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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 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```
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  • $\begingroup$ What does ls -l /data/201109_NB551126_0128_AH5G5KBGXF/ give? $\endgroup$ – M__ Nov 11 '20 at 13:47
  • $\begingroup$ 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! $\endgroup$ – Stewart Russell Nov 11 '20 at 13:58
  • $\begingroup$ I've got it .. just a minute $\endgroup$ – M__ Nov 11 '20 at 14:04
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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.

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  • 1
    $\begingroup$ 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 $\endgroup$ – Stewart Russell Nov 11 '20 at 14:17

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