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Can not locate the barcodes.tsv file

See original GitHub issue

I just installed velocyto, and want to run velocyto run10x -m repeat_msk.gtf mypath/sample01 somepath/refdata-cellranger-mm10-1.2.0/genes/genes.gtf according to tutorial.

My code is velocyto run10x /Cell_Ranger_Processed_Data/GTE001/out/filtered_feature_bc_matrix /Cell_Ranger/opt/refdata-cellranger-hg19-3.0.0/genes/genes.gtf

However, I got the error:

2020-02-26 13:10:05,451 - ERROR - This is an older version of cellranger, cannot check if the output are ready, make sure of this yourself
2020-02-26 13:10:05,451 - ERROR - Can not locate the barcodes.tsv file!
Traceback (most recent call last):
  File "/public-supool/home/wuhaoda/anaconda2/envs/Grim3.6.8/bin/velocyto", line 8, in <module>
    sys.exit(cli())
  File "/public-supool/home/wuhaoda/anaconda2/envs/Grim3.6.8/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/public-supool/home/wuhaoda/anaconda2/envs/Grim3.6.8/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/public-supool/home/wuhaoda/anaconda2/envs/Grim3.6.8/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/public-supool/home/wuhaoda/anaconda2/envs/Grim3.6.8/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/public-supool/home/wuhaoda/anaconda2/envs/Grim3.6.8/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/public-supool/home/wuhaoda/anaconda2/envs/Grim3.6.8/lib/python3.6/site-packages/velocyto/commands/run10x.py", line 91, in run10x
    bcfile = bcmatches[0]
IndexError: list index out of range

I updated Cellranger to the latest version (3.0.2 -> 3.1.0). And I unzip the “.gz” file. However, I got the same error. Should I run Cellranger one more time to get a new “out” file? Or any other solutions?

Issue Analytics

State:
Created 4 years ago
Comments:6

Top GitHub Comments

5reactions

ggruenhagen3commented, Feb 1, 2021

For me the problem was I provided a subdirectory of the directory velocyto was expecting. velocyto expects samplefolder to be the one that contains ‘outs/filtered_feature_bc_matrix/barcodes.tsv.gz’. Also it only worked for me when barcodes.tsv.gz was zipped.

1reaction

SiyiWanggoucommented, Mar 10, 2020

Try velocyto run10x /Cell_Ranger_Processed_Data/GTE001 /Cell_Ranger/opt/refdata-cellranger-hg19-3.0.0/genes/genes.gtf

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