Mira 4 Mapping Error

Question

[HG]

Hi everyone i was trying to do a hybrid mapping with 454 and illumina data to my reference fasta file. I am using MIRA 4 , and accoding to manual i made my .config file also but it does not help. Can anyone give some idea about the error. thank you advance.

Few line like that :

project = MyFirstAssembly job = genome,mapping,accurate parameters = SOLEXA_SETTINGS -CO:msr=no

  Fatal error (may be due to problems of the input data or parameters):

    ********************************************************************************
    * 4552974 reads were detected with names longer than 40 characters.            *
    *                                                                              *
    * While MIRA and many other programs have no problem with that, some older     *
    * programs have restrictions concerning the length of the read name.           *
    *                                                                              *
    * Example given: the pipeline                                                  *
    *      CAF -> caf2gap -> gap2caf                                               *
    * will stop working at the gap2caf stage if there are read names having > 40   *
    * characters where the names differ only at >40 characters.                    *
    *                                                                              *
    * This is a warning only, but as a couple of people were bitten by this, the   *
    * default behaviour of MIRA is to stop when it sees that potential problem.    *
    *                                                                              *
    * You might want to rename your reads to have <= 40 characters.                *
    *                                                                              *
    * On the other hand, you also can ignore this potential problem and force MIRA *
    * to continue by using the parameter: '-NW:cmrnl=warn' or '-NW:cmrnl=no'       *
    ********************************************************************************
->Thrown: void Assembly::checkForReadNameLength(uint32 stoplength)
->Caught: main

Aborting process, probably due to error in the input data or parametrisation.
Please check the output log for more information.
For help, please write a mail to the mira talk mailing list.
Subscribing / unsubscribing to mira talk, see: http://www.freelists.org/list/mira_talk

CWD: /home/hiren/Desktop/assembly/mira_4.0_linux-gnu_x86_64_static/bin
Thank you for noticing that this is *NOT* a crash, but a
controlled program stop.
Failure, wrapped MIRA process aborted.

[Martombo]

I don't really know how the error message could be easier to understand than this. your reads have a name that is too long, you either make it shorter or add the option -NW:cmrnl=no to ignore the warning.

[HG]

I hope you did not read my question properly i already mention in config file

parameters = SOLEXA_SETTINGS -CO:msr=no

Hope its now clear to you.

[lelle]

So? This parameter has nothing to do with the warning you are getting, does it?

[HG]

No I hope its a errror inside the program not a worning message, please have a look a brod view of that error.( i edited the error msg)

[HG]

For your information i made my config file according to MIRA manual : Its look like :

# Example for a manifest describing a mapping assembly with
# shotgun 454 and paired-end Illumina data, not merging reads and therefore keeping
# all pair information
# First part: defining some basic things
# In this example, we just give a name to the assembly
# and tell MIRA it should map a genome in accurate mode
# As special parameter, we want to switch off merging of Solexa reads
project = MyFirstAssembly
job = genome,mapping,accurate
parameters = SOLEXA_SETTINGS -CO:msr=no
# The second part defines the sequencing data MIRA should load and assemble
# The data is logically divided into "readgroups"
# first, the reference sequence
readgroup
is_reference
data = ../../data/NC_someNCBInumber.gff3
strain = bchoc_wt
# now the shotgun 454 data
readgroup = DataForShotgun454
data = ../../data/project454data.fastq
technology = 454
strain = bchoc_se1
# now the paired-end Illumina data
readgroup = DataForPairedEnd500bpLib
data = ../../data/project500bp-1.fastq ../../data/project500bp-2.fastq
technology = solexa
strain = bchoc_se1
template_size = 250 750
segment_placement = ---> <---

[Adrian Pelin]

It seems you are missing the point the program is making, and the input from other community members are giving you.

Tog get rid of the error, you need to replace the following lines in your manifest file:

project = MyFirstAssembly
job = genome,mapping,accurate
parameters = SOLEXA_SETTINGS -CO:msr=no

With this:

project = MyFirstAssembly
job = genome,mapping,accurate
parameters = SOLEXA_SETTINGS -CO:msr=no
parameters = -NW:cmrnl=no

Answer 1

[al-ash]

Include line

parameters = COMMON_SETTINGS -NW:cmrnl=no

in your manifest config file. Note that the string COMMON_SETTINGS is critical here. Writing just parameters = -NW:cmrnl=no as suggested here by Adrian and as seems the original error message to suggest gave me error:

* Parameter section: '-NW'
* Parameter 'cmrnl' can only be set as COMMON_SETTINGS, not individually for a specific sequencing type (SOLEXA_SETTINGS).

MIRA is there a bit misleading here, IMO.