Hi Dan,
That's a bug. Zero singletons does cause the pipeline to crash. The step
that analyzes singletons assumes there are always some singletons. You can
get past that for now by commenting out the singleton analysis steps 600-710
(Align singleton reads and analyzing breakpoints). Comment them out in the
amosvalidate script with '#' characters. I'll try and find time to make the
amosvalidate pipeline more robust in a future release of AMOS.
Best,
-Adam
On Tue, Mar 17, 2009 at 6:58 AM, Dan Bolser <dan.bolser@...> wrote:
> I am trying to validate several BAC assemblies using amosvalidate. The
> pipeline seems to run correctly for 8/11 BACs, but throws an error for
> 3/11. I tried to Google the error, but there were no hits that I could
> find.
>
> The log file for the pipeline says, for example:
>
> $ grep -C 3 "please file a bug report" PATH_BAC??.bnk.runAmos.log
> PATH_BAC01.bnk.runAmos.log-# (maximum input length is 536870908)
> PATH_BAC01.bnk.runAmos.log-# CONSTRUCTIONTIME mummer PATH_BAC01.ntref 0.01
> PATH_BAC01.bnk.runAmos.log-mummer: cannot open file
> "PATH_BAC01.singletons.seq" or file "PATH_BAC01.singletons.seq" is
> empty
> PATH_BAC01.bnk.runAmos.log:ERROR: mummer and/or mgaps returned
> non-zero, please file a bug report
> PATH_BAC01.bnk.runAmos.log-!!! 2009-03-17 10:32:25 Command: nucmer
> --prefix=PATH_BAC01 PATH_BAC01.fasta PATH_BAC01.singletons.seq exited
> with status: 1
> PATH_BAC01.bnk.runAmos.log-!!! END - Elapsed time: 0d 0h 0m 12s
> PATH_BAC01.bnk.runAmos.log-
>
>
> (where PATH is a longer file path, removed for clarity).
>
>
> Indeed, the '.singletons' file for the affected BACs are empty...
>
> wc -l PATH_BAC??.singletons.seq
> 0 PATH_BAC01.singletons.seq
>
>
> But I'm guessing that shouldn't cause the validation pipeline to terminate?
>
>
> Thanks for any suggestions.
> Dan.
>
>
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