Error while running velocyto run10x

[yurasong]

Hello, I have tried to run velocyto run10x on my data with velocyto run10x test_set/outs/ test_set/refdata-gex-mm10-2020-A.gtf However, it returns the error as below;

2021-10-25 15:35:07,730 - ERROR - This is an older version of cellranger, cannot check if the output are ready, make sure of this yourself 2021-10-25 15:35:07,730 - ERROR - Can not locate the barcodes.tsv file! Traceback (most recent call last): File "/home/audrey/anaconda3/envs/velocyto/bin/velocyto", line 8, in sys.exit(cli()) File "/home/audrey/anaconda3/envs/velocyto/lib/python3.8/site-packages/click/core.py", line 1137, in call return self.main(*args, **kwargs) File "/home/audrey/anaconda3/envs/velocyto/lib/python3.8/site-packages/click/core.py", line 1062, in main rv = self.invoke(ctx) File "/home/audrey/anaconda3/envs/velocyto/lib/python3.8/site-packages/click/core.py", line 1668, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/audrey/anaconda3/envs/velocyto/lib/python3.8/site-packages/click/core.py", line 1404, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/audrey/anaconda3/envs/velocyto/lib/python3.8/site-packages/click/core.py", line 763, in invoke return __callback(*args, **kwargs) File "/home/audrey/anaconda3/envs/velocyto/lib/python3.8/site-packages/velocyto/commands/run10x.py", line 91, in run10x bcfile = bcmatches[0] IndexError: list index out of range

Could you give me some advice about this issue? Thanks!

Best,

Yura

[hyjforesight]

Can not locate the barcodes.tsv file---- u need the barcodes.tsv change all the files into an absolute path

[yurasong]

Hi, sorry for the late response! It works now :) Thanks!!

[kragrawa]

Hi, were you able to just solve the problem by specifying the full filepath? I am having the same error, even though I am specifying the full file path.