[maker-devel] maker-devel post from dianad.mosa at gmail.com requires approval

[Carson Holt]

MAKER’s internal logic has not changed at all. The new release is a minimal update to handle newer versions of GeneMark, tRNAScan, RepeatMasker, and Swiss-Prot (slight deviations from historical output formats).

*Update to handle most recent tRNAScan output format.
*Update to handle most recent GeneMark output format.
*Update to downstream putative function scripts to handle newer Swiss-Prot FASTA header format
*Some version/configurations of RepeatMasker can report 0 as a start/end coordinate when it should be 1 (0 is out of bounds), so we fix it when we see it.

—Carson


> On Jul 17, 2020, at 3:42 PM, maker-devel-owner at yandell-lab.org wrote:
> 
> As list administrator, your authorization is requested for the
> following mailing list posting:
> 
>    List:    maker-devel at yandell-lab.org
>    From:    dianad.mosa at gmail.com
>    Subject: INCONSISTENCY BETWEEN PROTEINS AND GFF
>    Reason:  Post by non-member to a members-only list
> 
> At your convenience, visit:
> 
>    http://yandell-lab.org/mailman/admindb/maker-devel_yandell-lab.org
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> to approve or deny the request.
> 
> From: Diana Moreno Santillán <dianad.mosa at gmail.com>
> Subject: INCONSISTENCY BETWEEN PROTEINS AND GFF
> Date: July 17, 2020 at 3:32:20 PM MDT
> To: maker-devel at yandell-lab.org
> 
> 
> Hello,
> 
> I am using MAKER for mammalian genomes.
> I am running 3 rounds for most of them, as it seems to increase completeness according to BUSCO. 
> The issue is that the round 3 output has inconsistencies. 
> 
> For example, at the protein.fasta file I have sequences that after performing blast and rename are annotated, but at the gff file are missing, for example:
> 
> 
> %grep  AnoCau_scaffold_40730 acaudifer_3rd_run_all_maker_proteins_renamed_putative_function.fasta
> augustus_masked-AnoCau_scaffold_40730-processed-gene-0.0-mRNA-1 protein Name:"Similar to IFNL3 Interferon lambda-3 (Homo sapiens OX=9606)" AED:0.28 eAED:0.23 QI:0|0|0|1|1|1|4|0|183 
> 
> %grep  AnoCau_scaffold_40730 acaudifer_3rd_run_all_maker_renamed_putative_function.gff
> nothing
> 
> Why is the sequence present in my proteins file, but not at my gff3 file?
> 
> Is worth to notice that when I tried to run maps_id I got:
> WARNING:  No mapping available for  AnoCau_scaffold_40730 
> 
> I found that if I use the gff file from previous rounds of Maker as evidence, this could happen, but I haven't found a solution yet. What do you recommend to avoid these changes of names?
> Why I have sequences in my protein file but not in my gff file?
> 
> Thank you for your attention. 
> 
> Diana Moreno 
> 
> 
> 
> From: maker-devel-request at yandell-lab.org
> Subject: confirm 2fbcb7f0a71181de1fcea3c9d2bf4e09bbaca6e4
> Date: July 17, 2020 at 3:42:30 PM MDT
> 
> 
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