text: user2005: 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:
  >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
  
  >[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?
  
  user2005: 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.
  
original_text: 2005: <p>While running <code>cellranger count</code> using the following <code>.slurm</code> file:</p>
  
  <pre><code>#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
  </code></pre>
  
  <p>I got the error:</p>
  
  <pre><code>&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
  </code></pre>
  
  <p>What is going wrong here? How could I correct it?</p>
   2005: <p>The issue was that I supplied wrong indexes during <code>fastq</code> files generation, however, they were generated successfully, and only the next step failed with not that informative error.</p>
  