValueError(
ValueError: Parameter grid for parameter 'reduce_dim__n_components' need to be a non-empty sequence, got: []
Finish time is 2023/10/19--11:12

[jingydz]

when I changed the chrM into chr21.
I got this error.

Traceback (most recent call last):
File "", line 1, in
File "/xxx/.local/lib/python3.9/site-packages/joblib/init.py", line 120, in
from .parallel import Parallel
File "/xxx/.local/lib/python3.9/site-packages/joblib/parallel.py", line 26, in
from ._parallel_backends import (FallbackToBackend, MultiprocessingBackend,
File "/xxx/.local/lib/python3.9/site-packages/joblib/_parallel_backends.py", line 17, in
from .pool import MemmappingPool
File "/xxx/.local/lib/python3.9/site-packages/joblib/pool.py", line 40, in
import numpy as np
File "/xxx/software/miniconda3/lib/python3.9/site-packages/numpy/init.py", line 147, in
from . import lib
File "/xxx/software/miniconda3/lib/python3.9/site-packages/numpy/lib/init.py", line 44, in
all += type_check.all
NameError: name 'type_check' is not defined

[jingydz]

-pl positives.list -nl negatives.list
how many bam files are needed in the list?