assembling long reads using HASLR... failed ERROR

[koujiaodahan]

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?

[koujiaodahan]

asm_contigs_k49_a3_c250_lr25x_b500_s3_sim0.85.err.txt
I find the error in the outdir,so should i decrease the running thread to reduce consuming memory?

[haghshenas]

@koujiaodahan this doesn't seem like a problem with memory usage. It seems to be the same bug reported in #5 which doesn't happen all the time and is hard to reproduce.
I will try to find a small dataset that reproduces this bug.

[koujiaodahan]

oh,i have reproduce threee times...

[haghshenas]

Yes, but I need a small dataset to be able to debug things.
But just in case, is the dataset you are using publicly available?

[koujiaodahan]

the dataset is not yet published,MGI short reads and ONT long reads.

[koujiaodahan]

I want to konw what's you whole analysis pipeline using real datasets in article which is not described in table s1. The pipeline is just running halsr on the sequencing dataset? is there any processing before running halsr?

[koujiaodahan]

should i correct the ONT reads using some software before running Halsr?

[koujiaodahan]

Yes, but I need a small dataset to be able to debug things.
But just in case, is the dataset you are using publicly available?

hello,is any advise?

[koujiaodahan]

here is my running log
asm_contigs_k49_a3_c250_lr25x_b500_s3_sim0.85.err.txt
map_contigs_k49_a3_c250_lr25x.log.txt
sr_k49_a3.log.txt