Filing bugs

Before filing a bug collect the following information. The commands provided will provide useful answers to the questions.

If you are having a read ID error (ERR BADID), please try to find out what version of CASAVA, the Illumina pipeline, your sequencing centre is using; though many make this obnoxiously difficult. Many sequencing centres seem to pass reads through their own pipelines that mangle the headers. PANDAseq is very picky about sequence headers for your protection.

Otherwise, please run:

curl -s https://raw.github.com/neufeld/pandaseq/master/pandabug | sh

or

wget -O- https://raw.github.com/neufeld/pandaseq/master/pandabug | sh

to gather basic details about your system.

If you installed Ubuntu packages using apt-get, please run sudo apt-get install pandaseq-dbg to get extra debugging information.

When filing, please include:

1. The output of the above script.
2. The exact error message. If this is a compilation error, do not truncate the output. If this is a problem when assembling, keep the INFO ARG lines, and the last few lines, but you may truncate the middle (the sequences that assembled correctly).
3. If you have tried multiple different things, please list them all.
4. Your sequencing data may be requested. This usually does not necessitate all the reads. It is generally ideal if you can include at least one read pair for a failing sequence assembly, especially for crashes (segmentation faults). For name errors, this is less important as the bad sequence name is in the output.
5. If failing with a segmentation fault on Linux, please run catchsegv pandaseq ... to produce a backtrace.