SLURM script

[PopGenHamburg]

Hi, I am trying to get Juicer running on our uni HPC cluster and failing so far. I find it hard to find the locations that should be modified or commented out when not a member of the Aiden lab (ie user Rice/BCM/Voltron). At the beginning we are advised to set the load_bwa/java/gpu variables to work with our system, which I did. However there are several chunks of the juicer.sh scripts that start with a condition, for example if [ $isRice -eq 1] #line 76

Does it matter? I have the feeling I get plenty of error messages related to these conditions never being fulfilled.

Would it be possible to add notes indicating which lines exactly should be modified to adapt to our own clusters?

[nchernia]

All of the "is" flags will be 0 for your system. You just need to set the flags up top, e.g. load_java, load_bwa, load_gpu. Change lines 112-127. The other times this is looked at is for system specific memory requirements, so you might take over the "isVoltron" flag and have it be tailored to your system (some have restrictions on memory, e.g.)

On Tue, Mar 2, 2021 at 3:11 PM PopGen Lab Hamburg notifications@github.com wrote:

Hi, I am trying to get Juicer running on our uni HPC cluster and failing so far. I find it hard to find the locations that should be modified or commented out when not a member of the Aiden lab (ie user Rice/BCM/Voltron). At the beginning we are advised to set the load_bwa/java/gpu variables to work with our system, which I did. However there are several chunks of the juicer.sh scripts that start with a condition, for example if [ $isRice -eq 1] #line 76

Does it matter? I have the feeling I get plenty of error messages related to these conditions never being fulfilled.

Would it be possible to add notes indicating which lines exactly should be modified to adapt to our own clusters?

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[PopGenHamburg]

Thank you, this is helpful! Now running better i.e. I get issues later on... At some point after line 818 I get the following error "sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified". Do you have an idea where it could come from?

[nchernia]

You might need to use the -A flag to specify account.

On Tue, Mar 2, 2021 at 3:43 PM PopGen Lab Hamburg notifications@github.com wrote:

Thank you, this is helpful! Now running better i.e. I get issues later on... At some point after line 818 I get the following error "sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified". Do you have an idea where it could come from?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/207#issuecomment-789202310, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW3OUDDYAYSJWZUQVDTTBVEXDANCNFSM4YPVCSYQ .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[nchernia]

And we use "queue" (-q) to specify partition.

On Tue, Mar 2, 2021 at 4:39 PM Neva Durand neva@broadinstitute.org wrote:

You might need to use the -A flag to specify account.

On Tue, Mar 2, 2021 at 3:43 PM PopGen Lab Hamburg < notifications@github.com> wrote:

Thank you, this is helpful! Now running better i.e. I get issues later on... At some point after line 818 I get the following error "sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified". Do you have an idea where it could come from?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/207#issuecomment-789202310, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW3OUDDYAYSJWZUQVDTTBVEXDANCNFSM4YPVCSYQ .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[PopGenHamburg]

I set both of them but still get the same error. I was wondering about the unit in which run time is given in lines 814 and 816. If I indeed coopt the isVoltron flag this is where max run times are defined, and I suppose this also should be adjusted to my cluster, right? Are these hours or minutes?

[nchernia]

You can also use the -L and -Q flags to set the time.

https://slurm.schedmd.com/sbatch.html

-t, --time=<time>Set a limit on the total run time of the job allocation. If the requested time limit exceeds the partition's time limit, the job will be left in a PENDING state (possibly indefinitely). The default time limit is the partition's default time limit. When the time limit is reached, each task in each job step is sent SIGTERM followed by SIGKILL. The interval between signals is specified by the Slurm configuration parameter KillWait. The OverTimeLimit configuration parameter may permit the job to run longer than scheduled. Time resolution is one minute and second values are rounded up to the next minute.

A time limit of zero requests that no time limit be imposed. Acceptable time formats include "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes" and "days-hours:minutes:seconds".

