Re: [Inchworm-users] Inchworm software usage problem

[Brian J H. <bh...@br...>]

Hi Jing,

If you run inchworm with '--monitor 1', you can follow its progress.  It'll
report how many sequences its parsed at certain intervals and also indicate
at what stage it's in in the process before it starts outputting assemblies.

If you want to capture the output to a file, be sure to direct the output to
a file:

   inchworm --reads $file.reads --run_inchworm --monitor 1 > inchworm.fasta

The 5G of data shouldn't be a problem, but it might take a while.   By
monitoring the progress (with the option above) and keeping an eye on your
resources (memory available via 'top'), you'll get a feel for what your
progress and any limitations are.  Hopefully, you have enough physical RAM,
which we estimate at around 1G of RAM per 1 M reads (~100 base), which in
your case might require ~50G of RAM.

Also, I should mention that our Trinity software is now available at:
http://TrinityRNASeq.sf.net, and provides a more rigorous solution to
RNA-Seq assembly. Inchworm is used as the first part of the process.

Best,

-brian



On Mon, Mar 21, 2011 at 12:22 PM, Jing Liu <jl...@mc...> wrote:

> Hi Inchworm group,
>
> I am a graduate student at Umass-Amherst. I am using Inchworm right
> now to assemble some mRNA data. I have met two problems in running and
> wonder if you can give me some help.
>
> 1, the data size I have is huge(over 5G). I found it seems to take a
> long time to run. In fact I ran on our server over 10 hours and
> nothing changed. I wonder for inchworm if there is a way to deal with
> such a huge amount of data?
>
> 2, I found the program will print result in standard output. Will it
> possible if I want to print result into a file?
>
> Thank you very much,
> Jing Liu
>
>
>
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-- 
-- 
Brian J. Haas
Manager, Bioinformatics Outreach, Genome Annotation and Analysis
The Broad Institute
http://broad.mit.edu/~bhaas