HI Elaine,
Nice job of troubleshooting! Let's find out where the problem is. At
this point, it is generally quickest when I look at the actual data. Are
you working on the public Main instance at http://usegalaxy.org? And if
not, are you able to duplicate the issue there, using a small test set
of your data (please test, as this is also informative for troubleshooting)?
Once the error is on Main, either share a history link with me or submit
one of the failed runs as a bug report. In the email/bug report
comments, note the meablast error and your account email if different
from this email. I'll look at everything, but also want to focus on the
most current troubleshooting run.
ex: #4 query .fasta + #5 custom .fasta = #7 megablast error
Datasets that are /_not permenently deleted_/ are best, as is including
the complete analysis in the same history (e.g. original upload dataset,
any grooming or other manipulations, etc.). Sometimes there are
secondary issues (related or not) - I'll give feedback about those - and
if there is a software or config problem, more info can only help.
Launch a re-run if you need to, for datasets key to the error that are
purged already, so I can see the exact UI parameters as displayed in the
tool forms (to compare versus the command-lines executed). You don't
need to wait for these to complete before sharing.
How to share/submit bugs reports (just do one, your choice):
https://wiki.galaxyproject.org/Support#Shared_and_Published_data
https://wiki.galaxyproject.org/Support#Reporting_tool_errors
If the problem is not reproducible on Main, and you are using a local,
cloud, or other public Galaxy instance, write back on list, and we can
work from there.
I'll watch for your reply. Avoid posting share links to the public list,
or 'publishing' (just 'share'), to keep data private.
Best,
Jen
Galaxy team
ps. Anyone else experience problems, the same guidelines apply. If
sharing a history, please start a galaxy-user thread first, then share
(this is when emailing team members direct with problems is best), it
help us with tracking. Bug reports from errors on Main can be sent in
directly from the history/dataset. I haven't posted the current
best-practice guidelines for error reporting yet this year to this list,
so took the opportunity to put this in our mail archives for
searches/reference. Please excuse the length.
On 2/20/14 8:09 AM, Elaine Youngman wrote:
Hello,
I am attempting to megablast a FASTA file containing ~45,000 records
of 100nt each against the nt database using the Galaxy web interface.
I am using a Galaxy-generated FASTA file produced from a groomed FASTQ
file using the 'FASTQ to tabular' and 'Tabular to FASTA' tools. When I
try to use this as input for the Megablast tool, I get the Required
metadata values are missing error. When I look at the attributes of
the FASTA file, the datatype is indeed set to FASTA. I have tried
downloading the FASTA file and reuploading it as a FASTA file
explicitly with the same result. I also tried changing the FASTA width
to 79, and trimming the records to 70nt each -- not the problem. If I
make a file containing only the first FASTA record, I get the same
error. Any suggestions?
Thanks!
Elaine
___
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
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org
___
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
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
