No filtered directory after running STARsolo with 10x v3 data

[Nicomakii]

Hi, I'm running an old dataset (from 2019) through cutadapt and then STARsolo for mapping. Here's my script:

#!/bin/bash
#SBATCH --time=24:00:00 -p day --ntasks=1 --cpus-per-task=8 --mem=60000M --job-name=AE_18_STARsolo -o ~/scripts/STARsolo/AE_18_STARsolo.sh.o%J -e ~/scripts/STARsolo/AE_18_STARsolo.sh.e%J
~software/STAR-2.7.10b/bin/Linux_x86_64_static/STAR --soloType CB_UMI_Simple --readFilesCommand zcat --soloBarcodeReadLength 0 --soloFeatures Gene GeneFull Velocyto --runThreadN 8 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --twopassMode None --soloStrand Forward --soloCBwhitelist ~/software/10x_Whitelists/3M-february-2018.txt --genomeDir ~/project/genome_indices/GRCh38.p13/gencode_release43/STARindex_no_GTF --sjdbGTFfile ~/project/genome_indices/GRCh38.p13/gencode_release43/GTF/gencode.v43.primary_assembly.annotation.gtf --readFilesIn ~/sample_out/AE_18/trimmed_merged_fastq/trimmed.R2.fastq.gz 
~/sample_out/AE_18/trimmed_merged_fastq/trimmed.R1.fastq.gz --outFileNamePrefix 
~/sample_out/AE_18/

There's no error and here's what's in the .o file:

    STAR version: 2.7.10b   compiled: 2022-11-01T09:53:26-04:00 :/home/dobin/data/STAR/STARcode/STAR.master/source
Nov 08 15:52:51 ..... started STAR run
Nov 08 15:52:53 ..... loading genome
Nov 08 15:53:05 ..... processing annotations GTF
Nov 08 15:53:21 ..... inserting junctions into the genome indices
Nov 08 15:57:31 ..... started mapping
Nov 08 16:12:11 ..... finished mapping
Nov 08 16:12:11 ..... started Solo counting
Nov 08 16:12:13 ..... finished Solo counting
Nov 08 16:12:13 ..... finished successfully

For all my previous runs a filtered directory would be generated under Solo.out/GeneFull but it's been missing for this run, did it again and it was not there. Did I do anything wrong causing this to happen, or is there something I need to add? Thank you

[alexdobin]

Hi @Nicomakii

it should be generated, please remove all output and restart it in a clean directory. If it does not help, please send me the Log.out file.

[malonzm1]

Hi @Nicomakii,

I encountered the same problem (no filtered folder). Did you by any chance figure out the problem and solution?

Thanks.

[Nicomakii]

Hi @Nicomakii

it should be generated, please remove all output and restart it in a clean directory. If it does not help, please send me the Log.out file.

Hi @alexdobin, Sorry for the super late response, I found the seurat object for the data I was processing last time so I gave up on that run. However, I was doing another alignment recently with the same exact script and encountered the same issue where there is no filtered folder, similar to @malonzm1's post too. Here is the Log.out.txt file

[alexdobin]

Hi @Nicomakii

Log.out.txt says that there were no barcodes detected, so something went wrong with the whole run. You can check that the raw matrix is empty.