Open tanger-code opened 10 months ago
And when I run it with PBS, there is another error: /var/spool/torque/mom_priv/jobs/534733.manager.SC: /data/home/tangen/workware/cactus-bin-v2.6.4/cactus_env/bin/cactus-pangenome: /data/home/tangen/workware/cactus-bin-v2.6.4/cactus_env/bin/python3: bad interpreter: No such file or directory
, but python does exist in this directory.
This seems to be the important part of the error:
/var/spool/torque/mom_priv/jobs/534728.manager.SC: line 6: _toil_worker: command not found
The only cluster environment we "officially" support for Cactus now is SLURM. Toil has options for a few others, including torque, but they are not as well-tested for Cactus. You can try raising in issue here https://github.com/DataBiosphere/toil/issues
I reinstalled the software for older CPU Architectures, and run it with PBS.
There is another error:
Then I set the PYTHONHOME=/data/home/tangen/workware/cactus-bin-v2.6.9/venv-cactus-v2.6.9/bin/python3:$PYTHONHOME
, but a similar error occurred.
Is this because of system incompatibility or some other problem?
You might need to run something like
pip install -U toil[all]==5.12.0
but again, Cactus is only tested with SLURM.
Okay, I got it. Thank you. I will try the docker later.
Normally, you cannot use your cluster from inside the Cactus docker image. You must install Cactus in a virtualenv on your head node and work from there.
I run a small test in windows docker desktop
to construct a small graph. The command I used is docker run -v e/HPRC_HG002:/home/tang/HPRC_HG002 quay.io/comparative-genomics-toolkit/cactus:v2.6.9 /bin/bash -c "cactus-pangenome /home/tang/HPRC_HG002/js-grch38 /home/tang/HPRC_HG002/hprc-v1.1-mc.seqfile --outName hprc-v1.1-mc-grch38 --outDir /home/tang/HPRC_HG002/hprc-v1.1-mc-grch38 --reference GRCh38 CHM13 --filter 9 --giraffe clip filter --vcf --viz --odgi --chrom-vg clip filter --chrom-og --gbz clip filter full --gfa clip full --vcf --logFile /home/tang/HPRC_HG002/hprc-v1.1-mc-grch38.log --batchSystem slurm --mgCores 64 --mapCores 16 --consCores 64 --indexCores 64 2> /home/tang/HPRC_HG002/hprc-v1.1-mc-grch38.stderr"
.
But there is still a mistake here : hprc-v1.1-mc-grch38.stderr.txt
This is the directory on Windows:
This is the seqfile that only contains CHM13,GRCh38 and HG002:
hprc-v1.1-mc.seqfile.txt
When I run without --batchSystem
parameter, It seems to be running correctly(at least it hasn't stopped). Are there any bad effects of not using this parameter?
And then it stopped, for the reason : toil.batchSystems.abstractBatchSystem.InsufficientSystemResources: The job 'minigraph_construct' kind-minigraph_construct/instance-dueekojc v1 is requesting 405415491274 bytes of memory, more than the maximum of 403933802496 bytes of memory that SingleMachineBatchSystem was configured with, or enforced by --maxMemory. Scale is set to 1.0.
I only used 4 haplotypes. Why does it request so much memory? If I use all 90 haplotypes, will the memory used be much higher?
There are three relevant --batchSystem
options for Cactus
1) --batchSystem single_machine
(this is the default if not specified): Run on one computer
2) --batchSystem slurm
: Run distributed on slurm cluster
3) --batchSystem mesos --provisioner aws
: Run distributed on AWS cluster
While others, including torque, are listed in the help
--batchSystem {aws_batch,parasol,single_machine,grid_engine,lsf,mesos,slurm,tes,torque,htcondor,kubernetes}
The type of batch system to run the job(s) with,
currently can be one of aws_batch, parasol,
single_machine, grid_engine, lsf, mesos, slurm, tes,
torque, htcondor, kubernetes. default=single_machine
and the Toil Documentation they are much less well-tested and I don't recommend using them.
Hi! I want to reconstruct a HPRC graph with HG002, and using the command
cactus-pangenome ./js-grch38 ./hprc-v1.1-mc.seqfile --outName hprc-v1.1-mc-grch38 --outDir hprc-v1.1-mc-grch38 --reference GRCh38 CHM13 --filter 9 --giraffe clip filter --vcf --viz --odgi --chrom-vg clip filter --chrom-og --gbz clip filter full --gfa clip full --vcf --logFile hprc-v1.1-mc-grch38.log --batchSystem torque --mgCores 64 --mapCores 16 --consCores 64 --indexCores 64
.But there seems to be an error related to
“pangenome_end_to_end_workflow”
. The .stderr and .log file are here: hprc-v1.1-mc-grch38.stderr.txt hprc-v1.1-mc-grch38.logMy cluster system is torque. Why does this happen?