[mira_talk] Re: Bug in 4.9 during
- From: Juan Daniel Montenegro Cabrera <jdmontenegroc@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Mon, 27 Oct 2014 10:29:31 +1000
It seems the like log is telling you that the parameter mhpb inside HS has
been renamed to mkpb in the section KS. Hash names have been renamed to
kmer.
On 27/10/2014 10:25 am, "Robert Willows" <robert.willows@xxxxxxxxx> wrote:
> Hi Bastien,
>
> I just downloaded and tried to use mira 4.9. I get the following error and
> don't get any files or folders made.
>
> I tried the older version with the same manifest and it works fine.
>
> Regards
> Robert
>
>
> This is MIRA 4.9.0 .
>
> Please cite: Chevreux, B., Wetter, T. and Suhai, S. (1999), Genome Sequence
> Assembly Using Trace Signals and Additional Sequence Information.
> Computer Science and Biology: Proceedings of the German Conference on
> Bioinformatics (GCB) 99, pp. 45-56.
>
> To (un-)subscribe the MIRA mailing lists, see:
> http://www.chevreux.org/mira_mailinglists.html
>
> After subscribing, mail general questions to the MIRA talk mailing list:
> mira_talk@xxxxxxxxxxxxx
>
>
> To report bugs or ask for features, please use the SourceForge ticketing
> system at:
> http://sourceforge.net/p/mira-assembler/tickets/
> This ensures that requests do not get lost.
>
>
> Compiled by: bach
> Sun Oct 26 19:15:37 CET 2014
> On: Linux vk10464 2.6.32-41-generic #94-Ubuntu SMP Fri Jul 6 18:00:34 UTC
> 2012 x86_64 GNU/Linux
> Compiled in boundtracking mode.
> Compiled in bugtracking mode.
> Compiled with ENABLE64 activated.
> Runtime settings (sorry, for debug):
> Size of size_t : 8
> Size of uint32 : 4
> Size of uint32_t: 4
> Size of uint64 : 8
> Size of uint64_t: 8
> Current system: Linux mira-cabog 3.2.0-60-virtual #91-Ubuntu SMP Wed Feb
> 19 04:13:28 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>
> Looking for files named in data ...Pushing back filename:
> "pacbio454only.fastq"
> Pushing back filename: "pacbio_SC.fastq"
> Manifest:
> projectname: OCT_2014_PB_ONLY
> job: genome,denovo,accurate
> parameters: -GE:not=16 -NW:cmrnl=warn PCBIOHQ_SETTINGS -CO:mrpg=3
> Manifest load entries: 1
> MLE 1:
> RGID: 1
> RGN: PacBio_HH SN: StrainX
> SP: SPio: 0 SPC: 0 IF: -1 IT: -1 TSio: 0
> ST: 3 (PcBioHQ) namschem: 7 SID: 0
> DQ: 20
> BB: 0 Rail: 0 CER: 0
>
> pacbio454only.fastq pacbio_SC.fastq
>
>
> ========================= Parameter parsing error(s)
> ==========================
>
> * Parameter section: '-KS'
> * Parameter: mhpb
> * Section -HASHSTATISTICS was renamed to section '-KMERSTATISTICS'.
> Furthermore, parameters with the term 'hash' were renamed with the term
> 'kmer'. Please look up the new name in the documentation, sorry about that.
>
> * Parameter section: '-KS'
> * unrecognised string or unexpected character: 4
> * (may be due to previous errors)
>
>
> ===============================================================================
>
> Internal logic/programming/debugging error (*sigh* this should not have
> happened)
>
>
> ********************************************************************************
> * Error while parsing MIRA-internal standard parameters:
> *
> *
> --job=denovo,fragments,accurate,sanger,454,iontor,pcbiolq,pcbiohq,text,solexa,solid*
> *
> *
> * There is nothing you can do about it, this is a blunder by the author.
> *
> * Please file a bug report immediately.
> *
>
> ********************************************************************************
> ->Thrown: void MIRAParameters::parse(istream & is, vector<MIRAParameters>
> & Pv)
> ->Caught: void MIRAParameters::parse(istream & is, vector<MIRAParameters>
> & Pv)
>
> Aborting process, probably due to an internal error.
>
> If you want to report the error, please do so on
> http://sourceforge.net/p/mira-assembler/tickets/
> and also give a short notice on the mira talk mailing list.
>
> If reporting, please do not delete the log and checkpoint directories,
> there may
> be files in them which could be needed to find the problem.
> Subscribing / unsubscribing to mira talk, see:
> //www.freelists.org/list/mira_talk
>
> CWD: /mnt
> Thank you for noticing that this is *NOT* a crash, but a
> controlled program stop.
> Failure, wrapped MIRA process aborted.
>
>
>
>
> Associate Professor Robert Willows
> Macquarie University
> Department of Chemistry and Biomolecular Sciences
> North Ryde, NSW 2109, Australia
> Ph: +61 2 9850 8146
> Fax: +61 2 9850 8313
> robert.willows@xxxxxxxxx
>
>
>
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