Answers.Body: <p>I repro the error.</p>
  <pre><code>ls /ml
  </code></pre>
  <blockquote>
  <p>ls: cannot access '/ml': No such file or directory</p>
  </blockquote>
  <p>If run</p>
  <pre><code>bcl2fastq --runfolder-dir ./data/201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0
  </code></pre>
  <p>I suspect it will work.</p>
  <p>At present you are attempting to call a directory <code>/data</code>, which doesn't exit. If you type <code>ls /etc</code> that will work. The difference between <code>./data</code> and <code>/data</code> in a file structure is alot, but on a command line it appears minimal.</p>
  <hr />
  <p>Wait ... if that doesn't work .. because I suspect the calling directory is <code>data</code> then the following will,</p>
  <pre><code>bcl2fastq --runfolder-dir ./201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0
  </code></pre>
  <p>OR</p>
  <pre><code>bcl2fastq --runfolder-dir ./data/201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./data/SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0
  </code></pre>
  <p>It depends on the path where you are making the call. You could sort this out using <code>$PWD</code> or just <code>echo $PWD</code> then copy and paste the path name.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-11T14:17:42.247Z
Answers.Text: Such a simple fix! Thanks for your solution. I simply ran this from the folder containing the folder and it worked: ```bcl2fastq --runfolder-dir 201109_NB551126_0128_AH5G5KBGXF --sample-sheet SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0```
Answers.UserDisplayName: Stewart Russell
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-11-11T14:07:59.013Z
Answers.LastActivityDate: 2020-11-11T14:07:59.013Z
Answers.UserDisplayName: M__
Body: <p>I'm attempting to demux a nextseq run which I've successfully done several times in the past on other runs. I uploaded the run from my PC to the server (Ubuntu 18.04.4 LTS) without issue. Then I ran:</p>
  <pre><code>```bcl2fastq --runfolder-dir /data/201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0```
  </code></pre>
  <p>From which I got the error:</p>
  <blockquote>
  <pre><code>'/data/201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml' file for
  reading```
  </code></pre>
  </blockquote>
  <p>However, the RunInfo.xml file is present and readable:</p>
  <pre><code>$ ls -l
  total 96
  drwxrwxrwx 10 user user 90112 Nov 11 08:08 201109_NB551126_0128_AH5G5KBGXF
  -rwxrwxr-x  1 user user 1929 Nov 11 07:37 SampleSheet.csv
  $ 
  $ ls -l 201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml
  -rwxrwxr-x 1 user user 28510 Nov 11 08:08 201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml
  $ 
  $ head 201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml
  &lt;?xml version=&quot;1.0&quot;?&gt;
  &lt;RunInfo xmlns:xsd=&quot;http://www.w3.org/2001/XMLSchema&quot; xmlns:xsi=&quot;http://www.w3.org/2001/XMLSchema-instance&quot; Version=&quot;4&quot;&gt;
    &lt;Run Id=&quot;201109_NB551126_0128_AH5G5KBGXF&quot; Number=&quot;128&quot;&gt;
      &lt;Flowcell&gt;H5G5KBGXF&lt;/Flowcell&gt;
      &lt;Instrument&gt;NB551126&lt;/Instrument&gt;
      &lt;Date&gt;201109&lt;/Date&gt;
      &lt;Reads&gt;
        &lt;Read Number=&quot;1&quot; NumCycles=&quot;75&quot; IsIndexedRead=&quot;N&quot; /&gt;
        &lt;Read Number=&quot;2&quot; NumCycles=&quot;6&quot; IsIndexedRead=&quot;Y&quot; /&gt;
      &lt;/Reads&gt;
  </code></pre>
  <p>Has anyone had this issue or know of a fix? Thanks!</p>
  <p>Update: contents of run folder</p>
  <pre><code>total 2452
  -rwxrwxr-x 1 stewart stewart   977 Nov 11 07:59 '2020-11-09__14_05_58_94F12309 GetBestZ Camera 1 Focus Red top surface.snr.csv'
  ....
  -rwxrwxr-x 1 stewart stewart   244 Nov 11 07:59 '2020-11-09__14_08_54_FE05AB9F SafeParabola called by CalculateSignalStd.snr.csv'
  -rwxrwxr-x 1 stewart stewart   253 Nov 11 07:59 '2020-11-09__14_08_54_FE0620BC SafeParabola called by FindPeakUsingParabolaFit.snr.csv'
  ....
  drwxrwxrwx 2 stewart stewart  4096 Nov 11 07:59  Config
  drwxrwxrwx 3 stewart stewart  4096 Nov 11 07:59  Data
  drwxrwxrwx 3 stewart stewart  4096 Nov 11 08:07  Images
  drwxrwxrwx 2 stewart stewart 12288 Nov 11 08:07  InstrumentAnalyticsLogs
  drwxrwxrwx 2 stewart stewart  4096 Nov 11 08:08  InterOp
  drwxrwxrwx 2 stewart stewart  4096 Nov 11 08:08  Logs
  drwxrwxrwx 2 stewart stewart  4096 Nov 11 08:08  Recipe
  -rwxrwxr-x 1 stewart stewart    48 Nov 11 08:08  RTAComplete.txt
  -rwxrwxr-x 1 stewart stewart  6200 Nov 11 08:08  RTAConfiguration.xml
  drwxrwxrwx 2 stewart stewart  4096 Nov 11 08:08  RTALogs
  -rwxrwxr-x 1 stewart stewart    36 Nov 11 08:08  RTARead1Complete.txt
  -rwxrwxr-x 1 stewart stewart    36 Nov 11 08:08  RTARead2Complete.txt
  -rwxrwxr-x 1 stewart stewart   925 Nov 11 08:08  RunCompletionStatus.xml
  -rwxrwxr-x 1 stewart stewart 28510 Nov 11 08:08  RunInfo.xml
  -rwxrwxr-x 1 stewart stewart 26802 Nov 11 08:08  RunParameters.xml
  -rwxrwxr-x 1 stewart stewart  1929 Nov 11 08:08  SampleSheet.csv```
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-11T13:47:29.983Z
Comments.Text: What does `ls -l /data/201109_NB551126_0128_AH5G5KBGXF/` give?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-11T13:58:41.513Z
Comments.Text: It was too long for a comment so see update above. Interestingly there are a lot of .csv files I'm not used to seeing but the files that should be there are present as far as I can tell!
Comments.UserDisplayName: Stewart Russell
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-11-11T14:04:57.150Z
Comments.Text: I've got it .. just a minute
Comments.UserDisplayName: M__
Tags: <illumina><demultiplexing>
Title: Error processing run file with bcl2fastq - Unable to open '.../RunInfo.xml' file for reading
ThreadText: # Error processing run file with bcl2fastq - Unable to open '.../RunInfo.xml' file for reading
  
