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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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mrp: command not found #41

Closed tiramisutes closed 5 years ago

tiramisutes commented 5 years ago

Dear, I have a problem when used the cellranger count. This is my command:

cellranger count --id=sample --transcriptome=genome_index --fastqs=PATH --sample=J1

But I get a stderr with cann't find mrp.

cellranger/bin/../tenkit/bin/common/_mrp: line 26: mrp: command not found

Any help is much appreciated. Thanks.

evolvedmicrobe commented 5 years ago

Did you follow the instructions here: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation, particularly the third step where you prepend to the PATH? It looks like that may have been missed.

tiramisutes commented 5 years ago

I have added the PATH to the environment variable, but I can't find an mrp script in the cellranger installation directory.

https://drive.google.com/file/d/1DB6EgOhmPyC7B1hEYFX18HZ6LhUDjb2Q/view?usp=sharing

evolvedmicrobe commented 5 years ago

The scripts in the top level bin/ directory know to look for the mrp program at .../cellranger-3.1.0/martian-cs/v3.2.3/bin/mrp which is why a "naked" call to something like which mrp or simply mrp at the terminal won't work, even if the PATH variable is set, yet the command line program for Cell Ranger will always still work.

At first glance this unusual error message indicates you're doing something unusual. However, to resolve this quickly, I'd recommend shooting an email to support@10xgenomics.com. The support group at 10X are specialized trouble shooters, and have a track record of either resolving these types of things quickly, or working through them on your behalf more efficiently than would otherwise be possible.

tiramisutes commented 5 years ago

I even can't find a directory named martian-cs at the top level. https://drive.google.com/file/d/1Kmb21jsGivah0G7TPZ9QkkUjvEIjn3fH/view?usp=sharing

So, maybe I should first install martian and then remake this cellranger.

tiramisutes commented 5 years ago

Now, It's work when I first install martian and then remake this cellranger.