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Adrian Madera

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

Avun Jahei  Follow

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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Joseph Braun  Follow
bcl2fastq --runfolder-dir 201109_NB551126_0128_AH5G5KBGXF --sample-sheet SampleSheet.csv --no-lane-splitting --barcode-mismatches 0More
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Jack Sullivan  Follow
Such a simple fix! Thanks for your solution. I simply ran this from the folder containing the folder and it worked: More
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