Bonjour, est-ce que vous avez déjà eu à utiliser nexdenovo
Je suis en dépression
J'ai fait un issue sur le git des développeurs.
Si jamais vous avez de l’expérience, je suis preneuse des bons conseils.
Merci
ouvert 12:41PM - 15 Jun 26 UTC
Hello,
I'm trying to assembly a plant diploid genome of 2.5Gb with nextDenovo v… ersion 2.5.2
I've filtered data to have **80Gb of initial ONT fastq** (30X).
Nextdenovo is running for 12 days and it is generating a huge data on correction step (already 7 Tera) !
```
$ ll cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align*/*ovl
-rw-rw----+ 1 jorjuela jorjuela 1.9T Jun 15 14:21 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align7/input.seed.001.2bit.6.ovl
-rw-rw----+ 1 jorjuela jorjuela 1.5T Jun 14 17:15 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align9/input.seed.003.2bit.8.ovl
-rw-rw----+ 1 jorjuela jorjuela 0 Jun 11 11:44 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align8/input.seed.003.2bit.7.ovl
-rw-rw----+ 1 jorjuela jorjuela 0 Jun 7 09:56 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align6/input.seed.001.2bit.5.ovl
-rw-rw----+ 1 jorjuela jorjuela 0 Jun 7 09:46 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align5/input.seed.001.2bit.4.ovl
-rw-rw----+ 1 jorjuela jorjuela 1.2T Jun 6 08:40 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align2/input.seed.002.2bit.1.ovl
-rw-rw----+ 1 jorjuela jorjuela 1.2T Jun 6 08:26 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align3/input.seed.002.2bit.2.ovl
-rw-rw----+ 1 jorjuela jorjuela 1.2T Jun 6 08:25 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align4/input.seed.002.2bit.3.ovl
-rw-rw----+ 1 jorjuela jorjuela 0 Jun 3 10:13 cte80G_nextdenovo/01.raw_align/03.raw_align.sh.work/raw_align1/input.seed.002.2bit.0.ovl
```
Here parameters I'm using.
$ more run_nextdenovo.sh
```
#!/bin/bash
#SBATCH --job-name=ndn80_chamadorea
#SBATCH --cpus-per-task 72
#SBATCH --mem 550G
#SBATCH -A plantropomics
#SBATCH -p bigmem
#SBATCH --qos bigmem
#SBATCH -o /shared/ifbstor1/projects/kmexplore/chamadorea/nextDenovo80G/slurm.%N.%j.out
#SBATCH -e /shared/ifbstor1/projects/kmexplore/chamadorea/nextDenovo80G/slurm.%N.%j.err
module load nextdenovo/2.5.2
cd /shared/ifbstor1/projects/kmexplore/chamadorea/nextDenovo80G
echo 'starting nextdenovo on chamadorea 80G ...'
time nextDenovo config.cfg
```
$ more config.cfg
```
[General]
job_type = local
job_prefix = cte
task = all
rewrite = no
deltmp = yes
parallel_jobs = 3
input_type = raw
read_type = ont
input_fofn = ./input.fofn
workdir = cte80G_nextdenovo
[correct_option]
genome_size = 2.5g
read_cutoff = 5k
pa_correction = 3
sort_options = -m 160g -t 24 -k 32 # -k, max depth of each overlap, should <= average sequencing depth
minimap2_options_raw = -t 24
correction_options = -p 24 -b
[assemble_option]
minimap2_options_cns = -t 24
nextgraph_options = -a 1 -E 10000
```
My questions:
How can I speed up the assembly process??? some suggestions?
How many terabytes are needed?
Thank you
Julie
?
avec cette outil qui pour l'assemblage suggère une étape de correction de reads. Seul bémol il génère des quantités montreuses de données. Il tourne depuis 12 jours, a déjà généré 7 T (5/9 jobs se sont lancé pour le moment). J'avais initialement 80G de données pour 30x pour un génome de 2.5G d'une plante diploïde.