pbpearman
commented
15 hours ago Hi Kathy, Did you ever get a response or figure out how to fix your problem? I have a very similar error upon submitting run_purge_dups.py. Some of the messages I received seem to be duplicated. In addition, I get a subsequent minimap error. But when I run the minimap command as shown, it seems to run ok. My slurm-xxx.out file has the following info: Job runing on nh001 Choosing scratch ... Forced gscratch selection /gscratch/bgppermp/64214 /gscratch/bgppermp/64214 directory /usr/bin/time -p /beegfs_agamede/gscratch/bgppermp/conda/env/purge_dups/bin/run_purge_dups.py /beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_flye_Q7_purge_dups_config2.json /beegfs_agamede/gscratch/bgppermp/conda/env/purge_dups/bin Phlomis calculate coverage and self-alignment Unknown option: K Unknown option: K Unknown option: R"select[mem>5000] rusage[mem Unknown option: R"select[mem>30000] rusage[mem Usage: Usage: bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode] [-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q Queue Name] [-W Time] [-x Exclusive] [-h] [script] bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode] [-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q Queue Name] [-W Time] [-x Exclusive] [-h] [script]
command /beegfs_agamede/gscratch/bgppermp/conda/env/purge_dups/bin/split_fa /beegfs_agamede/gscratch/bgppermp/flye_2_results/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.fa > /beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly/split_aln/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.split.fa failed, return code: 2 unkown error, please check error log command minimap2 -I 10G -x map-ont -t 12 /beegfs_agamede/gscratch/bgppermp/flye_2_results/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.fa /beegfs_agamede/gscratch/bgppermp/all_trimmedQ7_gt5Kbp_gtQ7.fastq >/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly/coverage/all_trimmedQ7_gt5Kbp_gtQ7.paf failed, return code: 2 unkown error, please check error log
Here are the contents of the config file I used: { "cc": { "fofn": "/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/pb.fofn", "isdip": 1, "core": 12, "mem": 30000, "queue": "normal", "mnmp_opt": "-x map-ont", "bwa_opt": "", "ispb": 1, "skip": 0 }, "sa": { "core": 12, "mem": 30000, "queue": "normal" }, "busco": { "core": 12, "mem": 30000, "queue": "long", "skip": 0, "lineage": "/beegfs_agamede/gscratch/bgppermp/busco_data/eudicots_odb10", "prefix": "phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly_purged", "tmpdir": "busco_tmp" }, "pd": { "mem": 30000, "queue": "normal" }, "gs": { "mem": 30000, "oe": 0 }, "kcp": { "core": 12, "mem": 30000, "fofn": "/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/pb.fofn", "prefix": "phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly_purged_kcm", "tmpdir": "kcp_tmp", "skip": 0 }, "ref": "/beegfs_agamede/gscratch/bgppermp/flye_2_results/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly.fa", "out_dir": "/beegfs_agamede/gscratch/bgppermp/purge_dups_phlomis/phlomis_all_trimmedQ7_gt5Kbp_gtQ7_assembly" }
Please post any understanding you have of this, and what you did to make progress. :-) --Peter
Hello,
I'm having some trouble getting purge_dups to run. No output or intermediate files are created in the process and this is the output in the .txt file:
calculate coverage and self-alignment command /N/slate/kdarrag/programs/purge_dups/bin/split_fa /N/slate/kdarrag/Costus/allenii/PB1055_KK0154_SpiralGinger_HiFiv3_Revio_cell1/Fasta_Fastq_7335/outputs/run2/allenii.ASM.p_ctg.fa > allenii.ASM.p_ctg/split_aln/allenii.ASM.p_ctg.split.fa failed, return code: 2 unkown error, please check error log purge duplicates
and in the .err file:
Unknown option: K Unknown option: R"select[mem>5000] rusage[mem Usage: bsub [-cwd Working Directory Path] [-e Error Path] [-I Interactive Mode] [-m Node List] [-M Memory Limit] [-n Min Process] [-o Output Path] [-q Queue Name] [-W Time] [-x Exclusive] [-h] [script]
slurmstepd: error: Detected 1 oom_kill event in StepId=3300451.batch. Some of the step tasks have been OOM Killed.
I am running with 480Gb for a 1.1Gb genome. Is there some way that by split_fa failing this is causing the oom by not splitting up the genome? Any idea what return code 2 is? There is no error log information to check.
Thank you, Kathy