Question: Canu Pacbio assembly
0
gravatar for BioRyder
2.2 years ago by
BioRyder140
India
BioRyder140 wrote:

Hello All,

I was trying to use canu assembler for pacbio read.In test case-1 I have used 3Gb data (not used HPC) and all the process, correction ,trimming & assembly, has finished in three days.When I used 30Gb data in HPC machine with SLURM , assembly process got failed after two days of run. Looking for advise from someone,who has canu experience in HPC with SLURM.

Following commands used for canu correction

srun canu -p datepalm -d correct_file -correct genomeSize=650m -pacbio-raw first_30gb.fasta

Log file report is showing as : gatekeeperCreate finished successfully.

really appreciate your valuable suggestion.

assembly • 2.6k views
ADD COMMENTlink modified 2.2 years ago by Philipp Bayer5.5k • written 2.2 years ago by BioRyder140

what is the error message

ADD REPLYlink written 2.2 years ago by gangireddy160

there was no error message and program got exit.

ADD REPLYlink written 2.2 years ago by BioRyder140

what were last lines before program got exit

ADD REPLYlink modified 2.2 years ago • written 2.2 years ago by gangireddy160

In last test case, canu command failed with the following error message (job submitted with sbatch command instead of srun)

-- Starting command on Thu Mar 24 14:55:30 2016 with 256586.2 GB free disk space

sbatch --mem=64g --cpus-per-task=16 -D pwd -J "meryl_datepalm_myassembly" -a 1-1 -o /data/labs/genomics_lab/shared/shameem/projects/datePalmDeNovo/Assembly_30gb/correct_file/correction/0-mercounts/meryl.%A_%a.out /data/labs/genomics_lab/shared/shameem/projects/datePalmDeNovo/Assembly_30gb/correct_file/correction/0-mercounts/meryl.sh

sbatch: invalid option -- 'a'

Try "sbatch --help" for more information

-- Finished on Thu Mar 24 14:55:30 2016 (0 seconds) with 256586.2 GB free disk space

ERROR: Failed with signal HUP (1)

================================================================================ Please panic. canu failed, and it shouldn't have.

Stack trace:

at /data/labs/genomics_lab/shared/shameem/apps/canu-1.0/Linux-amd64/bin/lib/canu/Defaults.pm line 220 canu::Defaults::caFailure('Failed to submit batch jobs', undef) called at /data/labs/genomics_lab/shared/shameem/apps/canu-1.0/Linux-amd64/bin/lib/canu/Execution.pm line 1125 canu::Execution::submitOrRunParallelJob('/data/labs/genomics_lab/shared/shameem/projects/datePalmDeNov...', 'datepalm', 'meryl', '/data/labs/genomics_lab/shared/shameem/projects/datePalmDeNov...', 'meryl', 1) called at /data/labs/genomics_lab/shared/shameem/apps/canu-1.0/Linux-amd64/bin/lib/canu/Meryl.pm line 333 canu::Meryl::merylCheck('/data/labs/genomics_lab/shared/shameem/projects/datePalmDeNov...', 'datepalm', 'cor') called at /data/labs/genomics_lab/shared/shameem/apps/canu-1.0/Linux-amd64/bin/canu line 402

canu failed with 'Failed to submit batch jobs'.

ADD REPLYlink written 2.2 years ago by BioRyder140
1
gravatar for Philipp Bayer
2.2 years ago by
Philipp Bayer5.5k
Australia/Perth/UWA
Philipp Bayer5.5k wrote:

That looks like the batch jobs it tries to submit to the cluster are not in the format your cluster wants.

You can change the format of the SGE parameters, it's described in the manual: http://canu.readthedocs.org/en/stable/parameter-reference.html#grid-engine-config

You can also start canu with useGrid=0 to run it all on one server.

ADD COMMENTlink written 2.2 years ago by Philipp Bayer5.5k
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