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FAQ

From bfast

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(Please read this before submitting a help request)
(Please read this before submitting a help request)
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== Please read this before submitting a help request ==
== Please read this before submitting a help request ==
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We apologize for any inconvenience due to the program not working as you expect.
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We apologize for any inconvenience that you have experience due to the program not working as you expect.
Nonetheless, please make it easy for us to debug using the steps below.
Nonetheless, please make it easy for us to debug using the steps below.

Revision as of 15:52, 21 July 2011

Contents


Please read this before submitting a help request

We apologize for any inconvenience that you have experience due to the program not working as you expect. Nonetheless, please make it easy for us to debug using the steps below.

To help expedite debugging your problem, please try isolating your error to a small test case. For example, you could try removing reads from your input FASTQ, or using the -s/-e options (found in "bfast match" and "bfast localalign"), to find the offending read(s). As it is difficult to debug gigabyte or large size datasets, reducing the input data to a manageable size is greatly appreciated. If this is not possible, please host your data in a publicly accessible location for easy download (please add suggestions). Access to all inputs are required.

Also include the full output of the program including the full error message and command line parameters The best way for us to help is to be able to reproduce the error, and hence the need for the error message.

Thanks again, and happy debugging!

Installation

I am getting "undefined reference to `BZ2_bzwrite" or "fatal error: bzlib.h" when trying to install BFAST

You need to install the bzip2 developer package. This can be done with apt or yum on GNU/linux systems. If you do not want to install these, add the following flag when running the configure script: "--disable-bz2".

I am getting a warning when running "make check" on Mac OS X: "I can't find md5sum in your system"

Try installing md5sum from Fink, a great package manager on Mac OS X.

Postprocess

The postprocess command is slow, and/or is taking hours to complete

Try using the "-U" option. The slowness is most likely due to the pairing step in bfast taking to long. In most cases this will not affect the results dramatically.

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