On Wed, Mar 3, 2021 at 9:52 AM PopGen Lab Hamburg notifications@github.com wrote:

I set both of them but still get the same error. I was wondering about the unit in which run time is given in lines 814 and 816. If I indeed coopt the isVoltron flag this is where max run times are defined, and I suppose this also should be adjusted to my cluster, right? Are these hours or minutes?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/207#issuecomment-789769721, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW6HE6LBHJELNHST2YDTBZELBANCNFSM4YPVCSYQ .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[PopGenHamburg]

Thank you for your very fast and helpful answers! Sadly setting up all the flags still doesn't help on my cluster :( I hev started the job with the following command: ./juicer.sh -g hg19 -q std -l std -d $WORK/HIC003 -s MboI -a 'test' -p $HOME/juicedir/references/hg19.chrom.sizes -y $HOME/juicedir/restriction_sites/hg19_MboI.txt -z $HOME/juicedir/references/Homo_sapiens_assembly19.fasta -D $HOME/juicedir -Q 12:00:00 -L 12:00:00 -t 1 -A fbnv336

There seems to be also a dependency issue, but the error message doesn't show which one.

module: loaded site/slurm module: loaded site/tmpdir module: loaded site/hummel module: loaded env/system-gcc ./juicer.sh: line 71: host: command not found ./juicer.sh: line 72: host: command not found ./juicer.sh: line 76: [: -eq: unary operator expected ./juicer.sh: line 100: [: -eq: unary operator expected Using /home/fbnv336/juicedir/restriction_sites/hg19_MboI.txt as site file ./juicer.sh: line 374: [: -eq: unary operator expected ./juicer.sh: line 374: [: -eq: unary operator expected (-: Looking for fastq files...fastq files exist (-: Aligning files matching /work/fbnv336/HIC003/fastq/_R.fastq* in queue std to genome hg19 with no fragment delimited maps. (-: Created /work/fbnv336/HIC003/splits and /work/fbnv336/HIC003/aligned. (-: Starting job to launch other jobs once splitting is complete ./juicer.sh: line 818: [: -eq: unary operator expected sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem (-: Finished adding all jobs... Now is a good time to get that cup of coffee... Last job id

The debug folder contains 6 files atm with align1-1374379.err still growing. From this I deduce bwa is still working and my input regarding the bwa path was correct.

[nchernia]

You don't have host installed on your system, but just get rid of that command and set those variables to 0. That will get rid of a bunch of those errors.

However the reason your script isn't running is this:

sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified

You will need to ask your cluster management IT person what is invalid about the account or partition.

On Wed, Mar 3, 2021 at 10:39 AM PopGen Lab Hamburg notifications@github.com wrote:

Thank you for your very fast and helpful answers! Sadly setting up all the flags still doesn't help on my cluster :( I hev started the job with the following command: ./juicer.sh -g hg19 -q std -l std -d $WORK/HIC003 -s MboI -a 'test' -p $HOME/juicedir/references/hg19.chrom.sizes -y $HOME/juicedir/restriction_sites/hg19_MboI.txt -z $HOME/juicedir/references/Homo_sapiens_assembly19.fasta -D $HOME/juicedir -Q 12:00:00 -L 12:00:00 -t 1 -A fbnv336

There seems to be also a dependency issue, but the error message doesn't show which one.

module: loaded site/slurm module: loaded site/tmpdir module: loaded site/hummel module: loaded env/system-gcc ./juicer.sh: line 71: host: command not found ./juicer.sh: line 72: host: command not found ./juicer.sh: line 76: [: -eq: unary operator expected ./juicer.sh: line 100: [: -eq: unary operator expected Using /home/fbnv336/juicedir/restriction_sites/hg19_MboI.txt as site file ./juicer.sh: line 374: [: -eq: unary operator expected ./juicer.sh: line 374: [: -eq: unary operator expected (-: Looking for fastq files...fastq files exist (-: Aligning files matching /work/fbnv336/HIC003/fastq/_R.fastq* in queue std to genome hg19 with no fragment delimited maps. (-: Created /work/fbnv336/HIC003/splits and /work/fbnv336/HIC003/aligned. (-: Starting job to launch other jobs once splitting is complete ./juicer.sh: line 818: [: -eq: unary operator expected sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem sbatch: error: Batch job submission failed: Job dependency problem (-: Finished adding all jobs... Now is a good time to get that cup of coffee... Last job id

The debug folder contains 6 files atm with align1-1374379.err still growing. From this I deduce bwa is still working and my input regarding the bwa path was correct.

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-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org