[mira_talk] Re: Please please help in debugging this
- From: Chris Hoefler <hoeflerb@xxxxxxxxx>
- To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
- Date: Fri, 26 Sep 2014 09:22:23 -0500
For your reference, specify a .fa file instead of a .fasta file. Or use
technology=text. Otherwise Mira will expect to find qualities in that
readgroup.
In addition, unless you have a specific requirement, it is a good idea to
leave -CO:msr on. It greatly reduces the memory burden on downstream
analysis software, and you won't lose any information (coverage or
qualites).
On Thu, Sep 25, 2014 at 11:48 PM, Mandar Bobade <mandar.bobade60@xxxxxxxxx>
wrote:
> Hi Felipe,
> I appreciate your reply. Following is my manifest.config file:
>
> #manifest file for basic mapping assembly with illumina data using MIRA 5
>
> project = initial-mapping-testpool-to-Salpinus-mt
>
> job=genome,mapping,draft
>
> parameters = -NW:mrnl=0 -AS:nop=1 SOLEXA_SETTINGS -CO:msr=no
> # first, the reference sequence
> readgroup
> is_reference
> data = elaeis_guineensis_ref.fasta
> technology = solexa
> strain = DatePalm
>
> readgroup = SomeMatePairIlluminaReadsIGotFromTheLab
> autopairing
> data = Sample_mito-AB_out_interleaved.fastq
> technology = solexa
> strain = testpool
>
>
>
>
>
> This was when I used encountered with error.
>
> Regards,
> Mandar
>
> On Thu, Sep 25, 2014 at 8:31 PM, Felipe Lira <felipelira3@xxxxxxxxxxxx>
> wrote:
>
>> We will appreciate to see the manifest.
>>
>> Copy and paste if it is possible.
>>
>> Felipe Lira
>> Spanish National Center of Biotechnology - CNB/ CSIC
>> *Microbial Biotechnology Department*
>> Fellow of http://obrasocial.lacaixa.es/
>>
>> Antes de imprimir este mensaje piense bien si es realmente necesario
>> hacerlo.
>> *Before you print this e-mail, think well if it is **really** necessary.*
>>
>>
>> El Jueves 25 de septiembre de 2014 15:56, Chris Hoefler <
>> hoeflerb@xxxxxxxxx> escribió:
>>
>>
>> Mira did not find qualities in the file you provided. Can you send your
>> manifest.conf file?
>>
>> On Thu, Sep 25, 2014 at 6:56 AM, Mandar Bobade <mandar.bobade60@xxxxxxxxx
>> > wrote:
>>
>> Hi,
>> I am using MITObim with MIRA for mitochondrial genome assembly using
>> related mitochondrial genome. I have reads of 100 nt readlength and
>> 600000+600000 in my interleaved.fastq file. I am encountering following
>> error after being ran sometime:
>>
>> Loading data from FASTA file:
>> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
>> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
>> [90%] ....|.... [100%]
>> Localtime: Thu Sep 25 17:09:24 2014
>> rnm size: 0
>> No FASTA quality file given, using default qualities for all reads just
>> loaded.
>> Localtime: Thu Sep 25 17:09:24 2014
>>
>> Done.
>> Loaded 22089 reads with 0 reads having quality accounted for.
>> baitrp.size(): 22089
>> Localtime: Thu Sep 25 17:09:24 2014
>> Writing temporary hstat files:
>> freemem: 245825040384
>> TNH: 658917495
>> XME 1: 26.183
>> XME 2: 16
>> NEPB 1: 16777216
>> NEPB 2: 16777216
>> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
>> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
>> [90%] ....|.... [100%] done
>> Flushing buffers to disk:
>> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] ....|.... [40%]
>> ....|.... [50%] ....|.... [60%] ....|.... [70%] ....|.... [80%] ....|....
>> [90%] ....|.... [100%] done
>> Localtime: Thu Sep 25 17:13:27 2014
>>
>> Analysing hstat files:
>> [0%] ....|.... [10%] ....|.... [20%] ....|.... [30%] .
>> Fatal error (may be due to problems of the input data or parameters):
>>
>>
>>
>> Please, please let me know way out from this error, since error is also
>> inconceivable to me.
>>
>> Regards,
>> Mandar
>>
>>
>>
>>
>> --
>> Chris Hoefler, PhD
>> Postdoctoral Research Associate
>> Straight Lab
>> Texas A&M University
>> 2128 TAMU
>> College Station, TX 77843-2128
>>
>>
>>
>
--
Chris Hoefler, PhD
Postdoctoral Research Associate
Straight Lab
Texas A&M University
2128 TAMU
College Station, TX 77843-2128
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