Hi Bjorn and Hans, We are running Galaxy on our local webserver, so there is no job scheduler. Instead, we are using the localJobRunner configuration in the job_conf.xml <?xml version="1.0"?> <job_conf> <plugins> <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/> <plugin id="multilocal" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="2"/> </plugins> <destinations default="local"> <destination id="local" runner="local"/> <destination id="multicore6" runner="multilocal"> <param id="local_slots">6</param> </destination> </destinations> <tools> <tool id="bowtie2" destination="multicore6" /> <tool id="spades" destination="multicore6" /> <tool id="bbmap_1" destination="multicore6" /> <tool id="iuc_pear" destination="multicore6" /> <tool id="abyss-pe" destination="multicore6" /> <tool id="fastq_groomer_parallel" destination="multicore6" /> </tools> <handlers> <handler id="main"/> </handlers> </job_conf> Also, normally, we run galaxy in the daemon mode, but recently to help debug this issue, we have been running galaxy in interactive mode in a screen session. @Hans - The processes run under the galaxy user and everything seems to run fine. I am trying to get a concrete example, but run.sh usually crashes during our trimming/assembly steps for NGS data. Sometimes these workflows run to completion, but sometimes they crash the run.sh process. When run.sh crashes, the individual running programs keep running as the galaxy user. We cannot restart galaxy until we manually kill those running processes. Here are what the running processes look like on the system. galaxy 21162 99.4 0.0 2432784 616 s014 R 2:08PM 1425:10.57 seqtk seq -q 0 -X 255 -l 0 -Q 33 -s 11 -f 1.0 -L 0 -1 /Users/galaxy/data_galaxy/test_BACs/all-merged.interleaved.fq galaxy 21159 99.4 0.0 2432784 616 s014 R 2:08PM 1425:16.72 seqtk seq -q 0 -X 255 -l 0 -Q 33 -s 11 -f 1.0 -L 0 -2 /Users/galaxy/data_galaxy/test_BACs/all-merged.interleaved.fq galaxy 21118 92.5 0.5 3015188 367852 s014 R+ 2:07PM 791:21.54 python ./scripts/paster.py serve universe_wsgi.ini galaxy 21160 0.0 0.0 2433640 1044 s014 S 2:08PM 0:00.01 /bin/sh /Users/galaxy/galaxy-dist/database/job_working_directory/002/2180/galaxy_2180.sh galaxy 21157 0.0 0.0 2433640 1044 s014 S 2:08PM 0:00.01 /bin/sh /Users/galaxy/galaxy-dist/database/job_working_directory/002/2179/galaxy_2179.sh galaxy 21113 0.0 0.0 2433640 1000 s014 S+ 2:07PM 0:00.00 sh run.sh Thank you for the help, -Hans