Thank you both for the feedback. I am trying on the public server today to see if the problem arises there. I suspect the problem is specific to my setup.
I agree, the problem is not specific to a version of minimap2, or minimap2 itself (BWA has the same issue for me). The issue arises when >1 alignments are executed at one time.
As I described above, when fastq files (e.g. SampleA_F1 and R1, SampleB_F1 and R1) were uploaded as a “list-of-pairs”, Only SampleB generated alignment data, while SampleA was empty. Not only are there no alignments for SampleA but, the stdout and stderr are empty as well.
To troubleshoot, I instead selected “paired” for the collection type, and uploaded each set individually (so SampleA is one collection and SampleB is another collection). If I wait for the minimap2 job on SampleA to finish prior to staring another minimap2 job, then both alignments work. But, if I start a minimap2 job for SampleB while minimap2 for SampleA is running, then SampleB generates an empty bam file and SampleA works.
Could it have something to do with the reference sequence? Can 2 jobs utilize the same reference sequence file at the same time?