Entering edit mode
8.1 years ago
BioRyder
▴
220
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.
what is the error message
there was no error message and program got exit.
what were last lines before program got exit
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.shsbatch: 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'.