Image Artist: Extracting the Batch Analysis log files

Batch Analysis log are not included as part of the ImA server log bundle, hence must be extracted separately. The methods of collecting the analysis log files differ between ImA versions.

• ImA v1.1 or greater

The analysis log files can be downloaded directly from the ImA Job Status page using the "Download logs" link for a given batch job.

• ImA v1.0

The ImA 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 ImA 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.