yonniejon
commented
2 hours ago This is a duplicate of https://github.com/deeptools/deepTools/issues/1322
Closed yonniejon closed 2 hours ago
yonniejon
commented
2 hours ago This is a duplicate of https://github.com/deeptools/deepTools/issues/1322
Welcome to deepTools GitHub repository! Before opening the issue please check that the following requirements are met :
[x] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below.
[x] Paste your deepTools version (
deeptools --version) and your python version (python --version) below. deeptools 3.5.5 computeMatrix 3.5.5 Python 3.11.2 (main, May 2 2024, 11:59:08) [GCC 12.2.0] on linux[x] Paste the full deepTools command that produces the issue below (ignore if you simply spotted the issue in the code/documentation). computeMatrix reference-point -S origins_hg19.Q1_or_Q2.bw -R check.bed -o check.bin_size_10000.11000000_before_after.matrix --referencePoint center --binSize 10000 --beforeRegionStartLength 1000000 --afterRegionStartLength 1000000 --missingDataAsZero -p 16
[x] Paste the output printed on screen from the command that produces the issue below (ignore if you simply spotted the issue in the code/documentation).
multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/usr/lib/python3.11/multiprocessing/pool.py", line 125, in worker result = (True, func(*args, *kwds)) ^^^^^^^^^^^^^^^^^^^ File "/usr/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar return list(map(args)) ^^^^^^^^^^^^^^^^ File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/heatmapper.py", line 174, in compute_sub_matrix_wrapper return heatmapper.compute_sub_matrix_worker(*args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/heatmapper.py", line 379, in compute_sub_matrix_worker sub_matrix[:] = np.NAN ^^^^^^ File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/numpy/init.py", line 414, in getattr raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'NAN' """
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/cs/usr/jrosensk/.local/bin/computeMatrix", line 8, in
sys.exit(main())
^^^^^^
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/computeMatrix.py", line 398, in main
hm.computeMatrix(scores_file_list, args.regionsFileName, parameters, blackListFileName=args.blackListFileName, verbose=args.verbose, allArgs=args)
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/heatmapper.py", line 252, in computeMatrix
res, labels = mapReduce.mapReduce([score_file_list, parameters],
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/cs/cbio/jon/jon_v/lib/python3.11/site-packages/deeptools/mapReduce.py", line 142, in mapReduce
res = pool.map_async(func, TASKS).get(9999999)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/multiprocessing/pool.py", line 774, in get
raise self._value
AttributeError: module 'numpy' has no attribute 'NAN'