mgatk tenx endless runtime

[AdrianParrilla]

Hi, I was trying to process a bam file coming from a scATAC sequencing, but after waiting for hours the process seems to be stuck at the beginning (see image attached). The input bam file is 33 Gb and has around 500,000,000 reads in total (246,780 reads per cell) and 11% of the reads covering the mt DNA.

The command I used was:

mgatk tenx -i /mnt/smb/TDA/scATAC_files/results/test_scARC_possorted_downsampled_bam.bam -n test_scARC -o test_scARC_mgatk -c 60 -bt CB -b /mnt/smb/TDA/scATAC_files/results/barcodes.tsv -g /mnt/smb/TDA/scATAC_files/masked_genome.fa --keep-temp-files

After 2 hours of running, the only output I got was empty folders:

Why is the process stuck at the first step? Is the bam file too big?

Thanks in advance for your help,