STARsolo doesn't generate filtered folder

[malonzm1]

Hi,

When I run STAR with a particular sample no filtered folder is generated. It works fine with other samples.

STAR --limitBAMsortRAM 250000000000 --outSAMattributes NH HI AS nM NM MD jM jI MC ch XS CR UR GX GN sM CB UB --outSAMtype BAM SortedByCoordinate --quantMode GeneCounts --readFilesCommand gunzip -c --runThreadN 12 --sjdbGTFfile /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/GRCh38/genes/genes.gtf --outReadsUnmapped Fastx --outMultimapperOrder Random --genomeDir /scratch/cs/pan-autoimmune/utilities/STAR/hg38 --readFilesIn /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_3.fastq.gz /scratch/cs/pan-autoimmune/data/raw_data/scRNAseq/GSE169440/SRR13716262/SRR13716262_2.fastq.gz --outFileNamePrefix SRR13716262 --soloType CB_UMI_Simple --soloBarcodeReadLength 0 --soloCBwhitelist /scratch/cs/pan-autoimmune/utilities/GRCh38-2020-A/whitelists/737K-august-2016.txt --soloUMIlen 10 --soloCBlen 16 --soloUMIstart 17
STAR version: 2.7.10b   compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Nov 22 09:28:40 ..... started STAR run
Nov 22 09:28:40 ..... loading genome
Nov 22 09:28:53 ..... processing annotations GTF
Nov 22 09:29:06 ..... inserting junctions into the genome indices
Nov 22 09:30:46 ..... started mapping
Nov 22 09:40:02 ..... finished mapping
Nov 22 09:40:07 ..... started Solo counting
Nov 22 09:40:08 ..... finished Solo counting
Nov 22 09:40:08 ..... started sorting BAM
Nov 22 09:42:09 ..... finished successfully

Any thoughts? Thanks.

[alexdobin]

Hi @malonzm1

please check or post the Log.out file, which may contain some messages about what happened with cell filtering.

[malonzm1]

Thanks. Here's the log file.
SRR13716262Log.txt

[alexdobin]

Hi @malonzm1

it looks like no cell barcodes were detected (nCB=0 in the Log.out.txt file), so the raw matrix is empty and the filtered one is not generated. You need to check that your inputs are correct.

[malonzm1]

Thanks.