10X cellranger count, [error] The chemistry was unable to be automatically determined While running cellranger count using the following .slurm file:

#SBATCH -p standard
#SBATCH -A overall 
#SBATCH --time=48:00:00
#SBATCH --mail-type=end
#SBATCH --mail-user=nv4e@virginia.edu
#SBATCH --output=generate_count_%j.out
#SBATCH --error=generate_count_%j.err
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=20
#SBATCH --mem=120000


# Run driver program
FASTQS="/scratch/nv4e/kipnis/AHN3LLBGX5/outs/fastq_path/HN3LLBGX5"
TR="/scratch/nv4e/kipnis/refdata-cellranger-mm10-1.2.0"

cellranger count --id=17R_1 --transcriptome=${TR} --fastqs=${FASTQS} --sample=17R --expect-cells=2000


I got the error:

&gt;2018-04-28 20:04:37 [runtime] (progress)        
ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMI
STRY.fork0.chnk0: Indexing genome...
2018-04-28 20:04:49 [runtime] (progress)        ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Building transcriptome...
2018-04-28 20:04:58 [runtime] (progress)        ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Building kmer index...
2018-04-28 20:05:25 [runtime] (progress)        ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.chnk0: Mapping reads...
2018-04-28 20:05:28 [runtime] (chunks_complete) ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY
2018-04-28 20:05:28 [runtime] (run:local)       ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY.fork0.join
2018-04-28 20:05:31 [runtime] (join_complete)   ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.CHEMISTRY_DETECTOR.DETECT_CHEMISTRY

2018-04-28 20:05:34 [runtime] (ready)           ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS
2018-04-28 20:05:37 [runtime] (split_complete)  ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS
2018-04-28 20:05:37 [runtime] (run:local)       ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS.fork0.chnk0.main
2018-04-28 20:05:40 [runtime] (failed)          
ID.17R_1.SC_RNA_COUNTER_CS.SC_RNA_COUNTER.SETUP_CHUNKS

&gt;[error] The chemistry was unable to be automatically determined. This can happen if not enough reads originate from the given reference. Please verify your choice of reference or explicitly specify the chemistry via the --chemistry argument


What is going wrong here? How could I correct it?
The issue was that I supplied wrong indexes during fastq files generation, however, they were generated successfully, and only the next step failed with not that informative error.