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Re: maker-devel post from requires approval

Carson Holt-2
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.


On Jul 17, 2020, at 3:42 PM, [hidden email] wrote:

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From: Diana Moreno Santillán <[hidden email]>
Date: July 17, 2020 at 3:32:20 PM MDT


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

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 

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Date: July 17, 2020 at 3:42:30 PM MDT

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