soloCellFiltering only output is features.tsv
marlmatos opened this issue · comments
Hi,
I am running soloCellFiltering and it goes through instantly saying it finished but the only output is a features.tsv and a _tempSTAR directory. I've tried with different versions of STAR
Thanks in advance,
Marliette
$STAR --runMode soloCellFiltering ./ ../filtered_counts/ --soloCellFilter EmptyDrops_CR 25000 0.99 10 45000 90000 500 0.01 20000 0.01 10000
STAR --runMode soloCellFiltering ./ ../filtered_counts/ --soloCellFilter EmptyDrops_CR 25000 0.99 10 45000 90000 500 0.01 20000 0.01 10000
STAR version: 2.7.9a compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Mar 18 15:10:28 ..... started STAR run
Mar 18 15:10:28 ..... starting SoloCellFiltering
Mar 18 15:10:28 ..... finished successfully
$ STAR --version
2.7.9a
Hi!
I originally closed this issue because I was getting a core dump error. I realized my matrix.mtx had the wrong formatting. But now, I am realizing that I am getting a segmentation error, and all the input variables are the right formatting. I also tried the script with the raw matrixes from STARsolo and I get the same result.
This is my script.
STAR --runMode soloCellFiltering ./ scGEX-A17. --soloCellFilter EmptyDrops_CR 25000 0.99 10 45000 90000 500 0.01 20000 0.01 10000
STAR --runMode soloCellFiltering ./ scGEX-A17. --soloCellFilter EmptyDrops_CR 25000 0.99 10 45000 90000 500 0.01 20000 0.01 10000
STAR version: 2.7.9a compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
Mar 20 12:08:40 ..... started STAR run
Mar 20 12:08:40 ..... starting SoloCellFiltering
Command error:
INFO: Converting SIF file to temporary sandbox...
.command.sh: line 2: 15 Segmentation fault (core dumped) STAR --runMode soloCellFiltering ./ scGEX-A17. --soloCellFilter EmptyDrops_CR 25000 0.99 10 45000 90000 500 0.01 20000 0.01 10000
INFO: Cleaning up image...