Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-03T18:10:42.313Z
Answers.LastActivityDate: 2018-05-03T18:10:42.313Z
Answers.UserDisplayName: Nikita Vlasenko
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-29T06:08:18.803Z
Comments.Text: You presumably aligned against the wrong reference transcriptome.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-04-29T22:55:52.583Z
Comments.Text: It is very weird: the thing that the first time I ran it, it worked. Then, because we got bad results after running `cellranger count` ('bad' means biologically not what we want to see. It would mean that the biology was done in the wrong way), we transferred the raw data again, generated `fastq` files again and somehow now I am having this issue for the first replica, but not for the second one which ran successfully. I am wondering where in this chain of actions I did a mistake. Can it be that the data got corrupted while I was transferring it, however, `fastq` generation worked still?
Comments.UserDisplayName: Nikita Vlasenko
Tags: <10x-genomics><cellranger><slurm>
Title: 10X cellranger count, [error] The chemistry was unable to be automatically determined
ThreadText: # 10X cellranger count, [error] The chemistry was unable to be automatically determined
  
  (Asked by: username_0 on 2018-04-29)
  
  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?
  
  **Tags:** 10x-genomics, cellranger, slurm
  
  > **Comments:**
  > **username_1**: You presumably aligned against the wrong reference transcriptome.  
  > **username_0**: It is very weird: the thing that the first time I ran it, it worked. Then, because we got bad results after running `cellranger count` ('bad' means biologically not what we want to see. It would mean that the biology was done in the wrong way), we transferred the raw data again, generated `fastq` files again and somehow now I am having this issue for the first replica, but not for the second one which ran successfully. I am wondering where in this chain of actions I did a mistake. Can it be that the data got corrupted while I was transferring it, however, `fastq` generation worked still?  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2018-05-03. Score: 2
  
  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.
  
  
  ---
  
  