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JiekaiLab / scTE

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'Calculating expression' getting killed #66

Open noranekonobokkusu opened 1 year ago

noranekonobokkusu commented 1 year ago

Hi,

I am trying to analyze human bam file, and it crashes at 'calculating expression' step.

My command is ~/.local/bin/scTE -i $bam -o out -x hg38.exclusive.idx --hdf5 True -p 1 -CB CR -UMI UR I am requesting 24 Gb and using one thread. Is it not enough for the job? I tried using 2 threads 12 Gb each and it also got killed.

Full log:

DEBUG   : Creating converter from 7 to 5
DEBUG   : Creating converter from 5 to 7
DEBUG   : Creating converter from 7 to 5
DEBUG   : Creating converter from 5 to 7
INFO    : Parameter list:
Sample = out
Reference annotation index = hg38.exclusive.idx
Minimum number of genes required = 200
Minimum number of counts required = None
Number of threads = 1 

INFO    : Loading the genome annotation index... 2023-07-07 01:22:33
INFO    : Loaded 'hg38.exclusive.idx' binary file with 5400305 items
INFO    : Finished loading the genome annotation index... 2023-07-07 01:24:46 

INFO    : Processing BAM/SAM files ...2023-07-07 01:24:46
INFO    : Input SAM/BAM file appears to be valid
INFO    : Done BAM/SAM files processing ...2023-07-07 02:31:14 

INFO    : Splitting ...2023-07-07 02:31:14
INFO    : Executing single thread path
INFO    : Finished processing sample files 2023-07-07 03:32:18 

INFO    : Fetching from the annotation index... 2023-07-07 03:32:18
INFO    : Done fetching... 2023-07-07 04:51:48 

INFO    : Calculating expression... 2023-07-07 04:51:48
/var/spool/uger-8.5.5/uger-r7-c011/job_scripts/39670178: line 16: 212796 Killed                  ~/.local/bin/scTE -i $bam -o out -x hg38.exclusive.idx --hdf5 True -p 1 -CB CR -UMI UR

It seems it is crashing after 20 minutes of calculating expression. My bam file is 12 Gb. Should I just keep increasing memory?

Thanks!

jphe commented 1 year ago

Without more information about the specific problem you're encountering, it's difficult to provide a more detailed solution. However, increasing memory can often help improve system performance and stability, especially if you are running memory-intensive applications or multitasking.

I agree that one possible solution to try is increasing your memory.