error in mat2csv ValueError: Shape of passed values is (4926, 33694), indices imply (4926, 30585)

Question

[yueli7]

Hello, Everyone,

I tried to use mat2csv convert matrix to csv format.

Thanks in advance for any help!

Best,

Yue

li@li-0-p0xxx:~/opt/cellranger-3.1.0$ cellranger mat2csv ~/single_cell/gse112824_zebrafish samples12
/home/li/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin
cellranger mat2csv (3.1.0)


WARNING: this matrix has 30585 x 4926 (150661710 total) elements, 94.197432% of which are zero.
Converting it to dense CSV format may be very slow and memory intensive.
Moreover, other programs (e.g. Excel) may be unable to load it due to its size.
To cancel this command, press <control key> + C.

If you need to inspect the data, we recommend using Loupe Cell Browser.

Traceback (most recent call last):
File "/home/li/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin/mat2csv", line 79, in <module>
main()
File "/home/li/opt/cellranger-3.1.0/cellranger-cs/3.1.0/bin/mat2csv", line 73, in main
matrix.save_dense_csv(output_csv)
File "/home/li/opt/cellranger-3.1.0/cellranger-cs/3.1.0/lib/python/cellranger/matrix.py", line 414, in save_dense_csv
columns=self.bcs)
File "/home/li/opt/cellranger-3.1.0/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/lib/python2.7/site-packages/pandas/core/frame.py", line 361, in __init__
copy=copy)
File "/home/li/opt/cellranger-3.1.0/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/lib/python2.7/site-packages/pandas/core/frame.py", line 533, in _init_ndarray
return create_block_manager_from_blocks([values], [columns, index])
File "/home/li/opt/cellranger-3.1.0/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/lib/python2.7/site-packages/pandas/core/internals.py", line 4631, in create_block_manager_from_blocks
construction_error(tot_items, blocks[0].shape[1:], axes, e)
File "/home/li/opt/cellranger-3.1.0/miniconda-cr-cs/4.3.21-miniconda-cr-cs-c10/lib/python2.7/site-packages/pandas/core/internals.py", line 4608, in construction_error
passed, implied))
ValueError: Shape of passed values is (4926, 33694), indices imply (4926, 30585)

Answer 1

[yueli7]

should have a gene.tsv file