assembling long reads using HASLR... failed ERROR #20
Description
Hi：
I downsample the ONT data to 60X，and MGI data to 40X, and running the script as follow:
sh ~/USER/Assembly/haslr/script/lowdepth_script/haslr_base.sh ~/USER/Assembly/outdir2/fastq/ONT_60X/NA24385_ONT.60X.fastq.gz ~/USER/Assembly/outdir2/fastq/T7_40X/NA24385_T7.40X.clean_1.fq.gz ~/USER/Assembly/outdir2/fastq/T7_40X/NA24385_T7.40X.clean_2.fq.gz ~/Assembly/outdir2/haslr_out/T740_ONT60
and My haslr_base.sh :
ontfq=$1
r1=$2
r2=$3
outdir=$4
time ~/backup_data/anaconda3/haslr/bin/haslr.py -t 64 -o $outdir -g 3.1g -l $ontfq -x nanopore -s $r1 $r2
The errors is :
checking /home/ubuntu/backup_data/anaconda3/haslr/bin/haslr_assemble: ok
checking /home/ubuntu/backup_data/anaconda3/haslr/bin/minia_nooverlap: ok
checking /home/ubuntu/backup_data/anaconda3/haslr/bin/fastutils: ok
checking /home/ubuntu/backup_data/anaconda3/haslr/bin/minia: ok
checking /home/ubuntu/backup_data/anaconda3/haslr/bin/minimap2: ok
number of threads: 64
output directory: /home/ubuntu/USER/lizhichao/Assembly/outdir2/haslr_out/T740_ONT60
[27-Sep-2020 19:23:57] subsampling 25x long reads to /home/ubuntu/USER/lizhichao/Assembly/outdir2/haslr_out/T740_ONT60/lr25x.fasta... done
[27-Sep-2020 20:39:33] assembling short reads using Minia... done
[28-Sep-2020 03:27:39] removing overlaps in short read assembly... done
[28-Sep-2020 03:28:04] removing short sequences in short read assembly... done
[28-Sep-2020 03:28:11] aligning long reads to short read assembly using minimap2... done
[28-Sep-2020 04:11:15] assembling long reads using HASLR... failed
ERROR: "haslr_assemble" returned non-zero exit status
Command exited with non-zero status 70
366544.02user 252752.33system 12:17:11elapsed 1400%CPU (0avgtext+0avgdata 309192052maxresident)k
977298512inputs+838263248outputs (163major+24284513190minor)pagefaults 0swaps
so, could you tell me how can i handle it?