soloCellFiltering seg fault

[cnk113]

Hey Alex,

I was running --soloCellFiltering on my raw folder and I got a segfault close to completion. Attached is the Log file.
In terms of output files I got emptydropsfeatures.tsv

May 05 16:05:28 ..... started STAR run
May 05 16:05:29 ..... starting SoloCellFiltering
Segmentation fault (core dumped)

STAR version=2.7.9a
STAR compilation time,server,dir=2021-05-04T20:29:59-07:00 :/media/chang/HDD-3/chang/STAR/source
##### Command Line:
STAR --runMode soloCellFiltering raw emptydrops --soloCellFilter EmptyDrops_CR
##### Initial USER parameters from Command Line:
###### All USER parameters from Command Line:
runMode                       soloCellFiltering   raw   emptydrops        ~RE-DEFINED
soloCellFilter                EmptyDrops_CR        ~RE-DEFINED
##### Finished reading parameters from all sources

##### Final user re-defined parameters-----------------:
runMode                           soloCellFiltering   raw   emptydrops   
soloCellFilter                    EmptyDrops_CR   

-------------------------------
##### Final effective command line:
STAR   --runMode soloCellFiltering   raw   emptydrops      --soloCellFilter EmptyDrops_CR   
----------------------------------------

Number of fastq files for each mate = 1
ParametersSolo: using hardcoded filtering parameters for --soloCellFilterType EmptyDrops_CR
ParametersSolo: --soloCellFilterType EmptyDrops_CR filtering parameters: 3000 0.99 10 45000 90000 500 0.01 20000 0.01 10000
Finished loading and checking parameters
Solo output directory directory and its parents created: 
cellFiltering: simple: nUMImax=6229; nUMImin=623; nCellsSimple=13173
May 05 16:15:34 ... starting emptyDrops_CR filtering
May 05 16:15:34 ... finished ambient cells counting
May 05 16:15:34 ... finished SGT
May 05 16:15:34 ... finished ambient profile
May 05 16:15:34 ... candidate cells: minUMI=500; number of candidate cells=1288
May 05 16:15:34 ... finished observed logProb
May 05 16:15:35 ... finished simulations
May 05 16:15:35 ... finished emptyDrops_CR filtering: number of additional non-ambient cells=1286

[alexdobin]

Hi Chang,

could you please send the raw files to me? I need to reproduce the problem.

Thanks!
Alex

[cnk113]

I emailed you the file.

[bepoli]

I'm able to reproduce the error using the raw STARsolo matrices obtained from processing this data.
I get the same error if I use the raw Cell Ranger matrices downloaded from 10x genomics.

$ STAR --version
2.7.9a
$ wget https://cf.10xgenomics.com/samples/cell-exp/4.0.0/SC3_v3_NextGem_SI_PBMC_10K/SC3_v3_NextGem_SI_PBMC_10K_raw_feature_bc_matrix.tar.gz \
  && tar -xvf SC3_v3_NextGem_SI_PBMC_10K_raw_feature_bc_matrix.tar.gz \
  && gunzip raw_feature_bc_matrix/*.gz
$ STAR --runMode soloCellFiltering raw_feature_bc_matrix/ filtered/ --soloCellFilter EmptyDrops_CR
        STAR --runMode soloCellFiltering raw_feature_bc_matrix/ filtered/ --soloCellFilter EmptyDrops_CR
        STAR version: 2.7.9a   compiled: 2021-05-04T09:43:56-0400 vega:/home/dobin/data/STAR/STARcode/STAR.master/source
May 20 10:52:41 ..... started STAR run
May 20 10:52:41 ..... starting SoloCellFiltering
Segmentation fault (core dumped)

[piyushjo15]

Same issue with me. I generated the alignment and then just tried running --runMode soloCellFiltering. I only get a new features.tsv file and not the matrix.mtx file from filtering. I am also using --solocellFilter EmptyDrops_CR.

[pavsol]

Having the same issue with both, EmptyDrops_CR and CellRanger2.2 filtering methods.

[alexdobin]

Folks, sorry for the long delay.
I have fixed this bug, please try the latest commit on GitHub master.

[bepoli]

I ran it on the same data and it works perfectly now, thank you Alex!