  (Asked by: username_0 on 2020-11-11)
  
  I'm attempting to demux a nextseq run which I've successfully done several times in the past on other runs. I uploaded the run from my PC to the server (Ubuntu 18.04.4 LTS) without issue. Then I ran:
  
  ```
  ```bcl2fastq --runfolder-dir /data/201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0```
  
  ```
  
  From which I got the error:
  
  > ```
  > '/data/201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml' file for
  > reading```
  >
  > ```
  
  However, the RunInfo.xml file is present and readable:
  
  ```
  $ ls -l
  total 96
  drwxrwxrwx 10 user user 90112 Nov 11 08:08 201109_NB551126_0128_AH5G5KBGXF
  -rwxrwxr-x  1 user user 1929 Nov 11 07:37 SampleSheet.csv
  $ 
  $ ls -l 201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml
  -rwxrwxr-x 1 user user 28510 Nov 11 08:08 201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml
  $ 
  $ head 201109_NB551126_0128_AH5G5KBGXF/RunInfo.xml
  <?xml version="1.0"?>
  <RunInfo xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Version="4">
    <Run Id="201109_NB551126_0128_AH5G5KBGXF" Number="128">
      <Flowcell>H5G5KBGXF</Flowcell>
      <Instrument>NB551126</Instrument>
      <Date>201109</Date>
      <Reads>
        <Read Number="1" NumCycles="75" IsIndexedRead="N" />
        <Read Number="2" NumCycles="6" IsIndexedRead="Y" />
      </Reads>
  
