Open carla-hazelf opened 8 months ago
Describe the bug Hi, I am submitting ./nextDenovo run.cfg and after 35 mins of run time I get this error. I check the .log but not sure how to interpret what went wrong. I am submitting the job with 450G and 128CPUS per task. Any thoughts?
Error message
> [631262 INFO] 2023-11-03 12:35:35 NextDenovo start... > [631262 INFO] 2023-11-03 12:35:35 version:2.5.2 logfile:pid631262.log.info > [631262 WARNING] 2023-11-03 12:35:35 Re-write workdir > [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir > [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align > [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/02.cns_align > [631262 INFO] 2023-11-03 12:35:35 mkdir: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/03.ctg_graph > [631262 INFO] 2023-11-03 12:35:40 Total jobs: 1 > [631262 INFO] 2023-11-03 12:35:40 Submitted jobID:[301031] jobCmd: /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the slurm_cycle. > [631262 ERROR] 2023-11-03 13:33:24 db_stat failed: please check the following logs: > [631262 ERROR] 2023-11-03 13:33:24 /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.e
When I check the nextDenovo.sh.e, I find this:
hostname + hostname cd /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1 + cd /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1 ( time /ont/assemblies/nextdenovo/NextDenovo/bin/seq_stat -f 1k -g 650m -d 45 -o /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/input.reads.stat /ont/assemblies/nextdenovo/NextDenovo/input.fofn ) + /ont/assemblies/nextdenovo/NextDenovo/bin/seq_stat -f 1k -g 650m -d 45 -o /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/input.reads.stat /ont/assemblies/nextdenovo/NextDenovo/input.fofn real 57m1.747s user 2m17.870s sys 2m11.257s touch /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.done + touch /ont/assemblies/nextdenovo/NextDenovo/02_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh.done
Genome characteristics Genome size is expected to be ~650Mb.
Genome size is expected to be ~650Mb.
Input data ONT .fastq file. Total base count: 86,626,065,745 , sequencing depth x133.27, n50 length 13,995
ONT .fastq file. Total base count: 86,626,065,745 , sequencing depth x133.27, n50 length 13,995
Config file
[General] job_type = slurm # local, slurm, sge, pbs, lsf job_prefix = nextDenovo task = all # all, correct, assemble rewrite = yes # yes/no deltmp = yes parallel_jobs = 20 # number of tasks used to run in parallel input_type = raw # raw, corrected read_type = ont # clr, ont, hifi input_fofn = input.fofn workdir = 02_rundir [correct_option] read_cutoff = 1k genome_size = 650m # estimated genome size sort_options = -m 20g -t 30 minimap2_options_raw = -x ava-ont -t 32 pa_correction = 3 # number of corrected tasks used to run in parallel, each corrected task requires ~TOTAL_INPUT_BASES/4 bytes of memory usage. correction_options = -p 15 [assemble_option] minimap2_options_cns = -x ava-ont -t 32 -k 21 -w 21 nextgraph_options = -a 1
Operating system Which operating system and version are you using?
NAME="Rocky Linux" VERSION="8.8 (Green Obsidian)"
GCC GCCcore/11.3.0
Python Python/3.10.4
NextDenovo 2.5.2
It seems everything is ok, so just rerun the main task.
Describe the bug Hi, I am submitting ./nextDenovo run.cfg and after 35 mins of run time I get this error. I check the .log but not sure how to interpret what went wrong. I am submitting the job with 450G and 128CPUS per task. Any thoughts?
Error message
When I check the nextDenovo.sh.e, I find this:
Genome characteristics
Genome size is expected to be ~650Mb.
Input data
ONT .fastq file. Total base count: 86,626,065,745 , sequencing depth x133.27, n50 length 13,995
Config file
Operating system Which operating system and version are you using?
GCC GCCcore/11.3.0
Python Python/3.10.4
NextDenovo 2.5.2