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Job logs

Once a job enters the RUNNING state, BatchX starts collecting the logs (stderr and stdout) generated by your workload.

In order to see the logs of a job using the CLI:

  1. Make sure you have completed the CLI installation.
  2. Activate the environment where the job is running by using thebx env command.
  3. Inspect the logs using the bx logs command.

Example:

$ bx logs 1492
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:19:36] [M::bwa_idx_load_from_disk] read 0 ALT contigs
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:19:37] [M::process] read 99010 sequences (10000010 bp)...
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:19:37] [M::process] read 99010 sequences (10000010 bp)...
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:19:51] [M::mem_process_seqs] Processed 99010 reads in 14.521 CPU sec, 14.301 real sec
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:19:51] [M::process] read 51980 sequences (5249980 bp)...
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:20:06] [M::mem_process_seqs] Processed 99010 reads in 15.066 CPU sec, 14.854 real sec
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:20:14] [M::mem_process_seqs] Processed 51980 reads in 7.837 CPU sec, 7.670 real sec
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:20:14] [main] Version: 0.7.17-r1198-dirty
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:20:14] [main] CMD: /batchx/bwa/bwa mem -t 1 -R @RG\tID:1\tSM:sample /batchx/tmp/Homo_sapiens.GRCh38.dna.primary_assembly.fa /batchx/input/file1/sample.R1.fq.gz
[batchx@bioinformatics/bwa/mem:1.1.0] [2020/04/27 17:20:14] [main] Real time: 40.430 sec; CPU: 41.012 sec
info

Tip: You can get live logs from a running job with the bx attach command.

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