Hi!
I am analyzing WES data in a few samples. It had worked just fine until some days ago. However, for the remaining samples, it is not working anymore. I am running Mutect2 in all of them with the following command (running in docker):
gatk Mutect2 -R /gatk/my_data/reference/hg19_torrent/hg19.fasta -I IonXpress_041_rawlib.bam --f1r2-tar-gz IonXpress_041_f1r2.tar.gz -O /gatk/my_data/output/IonXpress_041_unfiltered.vcf --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' --independent-mates
I was able to process about half of the samples, with all the corresponding output files). But now, by using the exact same lines, Mutect2 executes until a certain point, and then stops (a , throwing some messages (file encosed).
All the sample have been sequenced on the same platform, and their bam files have been generated by the same pipeline (performed by IonTorrent platform), using the same reference build file (also used on the command line above - reference/hg19_torrent/hg19.fasta.
I have read in other threads that it might be due to lack of disk space. However, there are around 3TB available on the mounted volume being used.
Any help is greatly appreciated.