[maker-devel] Odd missing label bug

[Carson Holt]

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 Œmatch_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 Œmatch_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
>Œmatch_part¹ appears affected.
>
>Any ideas?
>
>chris
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