SOAPdenovo2

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#################### my config ########################### max_rd_len=150 [LIB] avg_ins=350 reverse_seq=0 asm_flags=3 rd_len_cutoff=150 rank=1 pair_num_cutoff=3 map_len=32 q1=~/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap_rd_1.fq.gz q2=~/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap_rd_2.fq.gz q=~/1/Pdong_data/Filter_bac/L7_wHAXPI020290-35_unmap.single.rd.fq.gz q1=~/1/Pdong_data/Filter_bac/L6_rd_1.fq.gz q2=~/1/Pdong_data/Filter_bac/L6_rd_2.fq.gz q=~/1/Pdong_data/Filter_bac/L6.single.rd.fq.gz ##################### my cmd ############################### #!/bin/bash #SBATCH --nodes=3 #SBATCH --ntasks-per-node=56 #SBATCH --partition=D2Part_test...

WJT0925

SOAPdenovo2 installation error

3

Hello I tried to install SOAPdenovo2 using the following in ubuntu (22.04.2 LTS) terminal $ git https://github.com/aquaskyline/SOAPdenovo2.git $ cd SOAPdenovo2 #### Then tried to install using make and make clean...

AbRawoof

My command: SOAPdenovo-63mer all -s config_file -K 31 -R -o soapdenovo_asm 1>ass.log 2>ass.err config_file: max_rd_len=100 [LIB] avg_ins=200reverse_seq=0 asm_flags=3 rd_len_cutoff=100 rank=1 pair_num_cutoff=3 map_len=32 q1=/mnt/hgfs/ubt22share/2.HQdata1/data/CDC012_R1.fq.gz q2=/mnt/hgfs/ubt22share/2.HQdata1/data/CDC012_R2.fq.gz

cqh1

Hello there, I'm having a problem while attempting to create an assembly using SOAPdenovo2. The issue lies in the results I'm getting. I've experimented with various k-mer lengths using the...

Simon602

Hi developers, I am trying to build an assembly with SOAPdenovo2, but i have noticed a issue. My input files are a pair of compressed `fq.gz` files. When I use...

shiinachaos

Hi, I wanna assemble a genome of moose (about 2.7 GB). After filtering reads, I run this command several times with different threads as below, but the same issue occurred...

cnxiaobo94

Hi, I try many different parameter K while using SOAPdenovo to assemble Streptomyces spp. genomes( 7-10M), but good results were still not got. The size of the genome in the...

17863952296

Hello, I have negative numbers of edges built in pregraph section. And in contig section a warning message appear: Warning : Front edge -2147483647 is larger than -2147483646. Why is...

Aphrix

Compilling SOAPdenovo2 failed on Debian11/gcc10.2 for r242 as well as from git. Attached is patch that fixes this issue ``` commit 56fbd4afe3134a84346353e3bb8b0d5f7415d228 Author: Alois SCHLOEGL Date: Mon Oct 10 12:49:50...

schloegl

I'm trying to compile SOAPdenovo2 from source on a RedHat9 server, but it seems not to work. I'm getting a lot of `multiple definition of `b_ban'` error messages ```bash [eylenbt@by3acs]...

eylenth