Open Jixuan-Huang opened 1 year ago
Also encountering the same issue. Would appreciate any help regarding this. Thanks.
Can you edit the conf like the following (adding -o and -e to redirect error logs to local files) and try again?
lsf-leader-job-resource-param=-W 2880 -M 4G -q ser -o /YOUR/HOME/stdout.txt -e /YOUR/HOME/stderr.txt
Define /YOUR/HOME
as a directory that you have access to.
And please post those two log files here.
Hi! I am also dealing with this exact issue on an LSF cluster. I edited the conf file to include the line:
lsf-leader-job-resource-param=-W 2880 -M 4G -q ser -o /YOUR/HOME/stdout.txt -e /YOUR/HOME/stderr.txt
as suggested by leepc12. The output and error files are as follows:
stderr.txt
/home/lewks/.lsbatch/1708824945.82031239: line 8: /home/lewks/6pcgf87d.sh: No such file or directory
stdout.txt
Sender: LSF System lsfadmin@node184.hpc.local [Subject: Job 82031239:
in cluster Exited] Job was submitted from host by user in > cluster at Sat Feb 24 20:35:45 2024 Job was executed on host(s) , in queue , as user in cluster at Sat Feb 24 20:35:45 2024 </home/lewks> was used as the home directory. </home/lewks/atac-seq-pipeline> was used as the working directory. Started at Sat Feb 24 20:35:45 2024 Terminated at Sat Feb 24 20:35:45 2024 Results reported at Sat Feb 24 20:35:45 2024 Your job looked like:
LSBATCH: User input
/home/lewks/6pcgf87d.sh
Exited with exit code 127.
Resource usage summary:
CPU time : 0.02 sec. Max Memory : - Average Memory : - Total Requested Memory : - Delta Memory : - Max Swap : - Max Processes : - Max Threads : - Run time : 0 sec. Turnaround time : 0 sec.
The output (if any) follows:
PS:
Read file </home/lewks/stderr.txt> for stderr output of this job.
Thank you so much for any insight you might have as to how to fix this!
Best, Stephanie
I'm truly sorry to hear about the difficulties you're experiencing with running CAPER. Unfortunately, due to our current bandwidth and personnel limitations, we are unable to provide immediate attention to resolving this particular issue. We sincerely apologize for any inconvenience this may cause and greatly appreciate your understanding.
No problem! Thanks for letting us know.
Bump - I am experiencing this same issue. Error logs show calls to supposedly generated shell script that system checks for and finds does not exist...
Hi,
when I tried to run caper with encode-atac-pipeline, I could see the job was submitted to the lsf system, but the job disappear immediately without any reports.
when I looked into the detailed record of the job, I could find an "exit code 127", and I think maybe the shell script was never been created in the home directory, but I have no ideas how to solve it. Here are the command and the job reports:
Here is the config file for caper:
And here is the information about the software and environment:
Thanks for responding!