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Nextomics / NextDenovo

Fast and accurate de novo assembler for long reads

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When run nextdenovo with test_data failed

sumoii opened this issue · comments

commented

Dear developer:

When I run nextdenovo wiht test_data failed

my command is :
./nextDenovo ./test_data/run.cfg

and get a Error:
Exception: Command '/bin/bash ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/nextDenovo.sh > ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/nextDenovo.sh.o 2> ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/nextDenovo.sh.e' returned non-zero exit status 1, error info: .
[47253 ERROR] 2024-02-28 10:19:14 ctg_align failed: please check the following logs:
[47253 ERROR] 2024-02-28 10:19:14 ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align1/nextDenovo.sh.e
[47253 ERROR] 2024-02-28 10:19:14 ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align2/nextDenovo.sh.e
[47253 ERROR] 2024-02-28 10:19:14 ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align3/nextDenovo.sh.e

and the ctg_align1/nextDenovo.sh.e ：

ctg_align.sh.work/ctg_align1/nextDenovo.sh.eovo/test_data/01_rundir/03.ctg_graph/02.
hostname

  • hostname
    cd ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align1
  • cd ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/02.ctg_align.sh.work/ctg_align1
    ( time ./software/NextDenovo/bin/minimap2-nd --step 3 -x map-pb -a -t 15 ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta ./software/NextDenovo/test_data/./01_rundir/01.raw_align/input.seed.002.2bit|./software/NextDenovo/bin/bam_sort -i -@ 15 -o input.seed.002.2bit.sort.bam )
  • ./software/NextDenovo/bin/minimap2-nd --step 3 -x map-pb -a -t 15 ./software/NextDenovo/test_data/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta ./software/NextDenovo/test_data/./01_rundir/01.raw_align/input.seed.002.2bit
  • ./software/NextDenovo/bin/bam_sort -i -@ 15 -o input.seed.002.2bit.sort.bam
    [M::mm_idx_gen::0.0261.15] collected minimizers
    [M::mm_idx_gen::0.035    3.13] sorted minimizers
    [M::main::0.0353.13] loaded/built the index for 1 target sequence(s)
    [M::mm_mapopt_update::0.038    2.94] mid_occ = 6
    [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 1
    [M::mm_idx_stat::0.040*2.83] distinct minimizers: 41571 (99.59% are singletons); average occurrences: 1.006; average spacing: 7.299
    samtools sort: couldn't allocate memory for bam_mem

Should I change the sort_options = -m 2g -t 2 ?

commented

I have solved