Comments (5)
After playing a bit with the suggested parameters I managed to obtain an assembly with the expected characteristics (1,492,648 bp; GC%=0.341) and BUSCO C of 97.3%.
In case it helps others, the values I used were -a 1 -z 4 -l 8 -q 0 -N 2 -u 2 -w 3 -B 300 -C 20 -L 5 -t 300
.
Thanks for the help!
from nextdenovo.
Could you paste the content of file /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/erebia_ligea.RO_EL_949.nonBfly.nextdenovo.sh.e
to here?
from nextdenovo.
Here it is:
hostname
+ hostname
cd /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0
+ cd /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0
time /ceph/users/amackintosh/software/NextDenovo/bin/nextgraph -a 1 -f /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.input.seqs /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta;
+ time /ceph/users/amackintosh/software/NextDenovo/bin/nextgraph -a 1 -f /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.input.seqs /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta
[INFO] 2023-03-06 18:00:08 Initialize graph and reading...
[INFO] 2023-03-06 18:00:09 Initial Node(s): 684, Edge(s): 7574
[INFO] 2023-03-06 18:00:09 Depth stat, Mid: 39.000 Max: 78000.000 Repeat: 58.500 L:N:H: 0.040:0.960:0.000
[INFO] 2023-03-06 18:00:09 Outdegree stat, Mid: 11.000 Max: 22000.000 Repeat: 16.500 L:N:H: 0.052:0.948:0.000
[INFO] 2023-03-06 18:00:09 Chimeric node ratio: 0.073% (candidate: 1.169%)
[INFO] 2023-03-06 18:00:09 Assembly done and outputting...
[INFO] 2023-03-06 18:00:09 CMD:
/ceph/users/amackintosh/software/NextDenovo/bin/nextgraph -a 1 -f /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.input.seqs -o nd.asm.p.fasta /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.input.ovls
[INFO] 2023-03-06 18:00:09 Real time: 1.019 sec; CPU: 1.020 sec; Peak RSS: 0.376 GB
0.74user 0.27system 0:01.02elapsed 99%CPU (0avgtext+0avgdata 393792maxresident)k
0inputs+0outputs (0major+99669minor)pagefaults 0swaps
touch /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/erebia_ligea.RO_EL_949.nonBfly.nextdenovo.sh.done
+ touch /scratch/etoro/erebia/nextdenovo/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/erebia_ligea.RO_EL_949.nonBfly.nextdenovo.sh.done
from nextdenovo.
Try to reduce -z -l
first and if the result is still empty then reduce these options: -q -N -u -w -B -C -z -l -L -t
.
from nextdenovo.
I also meet the same problem, but my read type is ont and I don't know how to fix it
from nextdenovo.
Related Issues (20)
- sort_align step erro HOT 1
- Does NEXTDENOVO filter the contig before output? HOT 2
- Error: db_stat failed ? HOT 1
- ERROR:the input data is insufficient for an assembly HOT 3
- Question about error rate for correction HOT 1
- ctg_align failed HOT 4
- When run nextdenovo with test_data failed HOT 1
- hello , i used the nextdenovo to assemble the ultra large size genome of 23g, the fq only 270g, just want to assemble the grapgh HOT 7
- How to improve the N50 and reduce contigs numbers? HOT 7
- Test won't run HOT 1
- For low base quality of sequences HOT 1
- Timing out on minimap-nd tasks HOT 4
- I want to correct ONT with HiFi data HOT 1
- db_stat failed, @d84e39c8-130c-4159-bfa9-5393ad703a1a does not exist! HOT 2
- assembly problem HOT 2
- ctg_graph error, (core dumped), returned non-zero exit status 134".
- NextDeNovo running for >4days with no expected outputs HOT 22
- ModuleNotFoundError: No module named 'paralleltask' HOT 4
- Running out of disk space HOT 5
- Accepted a killed signal and killing all running jobs, please wait... HOT 1
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