bcl2fasta writing file in read only directory

Question

[alex]

I am running:

/usr/local/bin/bcl2fastq --runfolder-dir /runFolderReadOnly --output-dir /fastqReadAndWrite

However, getting the error:

Unable to open InterOp file '/runFolderReadOnly/InterOp/IndexMetricsOut.bin' for writing

Why is this trying to write to the non-output folder? Thanks!

[komal.rathi]

I might be wrong but shouldn't it be --input-dir instead of --runfolder-dir?

[Keith Callenberg]

--runfolder-dir is fine if you are using the v2.1.5 tool for NextSeq or HiSeq X. If you give --runfolder-dir it assumes input-dir is <runfolder-dir>/Data/Intensities/BaseCalls/.

http://support.illumina.com/downloads/bcl2fastq-conversion-user-guide-v2-15-15051736.html

However, there is a separate tool v1.8.x for all other Illumina instruments that does not have the runfolder-dir argument: http://support.illumina.com/downloads/bcl2fastq_conversion_software_184.html

[GouthamAtla]

Are you sure the directory names are /runFolderReadOnly instead of /fullpath/to/runFolderReadOnly? Something odd that they are located in root dir.

[alex]

Its actually a full path that was previously set up with many subdirectories but I changed it to other ones for simplicity

Answer 1

[coldrecd]

If you are using v2, use the flag --interop-dir to direct that output to the desired folder. If you give no flag, bcl2fatq assumes you want it with the other interop data in the run folder containing the BCLs. This is my experience with v2.15.0.4 , good luck!