/var/spool/slurm/d/job15231496/slurm_script: 8: /var/spool/slurm/d/job15231496/slurm_script: source: not found
/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/sklearn/ensemble/weight_boosting.py:29: DeprecationWarning: numpy.core.umath_tests is an internal NumPy module and should not be imported. It will be removed in a future NumPy release.
from numpy.core.umath_tests import inner1d
/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/utils.py:459: H5pyDeprecationWarning: The default file mode will change to 'r' (read-only) in h5py 3.0. To suppress this warning, pass the mode you need to h5py.File(), or set the global default h5.get_config().default_file_mode, or set the environment variable H5PY_DEFAULT_READONLY=1. Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. See the docs for details.
with h5py.File(file) as f:
Traceback (most recent call last):
File "/home/nicholas/miniconda3/envs/mutsig/bin/signatureanalyzer", line 8, in <module>
sys.exit(main())
File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/__main__.py", line 181, in main
**vars(args)
File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/signatureanalyzer.py", line 143, in run_maf
weighted_maf = assign_signature_weights_to_maf(maf, W, H)
File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/signatureanalyzer/utils.py", line 442, in assign_signature_weights_to_maf
signature_probabilities /= np.sum(signature_probabilities.values, axis=1, keepdims=True)
File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/ops.py", line 894, in f
result = method(self, other)
File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/ops.py", line 1517, in f
other = _align_method_FRAME(self, other, axis)
File "/home/nicholas/miniconda3/envs/mutsig/lib/python3.6/site-packages/pandas/core/ops.py", line 1440, in _align_method_FRAME
given_shape=right.shape))
ValueError: Unable to coerce to DataFrame, shape must be (3702, 3): given (3702, 1)
Ard NMF ran succesfully
---------------------------------------------------------
---------- S I G N A T U R E A N A L Y Z E R ----------
---------------------------------------------------------
* Creating output dir at test_mutsig_filtered
* Using GRCh38.p7.genome build
* Using cosmic3_exome signatures
* Loading spectra from test.maf
* Mapping contexts: 3701 / 3702
* Saving ARD-NMF outputs to test_mutsig_filtered/nmf_output.h5
* Running ARD-NMF...
0/9: nit= 1155 K=4 del=0.00000000
1/9: nit= 738 K=4 del=0.00000000
2/9: nit= 662 K=3 del=0.00000000
3/9: nit= 690 K=3 del=0.00000000
4/9: nit= 586 K=3 del=0.00000000
5/9: nit= 712 K=3 del=0.00000000
6/9: nit= 652 K=3 del=0.00000000
7/9: nit= 636 K=3 del=0.00000000
8/9: nit= 496 K=4 del=0.00000000
9/9: nit= 684 K=5 del=0.00000000
* Run 2 had lowest objective with mode (n=6) K = 3.
input:
Hugo_Symbol Tumor_Sample_Barcode Chromosome Start_Position Reference_Allele Tumor_Seq_Allele2 Variant_Type
358374 ATG4A 5369813 X 108091840 C A SNP
358407 TEX101 3924644 19 43416479 C A SNP
358498 NME2 4396053 17 51168277 C A SNP
358759 ATPAF2 3924644 17 18021143 G T SNP
358783 C2CD5 4396053 12 22515087 G T SNP
358811 CD52 3375285 1 26320200 C A SNP
358914 SH3BGRL2 2543113 6 79673788 C A SNP
358917 COMMD9 2543113 11 36280719 G T SNP
358996 LCE2C 4396053 1 152676238 C A SNP
359174 ODF3L1 3585049 15 75727327 C A SNP
njbernstein
commented
3 years ago
Job errored out while writing results:
Ard NMF ran succesfully
input:
Any ideas?