  ```
  
  Has anyone had this issue or know of a fix? Thanks!
  
  Update: contents of run folder
  
  ```
  total 2452
  -rwxrwxr-x 1 username_0 username_0   977 Nov 11 07:59 '2020-11-09__14_05_58_94F12309 GetBestZ Camera 1 Focus Red top surface.snr.csv'
  ....
  -rwxrwxr-x 1 username_0 username_0   244 Nov 11 07:59 '2020-11-09__14_08_54_FE05AB9F SafeParabola called by CalculateSignalStd.snr.csv'
  -rwxrwxr-x 1 username_0 username_0   253 Nov 11 07:59 '2020-11-09__14_08_54_FE0620BC SafeParabola called by FindPeakUsingParabolaFit.snr.csv'
  ....
  drwxrwxrwx 2 username_0 username_0  4096 Nov 11 07:59  Config
  drwxrwxrwx 3 username_0 username_0  4096 Nov 11 07:59  Data
  drwxrwxrwx 3 username_0 username_0  4096 Nov 11 08:07  Images
  drwxrwxrwx 2 username_0 username_0 12288 Nov 11 08:07  InstrumentAnalyticsLogs
  drwxrwxrwx 2 username_0 username_0  4096 Nov 11 08:08  InterOp
  drwxrwxrwx 2 username_0 username_0  4096 Nov 11 08:08  Logs
  drwxrwxrwx 2 username_0 username_0  4096 Nov 11 08:08  Recipe
  -rwxrwxr-x 1 username_0 username_0    48 Nov 11 08:08  RTAComplete.txt
  -rwxrwxr-x 1 username_0 username_0  6200 Nov 11 08:08  RTAConfiguration.xml
  drwxrwxrwx 2 username_0 username_0  4096 Nov 11 08:08  RTALogs
  -rwxrwxr-x 1 username_0 username_0    36 Nov 11 08:08  RTARead1Complete.txt
  -rwxrwxr-x 1 username_0 username_0    36 Nov 11 08:08  RTARead2Complete.txt
  -rwxrwxr-x 1 username_0 username_0   925 Nov 11 08:08  RunCompletionStatus.xml
  -rwxrwxr-x 1 username_0 username_0 28510 Nov 11 08:08  RunInfo.xml
  -rwxrwxr-x 1 username_0 username_0 26802 Nov 11 08:08  RunParameters.xml
  -rwxrwxr-x 1 username_0 username_0  1929 Nov 11 08:08  SampleSheet.csv```
  
  ```
  
  **Tags:** illumina, demultiplexing
  
  > **Comments:**
  > **username_1**: What does `ls -l /data/201109_NB551126_0128_AH5G5KBGXF/` give?  
  > **username_0**: It was too long for a comment so see update above. Interestingly there are a lot of .csv files I'm not used to seeing but the files that should be there are present as far as I can tell!  
  > **username_1**: I've got it .. just a minute  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-11-11. Score: 1 | Accepted answer
  
  I repro the error.
  
  ```
  ls /ml
  
  ```
  
  > ls: cannot access '/ml': No such file or directory
  
  If run
  
  ```
  bcl2fastq --runfolder-dir ./data/201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0
  
  ```
  
  I suspect it will work.
  
  At present you are attempting to call a directory `/data`, which doesn't exit. If you type `ls /etc` that will work. The difference between `./data` and `/data` in a file structure is alot, but on a command line it appears minimal.
  
  ---
  
  Wait ... if that doesn't work .. because I suspect the calling directory is `data` then the following will,
  
  ```
  bcl2fastq --runfolder-dir ./201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0
  
  ```
  
  OR
  
  ```
  bcl2fastq --runfolder-dir ./data/201109_NB551126_0128_AH5G5KBGXF --sample-sheet ./data/SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0
  
  ```
  
  It depends on the path where you are making the call. You could sort this out using `$PWD` or just `echo $PWD` then copy and paste the path name.
  
  > **Comments:**
  > **username_0**: Such a simple fix! Thanks for your solution. I simply ran this from the folder containing the folder and it worked: ```bcl2fastq --runfolder-dir 201109_NB551126_0128_AH5G5KBGXF --sample-sheet SampleSheet.csv  --no-lane-splitting --barcode-mismatches 0```  
  
  ---
  
  