Hi Chris,

It sounds like the file is too large for your set up and there is a memory problem. There are a few options:


1 - If you really want to try to use your desktop computer, break the large file into smaller files before running the tools, then merge together data from the same barcode together once split away from the rest. This may get tedious depending on how many barcodes you are working with, but possible. Just double check that the tool you are running makes sense to run on the partial datasets you are providing as input (most of the tools you list will run on any partial dataset). I would suggest running some tests to see if these are small enough to work with in your environment before you invest too much in this strategy (you may find that you run into resource issues again in later steps, like mapping).

2 - Run Galaxy on a different local computer, one with more memory.

3 - Run Galaxy on a cloud instance with sufficient memory.
    http://usegalaxy.org/cloud

Going forward, the galaxy-...@bx.psu.edu mailing list would be a good choice for local/cloud install questions:
http://wiki.g2.bx.psu.edu/Support#Mailing_Lists

Best,

Jen
Galaxy team

On 10/10/12 3:28 PM, Chris Merrikh wrote:
Hi, I'm trying to solve an issue I'm having with my local installation
of Galaxy (installed on my own computer, rather than on a server). I'm
using data in the form of fastq files from an Illumina Hi-seq and I want
Galaxy to parse the bar coded sequences out into individual files for
me. I've been using the public server in the past, and I'm able to use
the Groomer, Joiner, Reverse-Complement, Trimmer, and Barcode Splitter
tools just fine. Now I'm trying to do the same thing locally on the same
files. Both the large file (38 GB) and a smaller file consisting of the
first 10k lines will upload just fine. However, I can only get the
Groomer to work on the small file. When I use it on the large file I get
an error: "Error executing tool: maximum recursion depth exceeded while
calling a Python object."

Any help on this would be greatly appreciated!

- Chris M.


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Jennifer Jackson
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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
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