<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>

CC BY-SA 4.0
2020-11-11T14:17:42.247Z
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```
Stewart Russell
CC BY-SA 4.0
2020-11-11T14:07:59.013Z
2020-11-11T14:07:59.013Z
M__
<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>

CC BY-SA 4.0
2020-11-11T13:47:29.983Z
What does `ls -l /data/201109_NB551126_0128_AH5G5KBGXF/` give?
M__
CC BY-SA 4.0
2020-11-11T13:58:41.513Z
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!
Stewart Russell
CC BY-SA 4.0
2020-11-11T14:04:57.150Z
I've got it .. just a minute
M__
<illumina><demultiplexing>
Error processing run file with bcl2fastq - Unable to open '.../RunInfo.xml' file for reading
# 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


  
    H5G5KBGXF
    NB551126
    201109
    
      
      
    

Has anyone had this issue or know of a fix? Thanks!
Update: contents of run folder
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```

**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```  

---

