SOAPdenovo2 in sleeping state for 4 days

[illinu]

Hi,

I am running SOAPdenovo2 with 1 set of paired-end and 1 set mate pair reads, fragments of 300bp with a total to 66X coverage on a genome with estimated 240Mb.

The sparse_pregraph module on SOAPdenovo2 launched more than 4 days ago and it showed the message below. When I do top it shows in sleeping mode what suggests it could be either reading the reads or writing something but I am concerned it is taking far too long with no verbose on the terminal.

Any one with experience with SOAPdenovo2 maybe can let me know whether it is normal that it takes this long...

$ ./SOAPdenovo-127mer sparse_pregraph -s file.config -K 127 -z 240000000 -o pregraph -p 64
Version 2.04: released on July 13th, 2012
Compile Apr 9 2014 15:54:20
********************
SparsePregraph
********************

Parameters: pregraph_sparse -s file.config -K 127 -g 15 -z 240000000 -d 1 -e 1 -r 0 -p 64 -o pregraph

Start to build the sparse de Brujin graph, round: 1
1 io thread initialized.
Import reads from file:
reads/pe_A520-R1.fastq
64 work threads initialized.
...still showing only this on terminal

$ top
PID USER PR NI VIRT RES SHR S %CPU %MEM TIME+ COMMAND
44528 x 20 0 9158m 4.4g 1208 S 2419.8 0.9 166092:11 SOAPdenovo-127m

[colindaven]

It should run through very fast, i.e. in minutes to hours, in my experience.
Are there memory issues ?
Try the low kmer option as well with the SOAPdenovo-63mer .

[illinu]

We have 512GB of RAM so no, memory should not be an issue. At the moment there are other processes running but they're not even close to half that memory. I ran kmergenie on the dataset and the best k size is 121 so I guess SOAPdenovo-127mer is the most appropriate?

[fankatt]

We have 512GB of RAM so no, memory should not be an issue. At the moment there are other processes running but they're not even close to half that memory. I ran kmergenie on the dataset and the best k size is 121 so I guess SOAPdenovo-127mer is the most appropriate?

Hi, have you figured out what the problem is? I am encountering the same problem. Even I tried 63mer, it is still "sleeping" there.

I ran this program before, and it went very well--only took ~30 mins to de novo a 8Mb genome. So I am very confused why it's not working now.

[illinu]

fankatt, I had asm_flags=3 for all three libraries (2 paired end and 1 mate pair), I changed asm_flags=1 for paired end and asm_flags=2 for mate pairs. Also I gave rank=1 to all three libraries (not sure if this influenced, it shouldn't). I then ran it manually step by step.

As a reference, my run took:
sparse pregraph: 9 hours
contig: 1 min
map: 22 min
scaff: 1 min

reads are 80X for a 240Mb genome.

[id0]

I had the same issue where SOAPdenovo would seem to be running forever. I waited for two weeks and there seemed to be no progress. I think the problem had to do with memory.

I solved the problem by trimming the FASTQs prior to using them for SOAPdenovo. Having remains of adapters in the input sequences makes a huge difference.

[Gambarini]

I had the same issue now, so I'm posting it in case someone else got into this.

It looks like SOAPdenovo requires the sequences to have just one line. I formatted my files and it run just fine. Something like 5 minutes for a 4 million reads file.