Cellranger count issue

[ojhdavid]

I tried to run cellranger count in my computer and everytime I try the computer is shutting down. I don't know why. I got site check from 10XGenomics and I got this answer below :

Hi Jung Han oh,

Thanks for your site check request.

The minimum requirements are:

8-core Intel or AMD processor (16 cores recommended) 64GB RAM (128GB recommended) 1TB free disk space 64-bit CentOS/RedHat 6.0 or Ubuntu 12.04

You have:

24-core 98GB 2.3T free disk space Ubuntu 18.04.6 LTS

You have met the minimum and recommended hardware requirements for RAM, and CPU's.

The ulimits -n are low at 1024.

Ideally this should be 16K. You can change this using the following command:

ulimit -n 16000

You may need assistance from your local network admin as the hard limit looks to be set to 4096.

Your global open file limit is set to 9827152. This meets the requirement of 10000 per GB RAM. 98 * 10000 = 9800000 < 9827152.

I can see no problems with respect to the site check.

Since ulimit are low I tried to change it by using ulimit -n 16000 and it didn't worked. So I use root account to change ulimit into 16000 and run cellranger program there. Hard limit of root account is around 1000000 and this time computer was shut down again.

I used code below

ylc@ylc-System-Product-Name:~$ su - root
암호: 
root@ylc-System-Product-Name:/data/ojh/VISIUM/SSU_cho(1)/SSU_cho/LU-ALK 36(S1746877) (CR_22_13332_FP_R_SSV_1)/Fastq# export PATH=/data/ojh/yard/apps/cellranger-7.0.1:$PATH
root@ylc-System-Product-Name:/data/ojh/VISIUM/SSU_cho(1)/SSU_cho/LU-ALK 36(S1746877) (CR_22_13332_FP_R_SSV_1)/Fastq# cellranger count --id=ALK36 \
> --fastqs=. \
> --transcriptome=/data/ojh/VISIUM/refdata-gex-GRCh38-2020-A/ \
> --localcores=12 \
> --localmem=64

Then What should I check to solve this problem?