How do I know bcftools mpileup command completed?
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!
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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.
Shoot no I did not. Do you know how I would do that?
You would normally use
-o file.out -e file.erronsbatch or sruncommand line submission (or#SBATCH -o file.outin a script).Great! I’ll give that a go, thanks!