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Nextomics / NextPolish

Fast and accurately polish the genome generated by long reads.

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slurmstepd: error: JOB CANCELLED DUE TO TIME LIMIT

VendelboNM opened this issue · comments

commented

Hi there!

I am experiencing the same issue as that in thread #103 [https://github.com//issues/103] - however, i cannot get it to work... I am attempting to polish a barley assembly generated using long-read nanopore R10.4 sequences.

Hope you can help me figure out what is going wrong.

run.cfg:

[General]
job_type = slurm
job_prefix = nextpolish
task = best
rewrite = yes
parallel_jobs = 3
multithread_jobs = 10
genome = /projects/mjolnir1/people/bgn602/steps/01_comp_study/flye/parameter_eval/t2/A3_em2/A3_em2_t2.fasta
genome_size = auto
workdir = /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2
polish_options = -p 10

[sgs_option]
sgs_fofn = /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/A3_em2_sgs.fofn
sgs_options = -max_depth 50 -bwa

Error:

[1177493 INFO] 2023-11-03 08:08:47 NextPolish start...
[1177493 INFO] 2023-11-03 08:08:47 version:v1.4.1 logfile:pid1177493.log.info
[1177493 WARNING] 2023-11-03 08:08:47 Re-write workdir
[1177493 WARNING] 2023-11-03 08:08:52 Delete task: 5 due to missing lgs_fofn.
[1177493 WARNING] 2023-11-03 08:08:52 Delete task: 5 due to missing lgs_fofn.
[1177493 WARNING] 2023-11-03 08:08:52 Delete task: 6 due to missing hifi_fofn.
[1177493 WARNING] 2023-11-03 08:08:52 Delete task: 6 due to missing hifi_fofn.
[1177493 INFO] 2023-11-03 08:08:52 scheduled tasks:
[1, 2, 1, 2]
[1177493 INFO] 2023-11-03 08:08:52 options:
[1177493 INFO] 2023-11-03 08:08:52
rerun: 3
rewrite: 1
kill: None
cleantmp: 0
use_drmaa: 0
submit: None
deltmp: False
job_type: slurm
sgs_unpaired: 0
sgs_rm_nread: 1
lgs_read_type:
parallel_jobs: 3
check_alive: None
sgs_max_depth: 50
align_threads: 10
task: [1, 2, 1, 2]
job_id_regex: None
lgs_max_depth: 100
lgs_max_read_len: 0
hifi_max_depth: 100
multithread_jobs: 10
lgs_block_size: 500M
lgs_min_read_len: 1k
hifi_max_read_len: 0
polish_options: -p 10
hifi_block_size: 500M
hifi_min_read_len: 1k
job_prefix: nextpolish
genome_size: 3900762858
sgs_block_size: 500000000
sgs_use_duplicate_reads: 0
lgs_minimap2_options: -x map-ont
hifi_minimap2_options: -x map-pb
sgs_align_options: bwa mem -p -t 10
workdir: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2
genome: /projects/mjolnir1/people/bgn602/steps/01_comp_study/flye/parameter_eval/t2/A3_em2/A3_em2_t2.fasta
sgs_fofn: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/A3_em2_sgs.fofn
snp_phase: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/%02d.snp_phase
snp_valid: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/%02d.snp_valid
lgs_polish: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/%02d.lgs_polish
kmer_count: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/%02d.kmer_count
hifi_polish: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/%02d.hifi_polish
score_chain: /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/%02d.score_chain
[1177493 INFO] 2023-11-03 08:08:52 step 0 and task 1 start:
[1177493 INFO] 2023-11-03 08:08:57 Total jobs: 3
[1177493 INFO] 2023-11-03 08:08:57 Submitted jobID:[5660526] jobCmd:[/projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/00.score_chain/01.db_split.sh.work/db_split1/nextpolish.sh] in the slurm_cy$
[1177493 INFO] 2023-11-03 08:08:57 Submitted jobID:[5660527] jobCmd:[/projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/00.score_chain/01.db_split.sh.work/db_split2/nextpolish.sh] in the slurm_cy$
[1177493 INFO] 2023-11-03 08:08:57 Submitted jobID:[5660528] jobCmd:[/projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/00.score_chain/01.db_split.sh.work/db_split3/nextpolish.sh] in the slurm_cy$
[1177493 ERROR] 2023-11-03 09:09:11 ^[[35mdb_split failed: please check the following logs:^[[0m
[1177493 ERROR] 2023-11-03 09:09:11 ^[[35m/projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/00.score_chain/01.db_split.sh.work/db_split1/nextpolish.sh.e^[[0m
[1177493 ERROR] 2023-11-03 09:09:11 ^[[35m/projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/00.score_chain/01.db_split.sh.work/db_split2/nextpolish.sh.e^[[0m

Split error:

hostname

  • hostname
    cd /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/00.score_chain/01.db_split.sh.work/db_split1
  • cd /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2/00.score_chain/01.db_split.sh.work/db_split1
    ( /maps/projects/mjolnir1/people/bgn602/packages/nextpolish/bin/seq_split -d /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2 -m 500000000 -n 3 -t 10 -i 1 -s 195038142900 -p input.s$
  • /maps/projects/mjolnir1/people/bgn602/packages/nextpolish/bin/seq_split -d /projects/mjolnir1/people/bgn602/steps/01_comp_study/nextpolish/parameter_eval/t2/A3_em2 -m 500000000 -n 3 -t 10 -i 1 -s 195038142900 -p input.sg$
    slurmstepd: error: *** JOB 5660526 ON mjolnircomp08fl CANCELLED AT 2023-11-03T09:08:58 DUE TO TIME LIMIT ***
commented

see #103