ERROR - Can not locate the barcodes.tsv file!

[chrismahony]

Hi

I am running hte following:

source my-virtual-env-${BB_CPU}/bin/activate

velocyto run10x /path/FASTQ/CON_A/Align/CON_A \ /path/mm10/Mus_musculus.GRCm39.105.gtf

but I get the following error: 2022-03-15 16:04:06,583 - ERROR - Can not locate the barcodes.tsv file! Traceback (most recent call last): File "/rds/homes/m/mahonyc/.local/bin/velocyto", line 8, in sys.exit(cli()) File "/rds/bear-apps/2021a/EL8-cas/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/rds/bear-apps/2021a/EL8-cas/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/rds/bear-apps/2021a/EL8-cas/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/rds/bear-apps/2021a/EL8-cas/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/rds/bear-apps/2021a/EL8-cas/software/Python/3.9.5-GCCcore-10.3.0/lib/python3.9/site-packages/click/core.py", line 610, in invoke return callback(args, **kwargs) File "/rds/homes/m/mahonyc/.local/lib/python3.9/site-packages/velocyto/commands/run10x.py", line 91, in run10x bcfile = bcmatches[0] IndexError: list index out of range

If you could help I would really appreciate it, thanks, Chris

[chrismahony]

my barcodes file is in CON_A>outs>filtered_feature_bc_matrix

I have tried putting it in other places, but I still get the same error?

[Sa753]

I am getting the same error as well when I run it on the output of cellranger multi?. Did you solve this issue please?

Thanks

[ganpha]

Hello, I have the same issue with cellranger multi output. I tried giving the full path to the barcodes.tsv file, but it gives error - "Can not locate the barcodes.tsv file!" Can anyone help resolve this issue? Thanks!