IlluminaBasecallsToSam Header error about picard HOT 1 CLOSED

Hi Nils, I was able to figure out the source of the problem. I was creating a library_params file that contained all the barcodes (AACAATGG, TGTTCCGA, etc.) as well as one for non-matches (N). The problem is that executing IlluminaBasecallsToSam.jar in a cluster (for each of the basecall files) resulted in multiple threads writing to the miOrphan.bam file and it led to writing errors to the other bam files. I solved the problem by creating individual library_params files where there were only two lines: one for the barcode of a single basecall file (TGTTCCGA) and another for the non-matches (N), making sure that the miOrphan path had a unique file name so that multiple threads would write to different files.

It seems like it should be possible to run IlluminaBasecallsToSam for multiple basecall files in a cluster using a single library_params file, but I found this not to be the case.

from picard.