Comments (3)
ShixiangWang
commented on June 17, 2024
I try reinstalling miniconda and this package and find another error when run an example:
Python 3.8.3 (default, May 19 2020, 18:47:26)
[GCC 7.3.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import SigProfilerExtractor
>>> from SigProfilerExtractor import sigpro as sig
>>> path_to_example_table = sig.importdata("matrix")
>>> data = path_to_example_table
>>> sig.sigProfilerExtractor("matrix", "example_output", data, opportunity_genome="GRCh38", minimum_signatures=1, maximum_signatures=3)
************** Reported Current Memory Use: 0.18 GB *****************
Extracting signature 1 for mutation type 96
The matrix normalizig cutoff is 11723
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Time taken to collect 100 iterations for 1 signatures is 89.23 seconds
Optimization time is 4.6821348667144775 seconds
The reconstruction error is 0.7125, average process stability is 1.0 and
the minimum process stability is 1.0 for 1 signatures
Extracting signature 2 for mutation type 96
The matrix normalizig cutoff is 11723
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Time taken to collect 100 iterations for 2 signatures is 104.89 seconds
Optimization time is 4.701096773147583 seconds
The reconstruction error is 0.059, average process stability is 1.0 and
the minimum process stability is 1.0 for 2 signatures
Extracting signature 3 for mutation type 96
The matrix normalizig cutoff is 11723
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Time taken to collect 100 iterations for 3 signatures is 118.52 seconds
Optimization time is 4.95683217048645 seconds
The reconstruction error is 0.0605, average process stability is 0.99 and
the minimum process stability is 0.97 for 3 signatures
Traceback (most recent call last):
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/reportlab/lib/utils.py", line 658, in open_for_read
return open_for_read_by_name(name,mode)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/reportlab/lib/utils.py", line 602, in open_for_read_by_name
return open(name,mode)
FileNotFoundError: [Errno 2] No such file or directory: '/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/src/Accolade_fermante.png'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/reportlab/lib/utils.py", line 661, in open_for_read
return getBytesIO(datareader(name) if name[:5].lower()=='data:' else urlopen(name).read())
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/urllib/request.py", line 222, in urlopen
return opener.open(url, data, timeout)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/urllib/request.py", line 509, in open
req = Request(fullurl, data)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/urllib/request.py", line 328, in __init__
self.full_url = url
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/urllib/request.py", line 354, in full_url
self._parse()
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/urllib/request.py", line 383, in _parse
raise ValueError("unknown url type: %r" % self.full_url)
ValueError: unknown url type: '/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/src/Accolade_fermante.png'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/sigpro.py", line 953, in sigProfilerExtractor
final_signatures = sub.signature_decomposition(processAvg, m, layer_directory2, genome_build=genome_build, add_penalty=add_penalty, remove_penalty=remove_penalty, mutation_context=mutation_context, make_decomposition_plots=make_decomposition_plots)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/subroutines.py", line 1356, in signature_decomposition
sp.run_PlotDecomposition(signatures_DF, denovo_name, sigDatabases_DF, basis_names, weights, nonzero_exposures, directory+"/Decomposition_Polts", "test", mtype_par)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/PlotDecomposition.py", line 290, in run_PlotDecomposition
gen_decomposition(denovo_name, basis_names, weights, output_path, project, mtype, reconstruction=True, statistics=statistics)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/PlotDecomposition.py", line 223, in gen_decomposition
spd_96.gen_decomposition(denovo_name, basis_names, weights, output_path, project, reconstruction, statistics)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/PlotDecomposition_SBS96.py", line 273, in gen_decomposition
gen_plot(denovo_name, sorted_list, output_path, project, c, reconstruction, statistics)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/PlotDecomposition_SBS96.py", line 250, in gen_plot
draw_bracket(num_bases, c)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/PlotDecomposition_SBS96.py", line 198, in draw_bracket
c_draw.drawImage(paths+"/src/Accolade_fermante.png", MID_WIDTH_LETTER - 15, BRACKET_SIZES[num_plts][0], width = 20, height = BRACKET_SIZES[num_plts][1], mask='auto')
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/reportlab/pdfgen/canvas.py", line 953, in drawImage
imgObj = pdfdoc.PDFImageXObject(name, image, mask=mask)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/reportlab/pdfbase/pdfdoc.py", line 2089, in __init__
src = open_for_read(source)
File "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/reportlab/lib/utils.py", line 663, in open_for_read
raise IOError('Cannot open resource "%s"' % name)
OSError: Cannot open resource "/home/anaconda3/envs/sigminer_sigprofiler/lib/python3.8/site-packages/SigProfilerExtractor/src/Accolade_fermante.png"from sigprofilerextractor.
ShixiangWang
commented on June 17, 2024
Install package from GitHub cannot fix this error.
from sigprofilerextractor.
ShixiangWang
commented on June 17, 2024
Set nmf_init = 'random' fix the error UnboundLocalError: local variable 'W' referenced before assignment.
There is a bug for nmf_init = 'alexandrov-lab-custom'.
from sigprofilerextractor.
Related Issues (20)
- interpretation for SBS 96D HOT 5
- SBS384 extraction problem HOT 5
- Strategies to improve cosine similarity per sample HOT 1
- error because of new pandas version HOT 1
- Minimum number of mutations or genome length. HOT 1
- Custom opportunities matrix HOT 8
- AttributeError: 'NoneType' object has no attribute 'keys (decomposition.py error) HOT 2
- Infinite loop HOT 1
- Issue with install HOT 2
- ValueError: operands could not be broadcast together with shapes (83,0) (0,0) HOT 3
- Sample filtering before extraction HOT 1
- question about the SigProfilerExtractor HOT 1
- Singularity container creation HOT 5
- Denovo Signature and Assigning Signature Matching Error HOT 1
- Asking for SBS96 contexts in SigProfilerExtractor but receiving CH1000 HOT 1
- New issue with Indels HOT 7
- sigProfilerExtractor for ID(INDELS) HOT 5
- The difference between SBS96_De-Novo_Solution and COSMIC_SBS96_Decomposed_Solution. HOT 3
- IndexError occurred when processing directory /app/output: index out of range HOT 4
- AttributeError: 'NoneType' object has no attribute 'keys' HOT 3
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from sigprofilerextractor.