search

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
301 stars 125 forks source link

.thanks... #80

Closed hjack123 closed 5 years ago

hjack123 commented 5 years ago

snaptools snap-add-bmat --snap-file=atac_pbmc_5k_nextgem.snap --bin-size-lis 5000 --verbose=True ===== reading the barcodes and bins ====== @AM nBinSize:1 @AM binSizeList: [5000] @AM binSize:5000 nBin:0 Traceback (most recent call last): File "h5py/_proxy.pyx", line 316, in h5py._proxy.needs_bkg_buffer KeyError: 'Conversion function not found (no appropriate function for conversion path)'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/anaconda3/bin/snaptools", line 38, in parse_args()
File "/anaconda3/lib/python3.7/site-packages/snaptools/parser.py", line 168, in parse_args verbose=args.verbose) File "/anaconda3/lib/python3.7/site-packages/snaptools/add_bmat.py", line 175, in snap_bmat f.create_dataset("AM/"+str(binsize)+"/binChrom",data=[np.string(key[0]) for key in bin_dict_list[bin_size]], dtype=h5py.special_dtype(vlen=bytes), compression="gzip", compression_opts=9); File "/anaconda3/lib/python3.7/site-packages/h5py/_hl/group.py", line 136, in create_dataset dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds) File "/anaconda3/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 170, in make_new_dset dset_id.write(h5s.ALL, h5s.ALL, data) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5d.pyx", line 221, in h5py.h5d.DatasetID.write File "h5py/_proxy.pyx", line 152, in h5py._proxy.dset_rw File "h5py/_proxy.pyx", line 318, in h5py._proxy.needs_bkg_buffer TypeError: Operation not defined for data type class (operation not defined for data type class)

r3fang commented 5 years ago

it’s python version issue. I don’t have time to test it on >python3.6. If you can use python2.7, it should be fine

-- Rongxin Fang Ph.D. Student, Ren Lab Ludwig Institute for Cancer Research University of California, San Diego

On Aug 30, 2019, at 11:48 AM, hjack123 notifications@github.com wrote:

snaptools snap-add-bmat --snap-file=atac_pbmc_5k_nextgem.snap --bin-size-lis 5000 --verbose=True ===== reading the barcodes and bins ====== @am https://github.com/am nBinSize:1 @am https://github.com/am binSizeList: [5000] @am https://github.com/am binSize:5000 nBin:0 Traceback (most recent call last): File "h5py/_proxy.pyx", line 316, in h5py._proxy.needs_bkg_buffer KeyError: 'Conversion function not found (no appropriate function for conversion path)'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/anaconda3/bin/snaptools", line 38, in parse_args() File "/anaconda3/lib/python3.7/site-packages/snaptools/parser.py", line 168, in parse_args verbose=args.verbose) File "/anaconda3/lib/python3.7/site-packages/snaptools/add_bmat.py", line 175, in snap_bmat f.create_dataset("AM/"+str(binsize)+"/binChrom",data=[np.string(key[0]) for key in bin_dict_list[bin_size]], dtype=h5py.special_dtype(vlen=bytes), compression="gzip", compression_opts=9); File "/anaconda3/lib/python3.7/site-packages/h5py/_hl/group.py", line 136, in create_dataset dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds) File "/anaconda3/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 170, in make_new_dset dset_id.write(h5s.ALL, h5s.ALL, data) File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5d.pyx", line 221, in h5py.h5d.DatasetID.write File "h5py/_proxy.pyx", line 152, in h5py._proxy.dset_rw File "h5py/_proxy.pyx", line 318, in h5py._proxy.needs_bkg_buffer TypeError: Operation not defined for data type class (operation not defined for data type class)

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/80?email_source=notifications&email_token=ABT6GG5EU3KC5B3SB5Y4663QHFTPDA5CNFSM4ISQFVLKYY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HIQRPJQ, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG73HGRCP3JIBNIOSB3QHFTPDANCNFSM4ISQFVLA.