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JiekaiLab / scTE

MIT License
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scTE freezes after beginning BAM file processing #33

Open martinkinisu opened 2 years ago

martinkinisu commented 2 years ago

Hello! I am trying to use scTE on BAM files generated from STARsolo. The tool gets to the point where it says that the BAM files look good but does not progress. I have ensured that I have installed the latest version = 1.0 from the JiekaiLab git and have tried adjusting the -p from 1 to 8 with no success. Below is the output from the tool, any advice on how to fix this would be appreciated!

/wynton/home/greenelab/mkinisu/scripts/scTE_virtualenv/bin/python 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 = /wynton/scratch/mkinisu/Weili_HIV_STAR/Weili_HIV/WKWG04_C1_S9_L004 Reference annotation index = /wynton/home/greenelab/mkinisu/ref/scTE/hg38.exclusive.idx Minimum number of genes required = 200 Minimum number of counts required = None Number of threads = 8

INFO : Loading the genome annotation index... 2022-03-10 15:51:28 INFO : Loaded '/wynton/home/greenelab/mkinisu/ref/scTE/hg38.exclusive.idx' binary file with 4750078 items INFO : Finished loading the genome annotation index... 2022-03-10 15:52:31

INFO : Processing BAM/SAM files ...2022-03-10 15:52:31 INFO : Input SAM/BAM file appears to be valid

jphe commented 2 years ago

How much memory does your sever has? it seems to me run out of memory

wjbsb commented 1 year ago

Hello,

I have the same problem, after a time (some hours): scTE is always in process but there are no activities on the threads and the memory is in low activity.

There are no error in log activities on threads

Temporary files are built and I have count/TE in bed format file.

Perhaps, scTE is in infinite loop and there is not exit door ?

Update : After checked (and merge bed files), I had only data on 20 "good" cells (which pass the classical filters and doublet detection).

jphe commented 1 year ago

How many threads did you use? Each thread in scTE requires around 15GB of memory. Make sure that your server has enough memory, otherwise, decrease the number of threads appropriately using the -p parameter.

wjbsb commented 1 year ago

It is probably that...I used 20 threads but I have only 168GB of memory....I don't read this detail before to launch