tg_index: Template name must be a prefix of..

John Nash
2011-11-02
2013-04-18
  • John Nash
    John Nash
    2011-11-02

    I just completed a genome assembly with MIRA. It has 450000 454 reads and 3 million illumina read pairs.

    When I ask tg_index to convert the CAF file to a gap5 database, I get the following error messages:

    With the Illumina reads:
    Template name '"HWI-ST813:68:B0202ABXX:2:1102:13848:91869:TTAGGC"' must be a prefix of the sequence name 'HWI-ST813:68:B0202ABXX:2:1102:13848:91869:TTAGGC/1'. Ignoring it.

    With the 454 reads:
    Template name '"GACYVPL01ELGAJ"' must be a prefix of the sequence name 'GACYVPL01ELGAJ'. Ignoring it.

    I think it happens a few million times. Should I be concerned? Can I switch it off?  Should I be asking this question on the MIRA list?

    John

     
  • James Bonfield
    James Bonfield
    2011-11-03

    Hmm that's clearly my bug and not MIRA as the error is wrong.  Template name '"GACYVPL01ELGAJ"' *is* a prefix of the sequence name 'GACYVPL01ELGAJ'.

    Is this the latest svn version? I'll try and construct a CAF to verify this.

     
  • John Nash
    John Nash
    2011-11-03

    Thanks for the quick response.

    My version was taken from svn on the 19th October. I usually check through the source updates about once a week to look for relevant bug fixes.  I noticed that your last change to the tg_index code was on the 30th Sept, and it was a duplicate name search.  Perhaps this broke it?

    John

     
  • James Bonfield
    James Bonfield
    2011-11-03

    We managed to reproduce it here on a data set too with the latest svn checkout. So we'll investigate why.
    Thanks for the bug report.

    James

     
  • John Nash
    John Nash
    2011-11-03

    I did the same thing on my Ubuntu box to make sure it wasn't just a Mac thing. Same result.

     
  • Hi John,

    It's objecting to the quotes around the template name.  So in our internal caf files the template entry is like this:

    Template FJ6CHWX01DO5I2

    but in MIRA caf it is like this:

    Template "FJ6CHWX01DO5I2"

    I'm going to have to get tg_index to handle quotes in caf files properly  but in the mean time you could try and remove the quotes from the template names.

    Andrew