usda-ars-gbru / guidemaker Goto Github PK

2022-10-13 11:40:38,001 root         INFO     Identifying guides that have a hamming distance <= 2 to all other potential guides
2022-10-13 11:40:38,248 numexpr.utils INFO     Note: detected 78 virtual cores but NumExpr set to maximum of 64, check "NUMEXPR_MAX_THREADS" environment variable.
2022-10-13 11:40:38,248 numexpr.utils INFO     Note: NumExpr detected 78 cores but "NUMEXPR_MAX_THREADS" not set, so enforcing safe limit of 8.
2022-10-13 11:40:38,248 numexpr.utils INFO     NumExpr defaulting to 8 threads.

streamlit run /GuideMaker/guidemaker/data/app.py --server.maxUploadSize 5000

2022-11-20 00:17:31,672 root         INFO     Creating Efficiency Score based on Doench et al. 2016 - only for NGG PAM...
2022-11-20 00:17:31,685 root         ERROR    GuideMaker terminated with errors. See the log file for details.
Traceback (most recent call last):
  File "/hpc/home/cjm124/.local/lib/python3.8/site-packages/guidemaker/cli.py", line 208, in main
    prettydf = guidemaker.core.get_doench_efficiency_score(df=prettydf, pam_orientation=args.pam_orientation, num_threads=args.threads)
  File "/hpc/home/cjm124/.local/lib/python3.8/site-packages/guidemaker/core.py", line 1155, in get_doench_efficiency_score
    doenchscore = doench_predict.predict(np.array(df.target_seq30), num_threads=num_threads)
  File "/hpc/home/cjm124/.local/lib/python3.8/site-packages/guidemaker/doench_predict.py", line 114, in predict
    sess = rt.InferenceSession(model_file)
  File "/hpc/home/cjm124/.local/lib/python3.8/site-packages/onnxruntime/capi/onnxruntime_inference_collection.py", line 347, in __init__
    self._create_inference_session(providers, provider_options, disabled_optimizers)
  File "/hpc/home/cjm124/.local/lib/python3.8/site-packages/onnxruntime/capi/onnxruntime_inference_collection.py", line 384, in _create_inference_session
    sess = C.InferenceSession(session_options, self._model_path, True, self._read_config_from_model)
RuntimeError: /onnxruntime_src/onnxruntime/core/platform/posix/env.cc:183 onnxruntime::{anonymous}::PosixThread::PosixThread(const char*, int, unsigned int (*)(int, Eigen::ThreadPoolInterface*), Eigen::ThreadPoolInterface*, const onnxruntime::ThreadOptions&) pthread_setaffinity_np failed, error code: 0 error msg: 

guidemaker \
		--fasta chr1_Hery.fasta \
		--gff chr1anno.gff \
		-p NGG \
		-o outputFiles/run3/ \
		--doench_efficiency_score \
		--cfd_score \
		--pam_orientation 3prime \
		--guidelength 20 \
		--before 100 \
		--into 500 \
		--knum 5 \
		--controls 1000 \
		--threads 96

echo "all done"

exit

sbatch -p common \
	-n 96 \
	--mem=1000G \
	--mail-type=END \
	--time=20-12:00:00 \
	--wrap="bash code/make_hery_guides$runNumber.sh"

guidemaker   \
   --fasta /genome/hg38.fa       \
   --gff /genome/Homo_sapiens.GRCh38.77.gtf   \
   -o /home/out       \
   -p NGG       \
   --pam_orientation 3prime    \
   --guidelength 20    \
   --lsr 11   \
   --threads 5  \

GTTGTGTCTGCTGTGAGTGCGGGGGGGCGN
AGATGGGGTCGGGAGGGAAAGTGGGGGGGN
GATGGGGTCGGGAGGGAAAGTGGGGGGGNN
ATGGGGTCGGGAGGGAAAGTGGGGGGGNNN
TGCGCTGAGCCGGGTGTCAGCCTGAGGCNN
CCACCCTCCCCACCCCACCCCCCCAGGANN
TGGAGGACCTAGTTGTGGGTCAGGAGGACN

2023-10-11 17:25:01,529 root         ERROR    GuideMaker terminated with errors. See the log file for details.
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
  File "/project/90daydata/gbru_fy22_amr_cooccurence/leghornenv/lib/python3.9/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
  File "/project/90daydata/gbru_fy22_amr_cooccurence/leghornenv/lib/python3.9/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/project/90daydata/gbru_fy22_amr_cooccurence/GuideMaker/guidemaker/doench_featurization.py", line 58, in featurize_data
    feature_sets["_nuc_pd_Order1"], feature_sets["_nuc_pi_Order1"], feature_sets["_nuc_pd_Order2"], feature_sets["_nuc_pi_Order2"] = get_nuc_features(data)
  File "/project/90daydata/gbru_fy22_amr_cooccurence/GuideMaker/guidemaker/doench_featurization.py", line 196, in get_nuc_features
    pi1dict[let] += 1
KeyError: 'N'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/project/90daydata/gbru_fy22_amr_cooccurence/GuideMaker/guidemaker/cli.py", line 218, in main
    prettydf = guidemaker.core.get_doench_efficiency_score(df=prettydf, pam_orientation=args.pam_orientation, num_threads=args.threads)
  File "/project/90daydata/gbru_fy22_amr_cooccurence/GuideMaker/guidemaker/core.py", line 1156, in get_doench_efficiency_score
    doenchscore = doench_predict.predict(np.array([x.upper() for x in df.target_seq30]), num_threads=num_threads)
  File "/project/90daydata/gbru_fy22_amr_cooccurence/GuideMaker/guidemaker/doench_predict.py", line 122, in predict
    feature_sets = parallel_featurize_data(
  File "/project/90daydata/gbru_fy22_amr_cooccurence/GuideMaker/guidemaker/doench_featurization.py", line 103, in parallel_featurize_data
    result = pool.map(partial_fd, dflist)
  File "/project/90daydata/gbru_fy22_amr_cooccurence/leghornenv/lib/python3.9/multiprocessing/pool.py", line 364, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
  File "/project/90daydata/gbru_fy22_amr_cooccurence/leghornenv/lib/python3.9/multiprocessing/pool.py", line 771, in get
    raise self._value
KeyError: 'N'