There are a few steps you can take when asking a question on the QIIME forum
to help get the quickest response.
*1.* Most importantly, you should *create a small test data set that
reproduces the* error that you're getting, and send that data to us along
with the exact command that is generating the error. This allows us to
attempt to reproduce the error on our end, which makes it much faster to
sort out what's going on than going back-and-forth with questions by e-mail.
For example, if you're trying to align 100,000 sequences with align_seqs.py,
and getting a failure, try to reduce that data set down to the smallest
number of sequences that will reproduce that error, and send that fasta
file. To do this, copy the fasta file (so you don't mess with your original)
and start extracting sequences from the file and re-testing. Try extracting
the first sequence and see if you get an error. From the command line, call:
head -n 2 seqs.fasta > first_seq.fasta
to extract the first sequence (assuming that your fasta file is using the
one-line-per-sequence format). If this gives the error, then sends us the
first_seq.fasta file. If not, try increasing the number of sequences in that
file, or try only running the last sequence in the file using 'tail' instead
of 'head'. If you're using a template alignment (e.g. with PyNAST), do the
same thing there: reduce to the smallest number of sequences that will
recreate the error.
Be sure to send *all* of the files necessary to generate the error, and any
files that are getting created in failed run. If this is a workflow script,
be sure to include the parameters file that you are using. The best thing to
do is create a directory (e.g., align_seqs_failure_<my_name>) which contains
all of the input files, run the command in that directory, save the command
and output in a notes.txt file in that directory, zip it up, and send it
with the command and output also in the e-mail.
*2.* Once you've reduced to the smallest set of sequences that recreate the
error, *send us the exact command that you ran and the full error
message*that is being generated. Cut and paste this from the terminal.
For tips on how to send us files, see the note on 'Sending files to the
QIIME developers' below.
*3.* Run:
print_qiime_config.py -t
in the terminal, and paste all of the text that is printed into the e-mail
to us. This gives us information on what version of QIIME and its
dependencies you are using.
If this seems like a lot of work to do before sending us a message, remember
that we will end up asking you for it anyway at some point. By not having to
wait for us to bounce questions back to you, you get your answer faster, and
putting it together will help you improve your skills at debugging command
line application issues. We find that in a lot of cases, running through
step 1 above allows the user to figure out what the problem is on their own
(e.g., a file ending with '.fasta' is not really a fasta file). Finally, the
less time that we spend on support, the more time we can spend on new
features in QIIME and our own research.
*Sending files to the QIIME developers*
Some convenient (and free!) tools for sharing small data sets are
Dropbox<http://www.dropbox.com>(OS X/Windows/Linux) and
CloudAPP <http://www.getcloudapp.com> (OS X only). These will allow you to
publicly share a zip file, for example.
