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segmentation fault after ctg_graph was done #153
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Could you share the failed subtask log here? |
I posted the running log and the **.e file in "ctg_graph1" directory which point to the last and the failed subtask. I am not sure that's what you need. If not, please let me know. |
See the instructions below: [ERROR] 2020-07-01 11:06:57,184 cns_align failed: please check the following logs: [ERROR] 2020-07-01 11:06:57,185 ~/NextDenovo/test_data/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align0/nextDenovo.sh.e |
Hi, For the segmentation falut, I guess this is caused by the
|
Hi, I replaced the calgs function in kit.py, and got these info: [56473 INFO] 2022-09-07 15:27:58 skip step: db_split |
oo, so, Next, try to change this line |
wow, great! ... It worked after changing those two lines, and now I can finally get the "nd.asm.fasta". I am just curious about the changes, will it affect the final contigs corrections when the total seed length was fixed to 1000? |
For your data, it should not. |
Thanks so much. I really appreciate your help in resolving this ! |
Describe the bug
I am running an assembly of about 300M genome(0.6% het rate) using a 512GB machine. The Ultralong reads is about 27X.
Error message
The program run well and get nd.asm.p.fasta after runing ctg_graph, but then the program stopped and reported segmentation fault (core dumped). This meant that the program failed to run "02.ctg_align" and "03.ctg_cns". I have tried many parameters in run.cfg and even change to a machine wit 2TB memory, but the error still occurred at the same point.
Input data
Total base count=8358015912bp, sequencing depth=27X, average/N50 read length=100709
Config file
[General]
job_type = local
job_prefix = nextDenovo
task = all
rewrite = yes
deltmp = yes
parallel_jobs = 2
input_type = raw
read_type = ont
input_fofn = input.fofn
workdir = 01_rundir
[correct_option]
read_cutoff = 1k
genome_size = 300m
sort_options = -m 40g -t 5
minimap2_options_raw = -t 5
pa_correction = 5
correction_options = -p 4
[assemble_option]
minimap2_options_cns = -t 5
nextgraph_options = -a 1 -q 10
Operating system
CentOS Linux release 7.9.2009
GCC
Python
Python 2.7.5 and Python 3.6.2
NextDenovo
2.5.0
As the FAQ mentioned that nd.asm.p.fasta contains more structural & base errors than nd.asm.fasta, so I really want to solve this. Any ideas or suggestions on how to fix this problem?
Thank you!
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