SOAPdenovo error

[guru1985]

We have been using this tool for assembling eukaryotic genomes from a long time now but have never encountered an error message "Trace: can't find kmer 0 0 0 2914096dd4 (input 0 0 0 2f74f2afb0) at step 1 " at all. The output file is full of these errors and we are not able to workout where the issue. Is could you please tell us what this error actually means ?

A few more error lines

"Trace: can't find kmer 0 0 0 2914096dd4 (input 0 0 0 2f74f2afb0) at step 1
Trace: can't find kmer 0 0 0 114096dd4c (input 0 0 0 26f74f2afb) at step 0
Trace: can't find kmer 0 0 0 5025b7531 (input 0 0 0 39bdd3cabe) at step 0
Trace: can't find kmer 0 0 0 5025b7531 (input 0 0 0 39bdd3cabe) at step 1
Trace: can't find kmer 0 0 0 1025b75319 (input 0 0 0 339bdd3cab) at step 0
Trace: can't find kmer 0 0 0 4cacf100 (input 0 0 0 2ab96426e) at step 1
Trace: can't find kmer 0 0 0 acf100ac (input 0 0 0 242ab9642) at step 0
Trace: can't find kmer 0 0 0 acf100ac (input 0 0 0 242ab9642) at step 1
Trace: can't find kmer 0 0 0 96dd4c66 (input 0 0 0 ce6f74f2a) at step 0"

I really appreciate your help in this matter.

Thanks a lot.

[SES]

If you can provide some information about the data and command you used then it is more likely we can help. I recall seeing these "can't find kmer" messages in the past, but I can't figure it out from just looking at the error message.

[guru1985]

Thanks for your reply!!

The errors occured when i was trying to assemble a eukaryotic genome (quiet big) using 100bp paired end illumina reads. The command line i gave was

"export PATH=/projects/a07/gurjeet/bin/

SOAPdenovo127mer all -s /projects/genome/config_p1.txt -K 51 -p 48 -R yes -D yes -o /project/flauro/gurjeet/assembly/p1/p1_51/soap51"

The assembly goes through as it makes all the files including .scafSeq but its really poor assembly (we have tried quiet a lot of kmer's) and all the assembly's give the above same error. The error comes in the output file "assembly.sh.0233"(the output file which we gen after running any job) . This file shows that when the assembler starts making scaffolds all these error lines come . there are like 10 -4 error lines like that.

[SES]

Is SOAPdenovo crashing when running the "KmerFreq" step? If so, this is not unheard of with large data sets, but unfortunately, I don't have a good explanation or solution (other than to try another program).

[Rockx]

Hi, I am working with guru1985 on this project.

The error is occuring when SOAPdenovo starts to fill the scaffold gaps with reads from the *.ReadInGap file.

From the error message "...0 0 0 96dd4c66..." seems to refer to a memory location.

We will attempt to use other assembly software, to see if we get similar errors.

[SES]

Hi, I am working with guru1985 on this project.

The error is occuring when SOAPdenovo starts to fill the scaffold gaps with reads from the *.ReadInGap file.

From the error message "...0 0 0 96dd4c66..." seems to refer to a memory location.

We will attempt to use other assembly software, to see if we get similar errors.

What you said about memory issues makes sense, and you may just be running out of memory. Have you watched the memory usage on your machine while running the assembly? If you are submitting this to a queue with SGE (I'm guessing based on your output filename) you can do:

qstat -j job_id | grep vmem

where job_id is the ID assigned to your assembly job. If you are using LSF,

bjobs -l

will give you the memory information. If you are not using any queueing system, just type "top" at the command line and observe.