Newbler seems stop

Question

[wpwupingwp]

I use Newbler to assembly chloroplast genome, with 2 fastq files. It's almost 1.2 million pair reads.

I run the program in my computer(Core i7, 16G RAM) since the day before yesterday.

From yesterday to this morning, the log files shows the same: Computing alignment, 1209000. And all reads are 1212000.

Please tell me how to set the parameters or do somethings else. I don't want to wait several days.

[TriS]

it might help to know which parameters you initially used to run your analysis.

have you ran it successfully before with the same settings you have now? The product's website says it might take 24 hours (which I believe it might be more) to assemble big genomes.

I'm not expert in chloriplast genomes but if you have access to computer clusters I'd use bowtie or BWA.

[wpwupingwp]

Thanks for your reply, I use default parameters. Chloroplast genome is very small, about 150k.

[lexnederbragt]

And what coverage do you have? If it is not extremely large this may be a cause by a bug...

[wpwupingwp]

It is large, more than 1000X.

Should I reduce the input size?

[lexnederbragt]

Yes, or use the -e flag, see https://contig.wordpress.com/2010/07/16/running-newbler-more-de-novo-assembly-parameters-and-a-hidden-one

[wpwupingwp]

Thanks for your link, recently I can't use my VPN to access outside Internet (from China, you understand it) I'll try it later.

Answer 1

[lexnederbragt]

I'll turn my comment into an answer: with such a high coverage reducing it to 50-100x will probably help. Another thing to try is to tell newbler your expected (average) depth with the -e flag.

[wpwupingwp]

Thanks, I'm using soapdenovo now, seems no matter how large the data is, it can eat up :)