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I am interested in the analysis of single-cell RNA-sequencing data. I installed Cell Ranger according to the instruction (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_in#download). I know, it should be easy, but I found an error occurring after test running as below.

[error] Pipestance failed. Error log at:
tiny/SC_RNA_COUNTER_CS/SC_RNA_COUNTER/_BASIC_SC_RNA_COUNTER/COUNT_GENES/fork0/chnk0-u6c389ca928/_errors

Within that file, it shows the following error:

Job failed in stage code. signal: killed.

So, what do you think about this problem?

Additional information:

  • a checksum test (to check the integrity of the downloaded files) was successful
  • I performed a test run on a personal laptop, mac.
  • I used SSH command to connect the server, but we are sharing the server with our lab members.

I found an error as follows:

WARNING: configured to use 112GB of local memory, but only 80.5GB is currently available.

However, at this time with unknown reasons, the installation is successfully completed, in spite of the warning. Do you have idea?

Thank you in advance.

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  • $\begingroup$ I think I am having the same issue. but the error occurred while running cellranger-arc. If I am sharing server (hpc) with other people how do i solve this problem ? Thanks $\endgroup$
    – Goku
    Jan 13, 2022 at 21:31
  • $\begingroup$ Hello @Goku, if you have a problem that is similar to this, but not really, open a new question, link this one and explain properly why this solution did not work for you. Posting answers as follow up questions is not the way of stack exchange :-). $\endgroup$
    – Kamil S Jaron
    Jan 13, 2022 at 22:21

1 Answer 1

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Answer from PPK, converted from comments:

The memory warning is only letting you know that the upper limit you set on memory (112 gb) was higher than the available memory. Do you share the server with other people? because the minimum amount of memory for Cell Ranger is 64 GB. In your initial run there may have been less than 64 GB free.

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