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.
Going forward, the galaxy-dev(a)bx.psu.edu mailing list would be a good
choice for local/cloud install questions:
On 10/10/12 3:28 PM, Chris Merrikh wrote:
Hi, I'm trying to solve an issue I'm having with my local
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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