Where on earth are the intermediate files

[dagarfield]

I don't actually know if I have an issue yet, but I am surprised that after 30 min running this command:

alignmentSieve -b /data/gpfs-1/users/amonaco_m/project_work/projects/12_DrosophilaF1Hyb_scSeq/2_10XscATAC/6_totalCounts/Hyb2Dsec/Hyb2Dsec/outs/possorted_bam.bam --minMappingQuality 10 --filterMetrics ~/scratch/bam_storage/dsec.sieve.log.txt -o ~/scratch/bam_storage/Dsec.shifted.bam --ATACshift

I still have no output. I'm wondering if there are some intermediate files somewhere I could check to see if anything is actually happening....

Thanks!