CheckIlluminaDirectory exception: TileMetricsOutReader expects the version number to be 2. Actual Version in Header( 3)

Question

[francisckantor]

I'm trying to extract some BCL files generated by a NovaSeq run. When I run CheckIlluminaDirectory it throws the following exception:

Exception in thread "main" picard.PicardException: TileMetricsOutReader expects the version number to be 2. Actual Version in Header( 3) at picard.illumina.parser.readers.TileMetricsOutReader.<init>(TileMetricsOutReader.java:48) at picard.illumina.parser.IlluminaFileUtil.getExpectedTiles(IlluminaFileUtil.java:174) at picard.illumina.CheckIlluminaDirectory.doWork(CheckIlluminaDirectory.java:117) at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:208) at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95) at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)

Googling TileMetricsOutReader I found this page

https://broadinstitute.github.io/picard/javadoc/picard/picard/illumina/parser/readers/TileMetricsOutReader.html

which says "The version number which MUST be 2 or an exception will be thrown". Anyone know what this means? The feeling I have is that the interops output generated by the run is of a different version and Picard tools only handles version 2... but I'm not sure.

I found the interops c++ library from Illumina online, if anyone knows of a way to get around the problem that way.

Thanks.

Answer 1

[francisckantor]

Our files were CBCL files and based on this comment

https://kb.10xgenomics.com/hc/en-us/articles/115005261903-What-do-I-need-to-demultiplex-NovaSeq-data-

probably bcl2fastq2 is the right tool for the job.

[GenoMax]

extract some BCL files generated by a NovaSeq run

If you are trying to generate sequence files and demultiplex the data from an Illumina NovaSeq run then bcl2fastq is the right software.