Segmentation fault with scaff step when use different MEGAHIT's output about soapdenovo2 HOT 5 CLOSED

Megahit and SOAPdenovo2 are two pieces of software , changing the parameters of Megahit won't affect it's compatibility to SOAPdenovo2. I'm not sure with the limited information you provided, but the problem might be some incorrect file sharing between the two experiments you carried out. I would suggest you to rerun the experiment again using some slightly different parameters like p32 and k61. Another suggestion is, using mate-pairs (insert size >1k) for generating contigs is not recommended. You might want to use 270, 500 and 800 in Megahit only.

from soapdenovo2.

I ran into the segment fault in the scaffolding step, too. After compiling SOAPdenovo2 with -g option, I executed it again. Any help is appreciate.

My command is here:
/home/ohmiya/tools/SOAPdenovo2/SOAPdenovo2-master/SOAPdenovo-127mer all -K 127 -s /home/ohmiya/soap.config -R -o /home/ohmiya/soap_out

My config file is here:
max_rd_len=300
[LIB]
avg_ins=500
reverse_seq=0
asm_flag=3
rank=1
q1=/sshare1/home/ohmiya/Forward.fastq
q2=/sshare1/home/ohmiya/Reverse.fastq
q=/sshare1/home/ohmiya/all.fastq

Stderr message in the scaffolding step is here:

Scaff

Parameters: scaff -g /home/ohmiya/soap_out

Files for scaffold construction are OK.

There are 1 grad(s), 4838366 read(s), max read len 300.
Kmer size: 127
There are 101094 edge(s) in edge file.
Mask contigs with coverage lower than 0.9 or higher than 18.0, and strict length 0.
Average contig coverage is 9, 14518 contig(s) masked.
Mask contigs shorter than 129, 9924 contig(s) masked.
42662 arc(s) loaded, average weight is 6.
50547 contig(s) loaded.
Done loading updated edges.
Time spent on loading updated edges: 0s.

File /home/ohmiya/data/soap_out/ensemble_soap.links exists, skip creating the links...
Time spent on loading paired-end reads information: 0s.

Start to construct scaffolds.

For insert size: 500
Total PE links 54278
PE links to masked contigs 43026
On same scaffold PE links 0
Cutoff of PE links to make a reliable connection: 3
Active connections 22496
Weak connections 15344
Weak ratio 68.2%
390 circles removed.
Start to remove transitive connection.
Total contigs 101094
Masked contigs 26002
Remained contigs 75092
None-outgoing-connection contigs 71799 (95.614716%)
Single-outgoing-connection contigs 3124
Multi-outgoing-connection contigs 4
Cycle 1
Two-outgoing-connection contigs 165
Potential transitive connections 1
Transitive connections 1
Transitive ratio 0.6%
Cycle 2
Two-outgoing-connection contigs 164
Potential transitive connections 0
Transitive connections 0
Transitive ratio 0.0%
Start to linearize sub-graph.
Picked sub-graphs 135
Connection-conflict 0
Significant overlapping 116
Eligible 0
Bubble structures 1
Mask repeats:
Puzzles 118
Masked contigs 114
Start to remove transitive connection.
Total contigs 101094
Masked contigs 26232
Remained contigs 74862
None-outgoing-connection contigs 71898 (96.040710%)
Single-outgoing-connection contigs 2960
Multi-outgoing-connection contigs 0
Cycle 1
Two-outgoing-connection contigs 4
Potential transitive connections 0
Transitive connections 0
Transitive ratio 0.0%
Start to linearize sub-graph.
Picked sub-graphs 1
Connection-conflict 0
Significant overlapping 1
Eligible 0
Bubble structures 0
Non-strict linearization.
Start to linearize sub-graph.
Picked sub-graphs 1
Connection-conflict 0
Significant overlapping 0
Eligible 0
Bubble structures 0
Start to mask puzzles.
Masked contigs 3
Remained puzzles 0
Segmentation error

Content of the core file is here:
Core was generated by /home/ohmiya/tools/SOAPdenovo2/SOAPdenovo2-master/SOAPdenovo-127mer all -K 127'. Program terminated with signal 11, Segmentation fault. #0 0x000000000044a1d8 in validConnect (ctg=101124, preCNT=0x0) at orderContig.c:890 890 if ( !cn_temp->deleted && !cn_temp->mask ) warning: File "/usr/local/lib64/libstdc++.so.6.0.20-gdb.py" auto-loading has been declined by your auto-load safe-path' set to "$debugdir:$datadir/auto-load:/home/ohmiya/go/src/runtime/runtime-gdb.py".
To enable execution of this file add
add-auto-load-safe-path /usr/local/lib64/libstdc++.so.6.0.20-gdb.py
line to your configuration file "/home/ohmiya/.gdbinit".
To completely disable this security protection add
set auto-load safe-path /
line to your configuration file "/home/ohmiya/.gdbinit".
For more information about this security protection see the
"Auto-loading safe path" section in the GDB manual. E.g., run from the shell:
info "(gdb)Auto-loading safe path"
(gdb) where
#0 0x000000000044a1d8 in validConnect (ctg=101124, preCNT=0x0) at orderContig.c:890
#1 0x000000000044a43c in getNextContig (ctg=101125, preCNT=0x2965d58, exception=0x7fff5142a237 "") at orderContig.c:969
#2 0x000000000044e9a2 in freezing () at orderContig.c:3136
#3 0x000000000044cc13 in ordering (deWeak=1 '\001', downS=0 '\000', nonlinear=1 '\001',
infile=0x74ac80 "/sshare1/home/ohmiya/data/project/P249_1707_Metagenome.TLR3KO_DNA_virus/d249_04_ensemble.SAVacC_kmax_cdhit.mix.KO_pel_9w.qcl/soap_out/ensemble_soap") at orderContig.c:2390
#4 0x000000000045908d in Links2Scaf (
infile=0x74ac80 "/sshare1/home/ohmiya/data/project/P249_1707_Metagenome.TLR3KO_DNA_virus/d249_04_ensemble.SAVacC_kmax_cdhit.mix.KO_pel_9w.qcl/soap_out/ensemble_soap") at orderContig.c:5903
#5 0x00000000004805d8 in call_scaffold (argc=3, argv=0x7fff5142a7f0) at scaffold.c:83
#6 0x0000000000444e13 in pipeline (argc=8, argv=0x7fff5142aa60) at main.c:542
#7 0x000000000044393e in main (argc=8, argv=0x7fff5142aa60) at main.c:96

from soapdenovo2.

@ohmiya it seems that you only have a paired-end library with 500bp insert size. With only that, scaffolding will not increase the contiguity of your assembly.

from soapdenovo2.

In addition to the paired-end reads, I have a single-end library. In my config file,
q=/sshare1/home/ohmiya/all.fastq
Why the scaffolding doesn't work with only a paired-end library even though we perform the assembly before it?

from soapdenovo2.

Scaffolding requires mate-pairs with insert size ≥1kbp. Paired-end reads can be used for scaffolding, but the improvement won't be significant.

from soapdenovo2.