Thank you for all your help. I will let you know if I run into any more issues. For whatever reason, putting the program on verbose has let it run with no issues that I can determine related to my initial problems.
Thanks,
~ Heather

On Wed, Jun 26, 2019 at 10:56 AM Assaf Gordon <assafgordon@gmail.com> wrote:
tag 36130 notabug
close 36130
stop

Hello,

On Mon, Jun 10, 2019 at 04:50:20PM -0600, Assaf Gordon wrote:
> On 2019-06-10 12:28 p.m., Heather Wick wrote:
> > Verbose: This seems to have made the same number of files this time; not
> > sure why the other 3-4 times I ran it it did not. They appear to be the
> > same size, with paired last reads
> [...]
>
> Glad to hear it worked.
>
> Could it be that in previous times the queued job ran out of disk space?
>
> That would be my first guess, as such things are common in shared
> grid/cluster environments, particularly if your job runs in a temporary
> and limited storage location (e.g. "/tmp/job-NNNN").


With no further comments, I'm closing this ticket.
If more issues arise (or this was not adequate solution) we can always
re-open this ticket.

regards,
 -assaf


--
Heather Wick
PhD Candidate, Human Genetics
Labs of Sarah Wheelan and Vasan Yegnasubramanian
Institute of Genetic Medicine
Johns Hopkins University School of Medicine