ctg_align aborting

[fengyuanli304]

Hi, I run nextdenovo2.3.0 a few days, and I meet the following error:

[ERROR] 2020-10-13 07:12:59,063 ctg_align failed: please check the following logs: [ERROR] 2020-10-13 07:12:59,075 /lustre2/nextdenovonewresult/03.ctg_graph/02.ctg_align.sh.work/ctg_align5/nextDenovo2.3.0.sh.e

the wrong file (nextDenovo2.3.0.sh.e):

hostname

hostname
cd /lustre2/nextdenovonewresult/03.ctg_graph/02.ctg_align.sh.work/ctg_align5
cd /lustre2/nextdenovonewresult/03.ctg_graph/02.ctg_align.sh.work/ctg_align5
time /lustre2/software/NextDenovo/bin/minimap2-nd -x map-pb -a -t 18 /lustre2/nextdenovonewresult/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta /lustre2/nextdenovonewresult/.//01.raw_align/input.seed.005.2bit|/lustre2/software/NextDenovo/bin/bam_sort -i -@ 18 -o input.seed.005.2bit.sort.bam
/lustre2/software/NextDenovo/bin/minimap2-nd -x map-pb -a -t 18 /lustre2/nextdenovonewresult/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta /lustre2/nextdenovonewresult/.//01.raw_align/input.seed.005.2bit
/lustre2/software/NextDenovo/bin/bam_sort -i -@ 18 -o input.seed.005.2bit.sort.bam
[M::mm_idx_gen::74.0331.76] collected minimizers
[M::mm_idx_gen::98.8371.99] sorted minimizers
[M::main::98.8381.99] loaded/built the index for 1084 target sequence(s)
[M::mm_mapopt_update::103.1241.95] mid_occ = 1322
[M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 1084
[M::mm_idx_stat::104.2571.94] distinct minimizers: 68259648 (45.72% are singletons); average occurrences: 6.155; average spacing: 8.329
[M::worker_pipeline::564.5245.46] mapped 9336 sequences
[M::worker_pipeline::1002.5955.80] mapped 9334 sequences
[M::worker_pipeline::1457.2465.93] mapped 9373 sequences
[M::worker_pipeline::1879.4736.03] mapped 9399 sequences
[M::worker_pipeline::2276.0416.18] mapped 9358 sequences
[M::worker_pipeline::2719.1116.14] mapped 9294 sequences
[M::worker_pipeline::3162.7256.09] mapped 9404 sequences
[M::worker_pipeline::3570.6946.10] mapped 9345 sequences
[M::worker_pipeline::4011.6326.10] mapped 9290 sequences
[M::worker_pipeline::4471.0936.09] mapped 9342 sequences
[M::worker_pipeline::4882.3066.15] mapped 9379 sequences
[M::worker_pipeline::5339.2726.12] mapped 9401 sequences
[M::worker_pipeline::5857.4836.06] mapped 9373 sequences
[M::worker_pipeline::6284.6736.06] mapped 9369 sequences
[M::worker_pipeline::6724.0656.05] mapped 9394 sequences
[M::worker_pipeline::7264.340*6.04] mapped 9409 sequences
[W::sam_read1] Parse error at line 1334846
samtools sort: truncated file. Aborting

Genome characteristics genome size: 2.9G, heterozygous rate: 1.30%, repeat content: 60.05%

Input data Total base count 244,238,273,438 bp, sequencing depth 84, average/N50 read length 37,906

Operating system Which operating system and version are you using? CentOS Linux relase 7.6.1810

GCC What version of GCC are you using? 4.8.5 20150623 (Red Hat 4.8.5-36)

Python What version of Python are you using? python2.7.18

NextDenovo What version of NextDenovo are you using? nextdenovo2.3.0

[General] job_type = local job_prefix = nextDenovo2.3.0 task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 8 input_type = raw input_fofn = ./input.fofn workdir = ./

[correct_option] read_cutoff = 1k seed_cutoff = 36k blocksize = 3g pa_correction = 4 seed_cutfiles = 4 sort_options = -m 80g -t 25 -k 45 minimap2_options_raw = -x ava-pb -t 12 correction_options = -p 20

[assemble_option] minimap2_options_cns = -x ava-pb -t 12 -k17 -w17 nextgraph_options = -a 1

Can you help me to figure out how to solve it? Thank you.

[moold]

Hi, could you try to run the following command manually?

/lustre2/software/NextDenovo/bin/minimap2-nd -x map-pb -a -t 18 /lustre2/nextdenovonewresult/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nd.asm.p.fasta /lustre2/nextdenovonewresult/.//01.raw_align/input.seed.005.2bit -o input.seed.005.2bit.sam
/lustre2/software/NextDenovo/bin/bam_sort -i -@ 18 -o input.seed.005.2bit.sort.bam input.seed.005.2bit.sam

[fengyuanli304]

Thanks a lot.