percolator error
kschweig
I have been getting an error in percolator on a good number of files,
and was wondering if anyone knows what might be going on.
The command I am running is:
/usr/local/bin/crux percolator --output-dir perc --fileroot
OCI_AML3_070111_2 uniprot-taxonomy_human_reviewed_020612 search
I get the following error:
OCI_AML3_070111_2.percolator.log.txt:ERROR: Rich match count exceeds
max match limit: 10000000
It seems to get through the search-for-matches OK with no errors.
Any ideas what to check?
thanks much!
-karl
kschweig
I am actually running a script to process, en mass, a bunch of ms2
files.
It iterates over ms2 files and runs search for matches followed by
percolator,
followed by spectral-counts for each one. It writes all the search
results into
a dir called search, percolator results into perc, spectral-counts
into NSAF.
I am guessing that percolator is collecting all the results in the
search dir
and processing them all together.
Is there any way to tell percolator just to process a file with
a given root filename?
thanks
B. Frewen
Your diagnosis is correct. Percolator will read all search results in a
directory. There is no way to specify a particular file. This allows
folks to break up their input file, write the multiple search result files
a directory, and process them as though the file were searched intact.
We have adopted a new format for how inputs are specified for q-ranker
that does allow you to list specific files and are considering extending
it to percolator. I will count your email as a vote in favor. :)
Please let me know if I can answer any more questions for you.
Thanks,
Barbara
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kschweig
-karl