Answers.Body: <p>Using more threads solves the problem.</p>
  <h1>Run FASTQC with increased memory allocation</h1>
  <pre><code>fastqc --outdir=&quot;<span class="math-container">$OUTPUT_QC" -t 10 "$</span>OUTPUT_PC&quot;
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-08-28T11:28:42.447Z
Answers.LastActivityDate: 2024-08-29T09:06:39.393Z
Answers.LastEditDate: 2024-08-29T09:06:39.393Z
Answers.UserDisplayName: dim
Body: <p>I'm running a bioinformatics pipeline to analyze large nanopore sequencing files using FastQC. However, I keep running into an <code>OutOfMemoryError</code>. Here's what happens:</p>
  <pre><code>Unknown option: memory
  Started analysis of SQK-NBD114-24_barcode16.fastq
  Approx 5% complete for SQK-NBD114-24_barcode16.fastq
  ...
  Approx 40% complete for SQK-NBD114-24_barcode16.fastq
  Exception in thread &quot;Thread-1&quot; java.lang.OutOfMemoryError: Java heap space
          at uk.ac.babraham.FastQC.Utilities.QualityCount.&lt;init&gt;(QualityCount.java:33)
          at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.processSequence(PerBaseQualityScores.java:141)
          at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:89)
          at java.base/java.lang.Thread.run(Thread.java:829)
  ^CError: FastQC failed for /home/jupyter/bioinfo_pipeline/demuxed_2/SQK-NBD114-24_barcode16.fastq. Exiting pipeline.
  </code></pre>
  <p>I attempted to allocate more memory by setting <code>FASTQC_MEMORY=&quot;4g&quot;</code> and running FastQC with the following script:</p>
  <pre class="lang-bash prettyprint-override"><code># Allocate more memory to FastQC (e.g., 4GB)
  FASTQC_MEMORY=&quot;4g&quot;
  
  # Loop over all .fastq files in the demuxed directory
  for filename in &quot;<span class="math-container">$DEMUX_DIR"/*.fastq; do
      echo -e "\nProcessing $</span>filename...&quot;
      
      #-= STEP 3 - SECOND quality control (FASTQC and NANOQC) =- 
      echo -e &quot;\n~~~~~~-= Step 3, QC =-~~~~~~\n&quot;
      OUTPUT_PC=&quot;$filename&quot;  # Assuming OUTPUT_PC refers to the current .fastq file
      
      # Run FASTQC with increased memory allocation
      fastqc --outdir=&quot;<span class="math-container">$OUTPUT_QC" --memory="$</span>FASTQC_MEMORY&quot; &quot;$OUTPUT_PC&quot;
      
      # Check if FastQC failed due to memory issues or other errors
      if [ <span class="math-container">$? -ne 0 ]; then
      echo "Error: FastQC failed for $</span>filename. Exiting pipeline.&quot;
          exit 1
      fi
  done
  </code></pre>
  <p>But it seems like 4GB isn't enough, as the process still crashes. The file I'm working with is quite large (Nanopore sequencing data):</p>
  <pre><code>-rw-r--r-- 1 jupyter jupyter 442198080 Aug 27 14:49 SQK-NBD114-24_barcode16.fastq
  </code></pre>
  <p>According to <code>free -h</code>, I have 22 GiB of available memory. How much memory should I allocate to FastQC to prevent these errors? Is there a rule of thumb or specific calculation I should use when working with large <code>.fastq</code> files?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-27T15:45:09.573Z
Comments.Text: For now I would say give it like 15-20 GB and see if you run into the same error. Which version of FastQC are you using?
Comments.UserDisplayName: Karthik Nair
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-27T16:13:09.720Z
Comments.Text: Where did you get this `--memory` option? That doesn't seem to exist. Note the first line of your error output: `Unknown option: memory`. On my fastqc version 0.12.1, the `--memory` option is known, but only takes values in megabytes. Check that your version i) has a `--memory` option and ii) it can accept the string `4g` as a valid value.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-08-28T10:02:02.343Z
Comments.Text: @Karthik Nair ```FastQC v0.11.9```
Comments.UserDisplayName: dim
Tags: <nanopore><fastqc>
Title: How much memory should I allocate to FastQC for analyzing large nanopore sequencing files?
ThreadText: # How much memory should I allocate to FastQC for analyzing large nanopore sequencing files?
  
