output & log problem

[chengarthur]

Hi~ I found this software and I was trying to compare different single cell TE quantify methods, I was using salmon before, thanks to your contribution!
When I was using your package and the log stopped at
"
INFO : Parameter list:
Sample = sort_out
Genome = mm10
Reference annotation index = /home/ccheng/scTE/mm10.exclusive.idx
Minimum number of genes required = 200
Minimum number of counts required = None
Number of threads = 16

INFO : Loading the genome annotation index... 2020-07-20 21:59:57
INFO : Loaded '/home/ccheng/scTE/mm10.exclusive.idx' binary file with 3900779 items
INFO : Finished loading the genome annotation index... 2020-07-20 22:00:25

INFO : Processing BAM/SAM files ...2020-07-20 22:00:25
INFO : Input SAM/BAM file appears to be valid
INFO : Done BAM/SAM files processing ...2020-07-20 22:17:18

INFO : Splitting ...2020-07-20 22:17:18
INFO : Executing multiple thread path with 16 threads
['X', '2', '16', '18', '11', '8', '17', '15', 'Y', '1', '6', '9', '10', '13', '14', '3', '19', '7', '12', '4', '5', 'M']
INFO : Finished processing sample files 2020-07-20 22:21:42

INFO : Fetching from the annotation index... 2020-07-20 22:21:42
INFO : Loaded '/home/ccheng/scTE/mm10.exclusive.idx' binary file with 3900779 items
INFO : Loaded '/home/ccheng/scTE/mm10.exclusive.idx' binary file with 3900779 items
INFO : Loaded '/home/ccheng/scTE/mm10.exclusive.idx' binary file with 3900779 items
INFO : Loaded '/home/ccheng/scTE/mm10.exclusive.idx' binary file with 3900779 items
INFO : Loaded '/home/ccheng/scTE/mm10.exclusive.idx' binary file with 3900779 items
"
and the memory is still occupied so I loock through at the "o3" folder , there are 4 sorted chromosome contains the TE-cell bar code sparse matrix information for 4 chromosome ,should I integrated and convert them to one file manually ？

and one more question for the output:
how your software count mutimapped repeats reads in bam , because I did saw any non-integer in your output

Thanks！

[jphe]

Hi,

Sorry for the late reply.

It seems run out of memory for your task, the memory cost of scTE is coreelated with the threads you use. You can set the it to be fewer such as 3-4. In my experience, usually only need 2-3hours for typical 10x genomics scRNA-seq with 3-4 threads.

scTE quantifiy TEs in the family level instead of individual copies, it sum all the multiper reads from the same TE family, it output the raw count of the reads mammped to the TE family, so as you see, all of them are intergers.

Best,
Jphe