I am experiencing the same issue as that in thread #103 [https://github.com/Nextomics/NextPolish/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.
moold
commented
1 year ago
Hi there!
I am experiencing the same issue as that in thread #103 [https://github.com/Nextomics/NextPolish/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