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dfguan / purge_dups

haplotypic duplication identification tool
MIT License
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Meet error:"normal: No such queue. Job not submitted." #151

Open DryadDataDiver opened 2 months ago

DryadDataDiver commented 2 months ago

@dfguan Hello! As a beginner, I have encountered some issues while using purge_dups. I humbly seek your assistance in resolving these problems: I am using the LSF system to submit tasks, but I encountered an error: “normal: No such queue. Job not submitted.” I have checked the queue name, and it matches the one I submitted. Here is my json:

{
  "cc": {
    "fofn": "/share/home/AAA/hicanu/result/defult/purge/config/pb.fofn",
    "isdip": 1,
    "core": 19,
    "mem": 20000,
    "queue": "compute",
    "mnmp_opt": "",
    "bwa_opt": "",
    "ispb": 1,
    "skip": 0
  },
  "sa": {
    "core": 19,
    "mem": 10000,
    "queue": "compute"
  },
  "busco": {
    "core": 19,
    "mem": 20000,
    "queue": "compute",
    "skip": 0,
    "lineage": "eudicots_odb10",
    "prefix": "defult_purged",
    "tmpdir": "busco_tmp"
  },
  "pd": {
    "mem": 20000,
    "queue": "compute"
  },
  "gs": {
    "mem": 10000,
    "oe": 1
  },
  "kcp": {
    "core": 19,
    "mem": 30000,
    "fofn": "",
    "prefix": "defult_purged_kcm",
    "tmpdir": "kcp_tmp",
    "skip": 1
  },
  "ref": "/share/home/AAA/hicanu/result/defult/purge/config/defult.fasta",
  "out_dir": "/share/home/AAA/hicanu/result/defult/purge/pipeline"
}

Here is my script:

python "/share/home/AAA/hicanu/result/defult/purge/purge_dups/scripts/run_purge_dups.py" \
 "/share/home/AAA/hicanu/result/defult/purge/config/defult.PL.json" \
 "/share/home/AAA/hicanu/result/defult/purge/purge_dups/bin" \
 PL > log.txt 2>&1

Here is my log:

calculate coverage and self-alignment
normal: No such queue. Job not submitted.
normal: No such queue. Job not submitted.
normal: No such queue. Job not submitted.
command /share/home/AAA/hicanu/result/defult/purge/purge_dups/bin/split_fa /share/home/AAA/hicanu/result/defult/purge/config/defult.fasta > defult/split_aln/defult.split.fa failed, return code: 255
unkown error, please check error log
command minimap2 -I 4G -x map-pb -t 12 /share/home/AAA/hicanu/result/defult/purge/config/defult.fasta "/share/home/AAA/full/hifidata/s2hifi.fa" >defult/coverage/s2hifi.paf failed, return code: 255
unkown error, please check error log
command minimap2 -I 4G -x map-pb -t 12 /share/home/AAA/hicanu/result/defult/purge/config/defult.fasta "/share/home/AAA/full/hifidata/s3hifi.fa" >defult/coverage/s3hifi.paf failed, return code: 255
unkown error, please check error log
purge duplicates