These are chat archives for nextflow-io/nextflow
hello, guys. we have runned a wgs pipeline through nextflow, in grid engine clutser. A batch jobs have been submitted. Everything is fine and most jobs can be finished successfully, except a few jobs hang at running states, without any error. But in fact the job is already finished. When log in to the compute node and dig into more detail, we found the job process is still there, hanged at tee .command.out. The entire process is shown below:
any idea how this happens?
3079 ? Sl 71:10 /usr/bin/sge_execd 25652 ? S 0:00 \_ sge_shepherd-43799 -bg 25653 ? Ss 0:00 \_ /bin/bash /var/spool/gridengine/default/DN-03/job_scripts/43799 25665 ? S 0:00 \_ tee .command.out
teeis used to save the program output while presenting the original
.exitcodefile. What is the content?
.exitcodefile means that the jobs has been killed hardly by the batch scheduler
qacct -j 43799should report the job exit status and the cause of the error
script.pl ... > out.txt
.command.shin that way