[mira_talk] Re: (no subject)
- From: Aaron Aunins <auninsaw@xxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 12 Jul 2013 14:20:38 -0400
Hi Jahcub - Did you try putting an '--solexa' after the .maf and before the
&> log? I use Ion Torrent data with the MITObim script, and I have to add
an '--iontor' in the same spot.
- Aaron
On Fri, Jul 12, 2013 at 11:10 AM, Jac Trew <jac.trew@xxxxxxxxx> wrote:
> Hello,
>
> I'm new to mira, and I'm just trying the tutorial on MITObim. There seems
> to be a problem with the step after I run the initial mira assembly. It
> stops at the 1st iteration, and the log output gives an error message (top):
>
> "All paramters seem to make sense:
> startiteration: 1
> enditeration: 10
> strainname: testpool
> refname: Salpinus_mt_genome
> readpool:
> /home/jahcub/tutorial1/initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq
> maf:
> /home/jahcub/tutorial1/initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf
> quick: 0
> paired: 0
> denovo: 0 (mapping=0, denovo=1)
> noshow: 0
> proofread: 0
> read trimming: 0 (off=0, on=1)
> platform: SOLEXA
> Starting MITObim
> ==============
> ITERATION 1
> ==============
> Jul 12 15:49:29
> recover backbone by running convert_project on maf file
> Parsing special MIRA parameters: SOLEXA_SETTINGS -CO:fnicpst=yes
> ========================= Parameter parsing error(s)
> ==========================
> * Seen parameters for Solexa, but no readgroup has that sequencing
> technology?
>
> ===============================================================================
> Fatal error (may be due to problems of the input data or parameters):
>
> *******************************************************************************
> * Error while parsing parameters, sorry. "
>
> This is the command used "MITObim.pl -start 1 -end 10 -strain testpool
> -ref Salpinus_mt_genome -readpool
> initial-mapping-testpool-to-Salpinus-mt_in.solexa.fastq -maf
> initial-mapping-testpool-to-Salpinus-mt_assembly/initial-mapping-testpool-to-Salpinus-mt_d_results/initial-mapping-testpool-to-Salpinus-mt_out.maf
> &> log"
>
> I would be greatful for any help,
>
> Thanks,
> Jahcub.
>
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