Hello,
I met a problem when I run the cellranger (cellranger-6.0.2) to align the fq files to ref genome on the supercomputer. I used the two parameters of multi-threads and a large memory, but the log file always reminds "[jobmngr] Need 20 GB of memory to start the next job (17.7 GB of memory available). Waiting for jobs to complete." The code I used as follows:
cellranger count --id TG2A-oligo-1 \ --transcriptome /public/home/hyhh/ref/refdata-gex-mm10-2020-A \ --fastqs /public/home/hyhh/data/10x/Reads/TG2A-oligo-1 \ --sample TG2A-oligo-1 \ --nosecondary \ --localcores 4 \ --localmem 64
The information of log file as follows:
Martian Runtime - v4.0.4 Serving UI at http://c4:34237?auth=BkSCcehH5mMFHH4XDggh1UWt3C7itmiddsPGeHmHum8
Running preflight checks (please wait)... 2021-07-13 16:52:39 [jobmngr] 45.9GB less memory than expected was free 2021-07-13 16:52:39 [jobmngr] cgroup rss usage is 0.5GB, vs. limit of 8589934592.0 2021-07-13 16:52:39 [runtime] (ready) ID.TG2A-oligo-1.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT_LOCAL 2021-07-13 16:52:39 [runtime] (run:local) ID.TG2A-oligo-1.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT_LOCAL.fork0.chnk0.main 2021-07-13 16:52:39 [runtime] (ready) ID.TG2A-oligo-1.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT 2021-07-13 16:52:39 [runtime] (run:local) ID.TG2A-oligo-1.SC_RNA_COUNTER_CS.CELLRANGER_PREFLIGHT.fork0.chnk0.main ...... 2021-07-13 17:02:09 [jobmngr] Need 20 GB of memory to start the next job (17.7 GB of memory available). Waiting for jobs to complete. 2021-07-13 17:02:12 [jobmngr] Need 20 GB of memory to start the next job (17.7 GB of memory available). Waiting for jobs to complete. 2021-07-13 17:02:18 [jobmngr] Need 20 GB of memory to start the next job (17.7 GB of memory available). Waiting for jobs to complete. .....
I am waiting for very long time and the tail hints are "[jobmngr] Need 20 GB of memory to start the next job (17.7 GB of memory available). Waiting for jobs to complete"
So how can I run the software properly? Thanks !
