[maker-devel] Odd missing label bug

[Fields, Christopher J]

Yeah, that seems to be it (crossing around 100kbp increments).  I’ll run a reduced example set locally to make sure and will send.

-c

On Nov 13, 2013, at 9:58 PM, Carson Holt <carsonhh at gmail.com> wrote:

> Could you put a contig and protein fasta into a test job that I could run
> on?  Based on the hit position I imagine this may only happens when the
> alignments spans two chunks (by default MAKER splits the input config into
> 100,000bp chunks).  The hit runs from 374736-401929.
> 
> <Carson
> 
> 
> On 11/13/13, 8:51 PM, "Fields, Christopher J" <cjfields at illinois.edu>
> wrote:
> 
>> I¹m seeing an odd bug in GFF output where the label is being sporadically
>> left off some child Omatch_part' features.  This is when using
>> maker-2.30p.  I found this while splitting out the data by source as
>> individual tracks for IGV viewing; I have several sets of ESTs from
>> individuals of the same species, so I have them labeled (from maker_opts):
>> 
>> est=./ESTs/Trinity_1128_v2_combined_pr2.clean.fasta:strain_1128
>> protein=./ESTs/xeno/Taeniopygia_guttata.taeGut3.2.4.73.pep.all.fa:TaeGut,.
>> /ESTs/xeno/Ficedula_albicollis.FicAlb_1.4.73.pep.all.fa:FicAlb
>> 
>> I planned on separating these into separate tracks, one for each BLASTX,
>> BLASTN, etc.  
>> 
>> After a test run on a few scaffolds, a small number of the BLASTX and
>> BLASTN look like this:
>> 
>> KB913263.1      blastx:TaeGut   protein_match   374736  401929  330     -
>>     .       ID=KB913263.1:hit:9:3.10.0.3;Name=ENSTGUP00000000074
>> KB913263.1      blastx  match_part      401756  401929  312     -       .
>> 
>> ID=KB913263.1:hsp:55:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M58;Tar
>> get=ENSTGUP00000000074 1 58
>> KB913263.1      blastx  match_part      394486  394665  186     -       .
>> 
>> ID=KB913263.1:hsp:56:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M42 D9
>> M9;Target=ENSTGUP00000000074 56 106
>> KB913263.1      blastx  match_part      392059  392178  204     -       .
>> 
>> ID=KB913263.1:hsp:57:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M40;Tar
>> get=ENSTGUP00000000074 97 136
>> KB913263.1      blastx  match_part      387479  387547  116     -       .
>> 
>> ID=KB913263.1:hsp:58:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M23;Tar
>> get=ENSTGUP00000000074 151 173
>> KB913263.1      blastx  match_part      383644  383742  156     -       .
>> 
>> ID=KB913263.1:hsp:59:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M33;Tar
>> get=ENSTGUP00000000074 172 204
>> KB913263.1      blastx  match_part      382860  383063  242     -       .
>> 
>> ID=KB913263.1:hsp:60:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M68;Tar
>> get=ENSTGUP00000000074 193 260
>> KB913263.1      blastx  match_part      382538  382648  186     -       .
>> 
>> ID=KB913263.1:hsp:61:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M37;Tar
>> get=ENSTGUP00000000074 247 283
>> KB913263.1      blastx  match_part      382072  382236  268     -       .
>> 
>> ID=KB913263.1:hsp:62:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M55;Tar
>> get=ENSTGUP00000000074 282 336
>> KB913263.1      blastx  match_part      379270  379458  330     -       .
>> 
>> ID=KB913263.1:hsp:63:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M63;Tar
>> get=ENSTGUP00000000074 336 398
>> KB913263.1      blastx  match_part      374736  374900  147     -       .
>> 
>> ID=KB913263.1:hsp:64:3.10.0.3;Parent=KB913263.1:hit:9:3.10.0.3;Gap=M55;Tar
>> get=ENSTGUP00000000074 4 58
>> 
>> Note the missing label in the source column for the Omatch_part¹ types.
>> Strangely, only a small # have this problem, but the exact same ones
>> appear to be consistently popping up on repeated runs (this is from a
>> test prior to a full launch using openmpi).  It does seem like only child
>> Omatch_part¹ appears affected.
>> 
>> Any ideas?
>> 
>> chris
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> 
>