TypeError: create() got an unexpected keyword argument 'matrix'

[zcaiwei]

Hi,

I ran into a bug at the last step. It seems it is caused by the loompy. But I followed the install instructions to install every package and the loompy is installed from source (loompy==3.0.7 ). The command I used is as follows: velocyto run10x -m /notebook/zhencaiwei/RNA_velocity/mm10_rmsk.gtf /notebook/zhencaiwei/RNA_velocity/processed/sample01 /notebook/zhencaiwei/RNA_velocity/refdata-gex-mm10-2020-A/genes/genes.gtf

Could anyone help me to figure out that?

Many thanks!

2023-11-11 06:58:51,087 - DEBUG - Creating converter from 3 to 5 Traceback (most recent call last): File "/opt/conda/lib/python3.7/site-packages/velocyto/commands/_run.py", line 286, in _run ds = loompy.create(filename=outfile, matrix=total, row_attrs=ra, col_attrs=ca, dtype="float32")

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/lib/python3.7/site-packages/loompy/loompy.py", line 1066, in create ds.layer[""] = layers[""] File "/opt/conda/lib/python3.7/site-packages/loompy/layer_manager.py", line 90, in setitem return self.setattr(name, val) File "/opt/conda/lib/python3.7/site-packages/loompy/layer_manager.py", line 141, in setattr compression_opts=2 File "/opt/conda/lib/python3.7/site-packages/h5py/_hl/group.py", line 161, in create_dataset dsid = dataset.make_new_dset(group, shape, dtype, data, name, **kwds) File "/opt/conda/lib/python3.7/site-packages/h5py/_hl/dataset.py", line 159, 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 232, in h5py.h5d.DatasetID.write File "h5py/_proxy.pyx", line 114, in h5py._proxy.dset_rw OSError: [Errno 5] Can't write data (file write failed: time = Sat Nov 11 06:58:52 2023 , filename = '/notebook/zhencaiwei/RNA_velocity/processed/sample01/velocyto/sample01.loom', file descriptor = 4, errno = 5, error message = 'Input/output error', buf = 0x55c3aa106160, total write size = 214, bytes this sub-write = 214, bytes actually written = 18446744073709551615, offset = 0)

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/opt/conda/bin/velocyto", line 8, in sys.exit(cli()) File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1128, in call return self.main(args, kwargs) File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1053, in main rv = self.invoke(ctx) File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1659, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 1395, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/conda/lib/python3.7/site-packages/click/core.py", line 754, in invoke return __callback(args, **kwargs) File "/opt/conda/lib/python3.7/site-packages/velocyto/commands/run10x.py", line 115, in run10x samtools_memory=samtools_memory, dump=dump, loom_numeric_dtype=dtype, verbose=verbose, additional_ca=additional_ca) File "/opt/conda/lib/python3.7/site-packages/velocyto/commands/_run.py", line 297, in _run loompy.create(filename=outfile, layers=tmp_layers, row_attrs=ra, col_attrs=ca, file_attrs={"velocyto.version": vcy.version, "velocyto.logic": logic}) File "/opt/conda/lib/python3.7/site-packages/loompy/loompy.py", line 1081, in create raise ve File "/opt/conda/lib/python3.7/site-packages/loompy/loompy.py", line 1076, in create ds.ca[key] = vals File "/opt/conda/lib/python3.7/site-packages/loompy/loompy.py", line 183, in exit raise ValueError("Newly created loom file must be filled with data before leaving the 'with' statement") ValueError: Newly created loom file must be filled with data before leaving the 'with' statement Traceback (most recent call last): File "h5py/_objects.pyx", line 201, in h5py._objects.ObjectID.dealloc OSError: [Errno 5] Driver write request failed (file write failed: time = Sat Nov 11 06:58:54 2023 , filename = '/notebook/zhencaiwei/RNA_velocity/processed/sample01/velocyto/sample01.loom', file descriptor = 4, errno = 5, error message = 'Input/output error', buf = 0x55c382bf25b0, total write size = 203, bytes this sub-write = 203, bytes actually written = 18446744073709551615, offset = 0) Exception ignored in: 'h5py._objects.ObjectID.dealloc' Traceback (most recent call last): File "h5py/_objects.pyx", line 201, in h5py._objects.ObjectID.dealloc OSError: [Errno 5] Driver write request failed (file write failed: time = Sat Nov 11 06:58:54 2023 , filename = '/notebook/zhencaiwei/RNA_velocity/processed/sample01/velocyto/sample01.loom', file descriptor = 4, errno = 5, error message = 'Input/output error', buf = 0x55c382bf25b0, total write size = 203, bytes this sub-write = 203, bytes actually written = 18446744073709551615, offset = 0) Traceback (most recent call last): File "h5py/_objects.pyx", line 201, in h5py._objects.ObjectID.dealloc RuntimeError: Dirty entry flush destroy failed (file write failed: time = Sat Nov 11 06:58:57 2023 , filename = '/notebook/zhencaiwei/RNA_velocity/processed/sample01/velocyto/sample01.loom', file descriptor = 4, errno = 5, error message = 'Input/output error', buf = 0x55c3828f67a0, total write size = 32, bytes this sub-write = 32, bytes actually written = 18446744073709551615, offset = 0) Exception ignored in: 'h5py._objects.ObjectID.dealloc' Traceback (most recent call last): File "h5py/_objects.pyx", line 201, in h5py._objects.ObjectID.dealloc RuntimeError: Dirty entry flush destroy failed (file write failed: time = Sat Nov 11 06:58:57 2023 , filename = '/notebook/zhencaiwei/RNA_velocity/processed/sample01/velocyto/sample01.loom', file descriptor = 4, errno = 5, error message = 'Input/output error', buf = 0x55c3828f67a0, total write size = 32, bytes this sub-write = 32, bytes actually written = 18446744073709551615, offset = 0) Segmentation fault (core dumped)