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alexdobin / STAR

RNA-seq aligner
MIT License
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soloCellFiltering only output is features.tsv #2095

Closed marlmatos closed 3 months ago

marlmatos commented 3 months ago

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

marlmatos commented 3 months ago

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...