CNV Matrix causes error

[Ott-Alexander]

Hi,

I'm trying to run SigProfilerExtractor on a small CNV dataset to assign cosmic cnv signatures. I'm using the call:

sig.sigProfilerExtractor("seg:FACETS", result_folder, input_file, reference_genome="mm10", minimum_signatures=1, maximum_signatures=10, nmf_replicates=100, cpu=5)

with the input file in the format: chr start end tcn.em lcn.em sample id

It seems to work until the matrix is generated but then throws this error:

************** Reported Current Memory Use: 0.33 GB ***************** Saved matrix to results/FACETS.CNV48.matrix.tsv Traceback (most recent call last): File "/mnt/users/ahott1a1/projects/Somatic/Issue139_SigProfiler/extractSignatures.py", line 128, in main(args) File "/mnt/users/ahott1a1/projects/Somatic/Issue139_SigProfiler/extractSignatures.py", line 36, in main sig.sigProfilerExtractor("seg:FACETS", result_folder, args.input, reference_genome=args.ref, minimum_signatures=args.minSig, File "/mnt/users/ahott1a1/opt/miniconda/lib/python3.9/site-packages/SigProfilerExtractor/sigpro.py", line 686, in >sigProfilerExtractor normalization_cutoff = sub.get_normalization_cutoff(genomes, manual_cutoff=100*genomes.shape[0]) File "/mnt/users/ahott1a1/opt/miniconda/lib/python3.9/site-packages/SigProfilerExtractor/subroutines.py", line 182, in >get_normalization_cutoff mean = np.mean(col_sums) File "<array_function internals>", line 180, in mean File "/mnt/users/ahott1a1/opt/miniconda/lib/python3.9/site-packages/numpy/core/fromnumeric.py", line 3432, in mean return _methods._mean(a, axis=axis, dtype=dtype, File "/mnt/users/ahott1a1/opt/miniconda/lib/python3.9/site-packages/numpy/core/_methods.py", line 180, in _mean ret = umr_sum(arr, axis, dtype, out, keepdims, where=where) TypeError: can only concatenate str (not "int") to str

Is that an error because of my input? I saw the closse issue #146 but there was no mention of what was happening.

Thank you for the help Alex

[marcos-diazg]

Dear @Ott-Alexander,

Could you please share your input files/mutational matrix, as well as your JOB_METADATA file to try to reproduce your issue? Happy to help also over email at [email protected]. Thanks!

Marcos

[mdbarnesUCSD]

Please update to v1.1.14, the issue should be resolved in that update. Thanks!