Error while flushing and closing output. Terminate called after throwing an instance of 'int'. Aborted (core dumped)

[Jeremy D Zucker]

Hi folks,

I am running Bowtie from within Trinity, and I ran into the following problem that I can reproduce from the command-line:

$  bowtie -a -m 20 --best --strata --threads 10 --quiet --chunkmbs 512 -q -S --sam-nohead  -f target both.fa > bowtie3.out
Error while flushing and closing output
terminate called after throwing an instance of 'int'
Aborted (core dumped)

I don't think this is a memory issue, because I am running on a machine with 1TB of RAM, (although I set my ulimit=100GB). Any clues?

Sincerely,

Jeremy Zucker

[Jeremy D Zucker]

Nevermind, I just ran out of disk space is all.

$ df -h
Filesystem                              Size  Used Avail Use% Mounted on
/dev/sdb1                               549G  521G  304K 100% /scratch
...