Error processing run file with bcl2fastq - Unable to open '.../RunInfo.xml' file for reading 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
&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;

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```
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.