[mira_talk] Re: Failure, wrapped MIRA process aborted

  • From: Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx>
  • To: "mira_talk@xxxxxxxxxxxxx" <mira_talk@xxxxxxxxxxxxx>
  • Date: Wed, 4 Jun 2014 17:37:26 +0100

On Wed, Jun 4, 2014 at 5:28 PM, Mendez Garcia, Celia
<cmendezg@xxxxxxxxxxxx> wrote:
> # Hi, I'm trying to assemble a genome (draft assembly as 1st attempt) and
> don't know why I get the error.
>
> # Here the log file I get:
> This is MIRA 4.0.2 .
>
> ...
>
>
> Fatal error (may be due to problems of the input data or parameters):
>
> ********************************************************************************
> * 19849572 reads were detected with names longer than 40 characters (see
> *
> * output log for more details).
> *
> *
> *
> * 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. Instead of
> *
> * renaming reads in the input files, maybe the 'rename_prefix' functionality
> *
> * of manifest files is useful for you there.
> *
> *
> *
> * 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:
> //www.freelists.org/list/mira_talk
>
> CWD: /home/a-m/cmendezg
> Thank you for noticing that this is *NOT* a crash, but a
> controlled program stop.
> Failure, wrapped MIRA process aborted.
>
> # I'm using 1 node of a computation queue, 256 GB RAM. Don't think that's
> limiting, even when my .fastq file's size is of 5.17 GB.
>
> # Thanks ...
>
> Celia Mendez

MIRA is trying very hard to tell you what the problem is, and how to fix it.
I've cut out most of the log leaving the key part above (sadly the email
line wrapping makes it a bit harder to read).

Your data has lots of reads with long names (more than 40 characters).
Some downstream tools would break, so MIRA stopped and warned
you about this.

MIRA tells you that you might want to edit your reads, or you can treat
this a warning with -NW:cmrnl=warn in your manifest, or simply ignore
this with -NW:cmrnl=no instead.

Personally I would tell MIRA to ignore the long read names.

Please ask if you need help adjusting your manifest.

Regards,

Peter

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