Batch Analysis log are not included as part of the SImA server log bundle, hence must be extracted separately. The methods of collecting the analysis log files differ between SImA versions.
- SImA v1.1 or greater
The analysis log files can be downloaded directly from the SImA Job Status page using the "Download logs" link for a given batch job.
- SImA v1.0
The SImA installation directory contains the get_slurm_job_data.sh which is used to collect the analysis log files from within the slurmd container. The script generates a zip package which contains logs and configuration files relating to a single analysis job.
Usage:get_slurm_job_data.sh <cluster job directory>
Where <cluster job directory> is the job directory as reported via the SImA Job Status page.
Note: Only the job directory should be passed, not the absolute path to that directory.
Given the job status entry show in the screenshot above, the logs would be collected with the following command:
get_slurm_job_data.sh SIMA-JLu_080612_Rhod_Mito_Hoe_40xW-2008-06-12_11_32_02_00_00-7c8e74c4-5f68-11ed-ba09-02420a00082f
The logs are outputted to a zip file with name like <cluster job directory>.zip.
See get_slurm_job_data.sh --help for further usage information.