SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SOAPdenovo2 Ambiguous output redirect. thh32 Bioinformatics 1 02-19-2014 07:29 AM
Maker2 running for 8 days! condomitti General 6 02-11-2014 07:36 AM
How excatly does SOAPdenovo2 calculates the total scaffold length? Petrichor Bioinformatics 0 06-19-2013 03:23 AM
SOAPdenovo2 standard deviation input? Petrichor Bioinformatics 1 05-13-2013 11:18 PM
SOAPdenovo2 pari_89 Bioinformatics 4 04-29-2013 02:14 AM

Reply
 
Thread Tools
Old 04-14-2014, 02:51 AM   #1
illinu
Member
 
Location: US

Join Date: Jul 2013
Posts: 55
Default SOAPdenovo2 in sleeping state for 4 days

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
illinu is offline   Reply With Quote
Old 04-16-2014, 12:20 AM   #2
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 385
Default

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 .
colindaven is offline   Reply With Quote
Old 04-17-2014, 06:32 AM   #3
illinu
Member
 
Location: US

Join Date: Jul 2013
Posts: 55
Default

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?
illinu is offline   Reply With Quote
Old 05-22-2014, 10:11 PM   #4
fankatt
Junior Member
 
Location: China

Join Date: May 2013
Posts: 3
Default

Quote:
Originally Posted by illinu View Post
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.
fankatt is offline   Reply With Quote
Old 05-22-2014, 11:46 PM   #5
illinu
Member
 
Location: US

Join Date: Jul 2013
Posts: 55
Default

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.
illinu is offline   Reply With Quote
Old 05-23-2014, 06:27 AM   #6
id0
Senior Member
 
Location: USA

Join Date: Sep 2012
Posts: 130
Default

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.
id0 is offline   Reply With Quote
Old 03-19-2017, 05:58 PM   #7
Gambarini
Junior Member
 
Location: Brazil

Join Date: Jan 2017
Posts: 1
Default

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.
Gambarini is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:59 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO