[mira_talk] Re: read names too long?
- From: Lionel Guy <guy.lionel@xxxxxxxxx>
- To: mira_talk@xxxxxxxxxxxxx
- Date: Fri, 16 Mar 2012 17:26:34 +0100
Right, I get that:
Misc (-MI):
Stop on max read name length (somrnl) : 40
Which means that the parameter -MI:somrnl=0 was probably not parsed... But I
also see that you ran it with the --job parameter after that. Can you try again
and run it as I suggested with all "--" parameters in the beginning and the
others after?:
mira --project=teu1-denovo-PE --job=denovo,genome,accurate,solexa --noclipping
-CL:pec=no -GE:not=4:mps=6 -MI:somrnl=0 SOLEXA_SETTINGS
-GE:tismin=100:tismax=650 > assembly_log.txt
Cheers,
Lionel
On 16 Mar 2012, at 16:37 , Christoph Hahn wrote:
> Hi,
>
> Attached please find the log. THanks again for your help!
>
> Much obliged,
> Christoph
>
> On 03/16/2012 02:36 PM, Lionel Guy wrote:
>> Mmh... strange.
>> Maybe you'll have to wait for Bastien's answer, I'm not too sure how to go
>> further. If you assembly log is not too long, could you post it on the
>> mailing list? Can you try:
>>
>> mira --project=teu1-denovo-PE --job=denovo,genome,accurate,solexa
>> --noclipping -CL:pec=no -GE:not=4:mps=6 -MI:somrnl=0 SOLEXA_SETTINGS
>> -GE:tismin=100:tismax=650> assembly_log.txt
>>
>> and post assembly_log.txt?
>>
>> Lionel
>>
>> On 16 Mar 2012, at 14:02 , Christoph Hahn wrote:
>>
>>> Hi Lionel,
>>>
>>> Sorry for not being specific enough! I am using MIRA V3.4.0 on linux 64
>>> bit. Here s the complete error message:
>>>
>>> Fatal error (may be due to problems of the input data or parameters):
>>>
>>> "
>>> Some read names were detected with more 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: '-MI:somrnl=0'
>>> "
>>>
>>> ->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:
>>> //www.freelists.org/list/mira_talk
>>>
>>> CWD: /xanadu/home/chrishah/data/mtgenomes/Mira/teu1-ACTTGAA/denovo/Mira
>>> Thank you for noticing that this is *NOT* a crash, but a
>>> controlled program stop.
>>>
>>>
>>> The command seems to have been parsed correctly. From the stdout:
>>>
>>> Parsing parameters: --project=teu1-denovo-iteration15-PE --noclipping
>>> -CL:pec=no -GE:not=4:mps=6 -MI:somrnl=0 --job=denovo,genome,accurate,solexa
>>> SOLEXA_SETTINGS -GE:tismin=100:tismax=650
>>>
>>> I ve tried to put -MI:somrnl=0 in the position you have suggested and also
>>> in many other positions - the error stays the same. Also, what is very
>>> strange is that I did use the same data in a mapping assembly with
>>> basically the same parameters and with stating the options in exactly the
>>> same sequence - it worked without any problem..
>>>
>>> Thanks for your help!
>>> Christoph
>>>
>>> On 03/16/2012 12:32 PM, Lionel Guy wrote:
>>>> Hi Christoph,
>>>>
>>>> Some arguments are positional (AFAIR). Have you tried putting the
>>>> arguments -GE:not=4:mps=6 -MI:somrnl=0 after
>>>> --job=denovo,genome,accurate,solexa?
>>>>
>>>> You can check in the beginning of the log file to see if the argument was
>>>> parsed correctly.
>>>>
>>>> BTW, posting the exact error message, the environment you work, which
>>>> version of MIRA you use generally speeds up problem solving ;)
>>>>
>>>> Cheers,
>>>>
>>>> Lionel
>>>>
>>>> On 16 Mar 2012, at 12:24 , Christoph Hahn wrote:
>>>>
>>>>> Hello,
>>>>>
>>>>> I am trying to do denovo Solexa assembly using MIRA:
>>>>>
>>>>> mira --project=teu1-denovo-PE "--noclipping -CL:pec=no" -GE:not=4:mps=6
>>>>> -MI:somrnl=0 --job=denovo,genome,accurate,solexa SOLEXA_SETTINGS
>>>>> -GE:tismin=100:tismax=650
>>>>>
>>>>> Unfortunately, MIRA stops because of the read names being longer than 40
>>>>> characters. I have seen that before so I have already included the option
>>>>> '-MI:somrnl=0' to ignore this. Also I did mapping assemblies using the
>>>>> same data and basically the same parameters before without any problems.
>>>>> Any idea? Bug?
>>>>>
>>>>> Much obliged,
>>>>> Christoph
>>
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