Re: [AMOS-help] Problems running minimus2

[Afif E. <ael...@sd...>]

Thanks for your reply. I just tried this, but it still didn't work.

I don't think it's a problem with parameters because I had tried setting 
OVERLAP to zero and MINID also to zero as a debugging measure to see if 
it would just join the ends together. Doing that still did not help...


Thanks and regards
Afif

On 05/15/2015 12:52 AM, Mohamed Kassam wrote:
> Hi,
> please try to change the parameter of conserr to 0.05 and try again
>
> Mohamed
>
> 2015-05-15 1:46 GMT+02:00 Afif Elghraoui <ael...@sd...
> <mailto:ael...@sd...>>:
>
>     Hello,
>     I have assembled a bacterial genome into one contig and I am trying
>     to circularize it using minimus2 as described at
>     <https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/Circularizing-and-trimming>.
>     The directions there say to introduce a break somewhere in contig
>     and then run minimus to circularize it. With the resulting two-entry
>     fasta file, I run the following:
>
>
>     $ toAmos -s chromosome.fasta -o circularized.afg
>     Max ID: 9
>     $ minimus2 circularized
>     The log file is: circularized.runAmos.log
>     Doing step 10:  Building AMOS bank & Dumping reads
>     Doing step 11
>     Doing step 12
>     Doing step 13
>     Doing step 20:  Getting overlaps
>     Doing step 21
>     Doing step 22
>     Doing step 23:  Converting overlaps
>     Doing step 24:  Loading overlaps to the bank
>     Doing step 25
>     Doing step 30:  Running contigger
>     Doing step 31
>     Doing step 32
>     Doing step 40:  Running consensus
>     Doing step 41
>     Command:
>     /share/apps/pacbio/smrtanalysis/current/analysis/bin/make-consensus
>     -B -e 0.06 -b circularized.bnk -w 15  exited with status: 1
>
>
>     The error I'm getting is at the make-consensus step:
>     "Could not open bank file, circularized.bnk/LAY.ifo, No such file or
>     directory". I'm attaching the run log. My problem looks similar to
>     another one in the mailing list archive
>     <http://sourceforge.net/p/amos/mailman/message/585583/>, but I did
>     not find any resolution there.
>
>
>     I'm using the version of Amos distributed with PacBio's SMRTAnalysis
>     v2.3.0
>
>     $ toAmos --version
>     toAmos $Revision: 1.44 $
>
>     I'd really appreciate any help. I tried installing and using the
>     current revision of Amos from git, but it had other
>     'not-implemented' types of errors.
>
>
>     Many thanks and regards,
>     Afif
>
>     ------------------------------------------------------------------------------
>     One dashboard for servers and applications across Physical-Virtual-Cloud
>     Widest out-of-the-box monitoring support with 50+ applications
>     Performance metrics, stats and reports that give you Actionable Insights
>     Deep dive visibility with transaction tracing using APM Insight.
>     http://ad.doubleclick.net/ddm/clk/290420510;117567292;y
>     _______________________________________________
>     AMOS-help mailing list
>     AMO...@li... <mailto:AMO...@li...>
>     https://lists.sourceforge.net/lists/listinfo/amos-help
>
>

-- 
Afif Elghraoui
Laboratory Manager
Laboratory for Pathogenesis of Clinical Drug Resistance and Persistence
6367 Alvarado Ct., Ste 206, Room 2
San Diego, CA 92120
p. 619-594-1710