# 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 <?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  • What does ls -l /data/201109_NB551126_0128_AH5G5KBGXF/ give? – M__ Nov 11 '20 at 13:47 • 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 Nov 11 '20 at 13:58 • I've got it .. just a minute – M__ Nov 11 '20 at 14:04 ## 1 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.

• 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 Nov 11 '20 at 14:17