  (Asked by: username_0 on 2024-08-27)
  
  I'm running a bioinformatics pipeline to analyze large nanopore sequencing files using FastQC. However, I keep running into an `OutOfMemoryError`. Here's what happens:
  
  ```
  Unknown option: memory
  Started analysis of SQK-NBD114-24_barcode16.fastq
  Approx 5% complete for SQK-NBD114-24_barcode16.fastq
  ...
  Approx 40% complete for SQK-NBD114-24_barcode16.fastq
  Exception in thread "Thread-1" java.lang.OutOfMemoryError: Java heap space
          at uk.ac.babraham.FastQC.Utilities.QualityCount.<init>(QualityCount.java:33)
          at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.processSequence(PerBaseQualityScores.java:141)
          at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:89)
          at java.base/java.lang.Thread.run(Thread.java:829)
  ^CError: FastQC failed for /home/jupyter/bioinfo_pipeline/demuxed_2/SQK-NBD114-24_barcode16.fastq. Exiting pipeline.
  
  ```
  
  I attempted to allocate more memory by setting `FASTQC_MEMORY="4g"` and running FastQC with the following script:
  
  ```bash
  # Allocate more memory to FastQC (e.g., 4GB)
  FASTQC_MEMORY="4g"
  
  # Loop over all .fastq files in the demuxed directory
  for filename in "$DEMUX_DIR"/*.fastq; do
      echo -e "\nProcessing $filename..."
      
      #-= STEP 3 - SECOND quality control (FASTQC and NANOQC) =- 
      echo -e "\n~~~~~~-= Step 3, QC =-~~~~~~\n"
      OUTPUT_PC="$filename"  # Assuming OUTPUT_PC refers to the current .fastq file
      
      # Run FASTQC with increased memory allocation
      fastqc --outdir="$OUTPUT_QC" --memory="$FASTQC_MEMORY" "$OUTPUT_PC"
      
      # Check if FastQC failed due to memory issues or other errors
      if [ $? -ne 0 ]; then
      echo "Error: FastQC failed for $filename. Exiting pipeline."
          exit 1
      fi
  done
  
  ```
  
  But it seems like 4GB isn't enough, as the process still crashes. The file I'm working with is quite large (Nanopore sequencing data):
  
  ```
  -rw-r--r-- 1 jupyter jupyter 442198080 Aug 27 14:49 SQK-NBD114-24_barcode16.fastq
  
  ```
  
  According to `free -h`, I have 22 GiB of available memory. How much memory should I allocate to FastQC to prevent these errors? Is there a rule of thumb or specific calculation I should use when working with large `.fastq` files?
  
  **Tags:** nanopore, fastqc
  
  > **Comments:**
  > **username_1**: For now I would say give it like 15-20 GB and see if you run into the same error. Which version of FastQC are you using?  
  > **username_2**: Where did you get this `--memory` option? That doesn't seem to exist. Note the first line of your error output: `Unknown option: memory`. On my fastqc version 0.12.1, the `--memory` option is known, but only takes values in megabytes. Check that your version i) has a `--memory` option and ii) it can accept the string `4g` as a valid value.  
  > **username_0**: @username_1 ```FastQC v0.11.9```  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2024-08-28. Score: 0
  
  Using more threads solves the problem.
  
  # Run FASTQC with increased memory allocation
  
  ```
  fastqc --outdir="$OUTPUT_QC" -t 10 "$OUTPUT_PC"
  
  ```
  
  
  ---
  
  