How do I know bcftools mpileup command completed?
0
0
Entering edit mode
7 months ago
gt • 0

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!

bcftools mpileup DNA-seq • 299 views
ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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).

ADD REPLY
0
Entering edit mode

Great! I’ll give that a go, thanks!

ADD REPLY

Login before adding your answer.

Traffic: 1723 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6