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vpc-ccg / haslr

A fast tool for hybrid genome assembly of long and short reads
GNU General Public License v3.0
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assembling long reads using HASLR... failed ERROR #20

Open koujiaodahan opened 3 years ago

koujiaodahan commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

@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 commented 3 years ago

oh,i have reproduce threee times...

haghshenas commented 3 years ago

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 commented 3 years ago

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

koujiaodahan commented 3 years ago

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 commented 3 years ago

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

koujiaodahan commented 3 years ago

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 commented 3 years ago

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