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bcl2fasta writing file in read only directory

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!

bcl2fasta
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updated by Ram Ram • written by alex alex

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

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written by komal.rathi komal.rathi

--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

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updated by Ram Ram • written by Keith Callenberg Keith Callenberg

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

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updated by Ram Ram • written by GouthamAtla GouthamAtla

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

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written by alex alex

1 answer

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!

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updated by Ram Ram • written by coldrecd coldrecd

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