How do I know bcftools mpileup command completed?

Question

[gt]

Hi there, I was wondering how I can tell that my bcftools command did in fact finish. The jobs took a very long time to run and I want to ensure that they did in fact finish. I have the following output within my slurm file:

[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250
[mpileup] 1 samples in 1 input files
[mpileup] maximum number of reads per input file set to -d 250

Does this mean that the job finished running? Thanks for your help!

[GenoMax]

Hard to tell. This looks like intermediate status output. Did you capture both STDOUT/STDERR to same SLURM log file? If not check the other file.

[gt]

Shoot no I did not. Do you know how I would do that?

[GenoMax]

You would normally use -o file.out -e file.err on sbatch or srun command line submission (or #SBATCH -o file.out in a script).

[gt]

Great! I’ll give that a go, thanks!