SOAPdenovo-Trans: Seg fault

[kenietz]

Hi guys,
today i tried SOAPdenovo-trans to assemble some Illumina paired-end reads. I have 3 sets from 3 different conditions. 2 of the sets finished without a glitch. But the 3rd set just does not want to proceed. the program exits with a seg fault and no any other error msg. I found it crashes at the first stage:

-------------------------
SOAPdenovo-Trans-31mer pregraph -K 31 -s config -o soap_out

The version 1.0: released on Nov 12th, 2011

In config, 1 libs, max seq len 76, max name len 256

8 thread created
read from file:
read1.fastq
read from file:
read2.fastq
Segmentation fault
------------------------

Was digging on the net but found only hints about the length of the reads. Namely i had to check if all the reads are longer than 31bp. So i wrote a script and it seems all of them are longer than that. They are all 76bp.
Also its not a memory issue as i have 64Gb on my machine and i see the program crashes before it even reaches 20Gb of used RAM.
I also tried to reduce the k-mer to 29 but it crashes again, the same if i use SOAPdenovo-Trans-127mer with -K 31.

I have no idea how to proceed further tho.

I would appreciate any idea or hint on how to debug that!

Thank you!

PS: forgot to mention. My config is like that:
------------------------
max_rd_len=76
[LIB]
avg_ins=280
rank=1
q1=read1.fastq
q2=read2.fastq
asm_flag=3
reverse_seq=0

[mariof]

Hi there!

I oberserve similar problems. I have preprocessed Illimina PE RNA-seq data where I merged overlapping paired-end reads. I filtered out short reads and removed all reads containing Ns since SOAPdenovo-trans doesnt seem to like that. I still run into segfaults. Any ideas on how to put SOAPdenovo-trans into positive mood?

[mruizm]

Hi everyone, i'm trying to run a SOAPdenovo-trans assembly but i don't know how to use de configuration file and finally execute the assembly, i don't know about the details of the file like the meaning of max_rd_len, avg_ins, rank, asm_flag, reverse_seq. Could you help me with this?

Best regards!

[riv]

Hi kenietz and mariof. I have exactly the same problem. I was running soapdenovotrans for 25 Illumina libraries together in a machine with 200Gb RAM and it crashed reaching 4Gb of RAM... so I don´t know what it is going on... mariof, do we know each other maybe?

[GenoMax]

Was SOAPdenovo compiled with 64-bit support on the machine you are trying to run it on?

[lovenlong]

Hi guys,
today i tried SOAPdenovo-trans to assemble some Illumina paired-end reads. I have 3 sets from 3 different conditions. 2 of the sets finished without a glitch. But the 3rd set just does not want to proceed. the program exits with a seg fault and no any other error msg. I found it crashes at the first stage:

-------------------------
SOAPdenovo-Trans-31mer pregraph -K 31 -s config -o soap_out

The version 1.0: released on Nov 12th, 2011

In config, 1 libs, max seq len 76, max name len 256

8 thread created
read from file:
read1.fastq
read from file:
read2.fastq
Segmentation fault
------------------------

Hi all,
According to my recent experience at Soapdenovo2 assembler, I found the Core dumpe (Seg fault) would have some relations with the input data.
When I conducted Soapdenovo assembly using PE reads with quality filtering(fastx,q30p90), 5'-end (first 12nt) and adapters trimmg, everything was ok (N50 was 2K).
Then, I did errors correction and trimming (seems trim the 3'-end) by using Soapec (parameters:-k 17 –x 8 –r 60 -Q 33), and Seg fault problem arised from 1st stage of Soapdenovo2.
Is there anyone can explain why this happened?
I'm a PhD candidate in rice breeding and absolutely a newcomer to NGS, I'm trying to detect SVs/CNVs between several rice cultivars through de novo assembly (all samples' raw reads would be ~35 fold in depth). If someone can give me some suggestions ?
Thank you for anyone's patiently answering.