[maker-devel] Error with Maker_functional_gff

[Daniel Ence]

Hi Emmanuel, I think this script is expecting the file “uniprot_sprot.fasta” downloaded from the uniprot download page at http://www.uniprot.org/downloads#uniprotkblink
The fasta headers in this file are different from the fasta header that the file you used has: 
>sp|Q6GZX4|001R_FRG3G Putative transcription factor 001R OS=Frog virus 3 (isolate Goorha) GN=FV3-001R PE=4 SV=1

Let us know if that helps, 
Daniel

> On Oct 2, 2017, at 1:03 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello,
> I intend to rename genes for Genebank submission
> 
> I downloaded swissprot.fa from NCBI and used blast MAKER generated file to swissprot. 
> 
> the output of BLAST RESULT looks like this
> snap_masked-contig_8151-processed-gene-0.8-mRNA-1       P10978.1        49.315  73      37      0       43      115     874     946     2.61e-14        71.6
> 
> I attempted to run maker_funtional_gff using the swissprot.fa downloaded and the blastp result
> 
> I got the following result
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 2897906.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 2897906.
> Can't parse details from FASTA header: >P11684.1 RecName: Full=Uteroglobin; AltName: Full=Clara cell phospholipid-binding protein; Short=CCPBP; AltName: Full=Clara cells 10 kDa secretory protein; Short=CC10; AltName: Full=Secretoglobin family 1A member 1; AltName: Full=Urinary protein 1; Short=UP-1; Short=UP1; Short=Urine protein 1; Flags: Precursor
> 
> 
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 139, <$IN> line 1608599.
> Use of uninitialized value $id in hash element at /Users/emmannaemeka/Desktop/Gpm/maker/bin/maker_functional_gff line 141, <$IN> line 1608599.
> Can't parse details from FASTA header: >Q9HZU2.1 RecName: Full=Precorrin-8X methylmutase; AltName: Full=HBA synthase; AltName: Full=Precorrin isomerase
> 
> What can I do?
> 
> 
> Nnadi Nnaemeka Emmanuel
> Department of Microbiology,
> Faculty of Natural and Applied Science,
> Plateau State University, Bokkos, Plateau State, Nigeria.
> Publications:  https://www.researchgate.net/profile/Emmanuel_Nnadi/publications <https://urldefense.proofpoint.com/v2/url?u=https-3A__www.researchgate.net_profile_Emmanuel-5FNnadi_publications&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=7rmmgamH7FxikQu8KYDcWQ&m=msPeT4AvwkrDUCIhCkT2pdBnv3544Aw7GH4-1EaBLTI&s=xZn3vRB6bh2Dmlo_j8z7oR65G_I__AaOd8cUEs1TIqA&e=>
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