[maker-devel] Error with Maker_functional_gff

[Daniel Ence]

Hi Emmanuel, 

I can’t tell whether it’s will work from the blast lines that you sent. It will depend on the full headers in the fasta lines, which you’ll run after all the blasts are complete. 

Assembly isn’t really my expertise or the topic of this mailing list, but assembling your contigs into scaffolds would probably help your annotations by connecting some parts of genes that are broken across contigs, and will definitely help downstream analysis if you need to know which genes are located next to each other. 

How much improvement you can get by scaffolding depends on the type of sequence data you have. Each scaffolder makes assumptions and has requirements, and some assemblers like velvet and SOAPdenovo have scaffolding built into their algorithms. I’d recommend starting with a  review like this one: http://www.sciencedirect.com/science/article/pii/S1672022912000095 <http://www.sciencedirect.com/science/article/pii/S1672022912000095>

~Daniel

> On Oct 2, 2017, at 10:47 AM, Emmanuel Nnadi <eennadi at gmail.com> wrote:
> 
> Hello Daniel,
> 
> Thanks for the tip, I was able to download uniprot_swiss.fa I am currently running the blast now
> 
> it looks like this
> 
> MUCPR_041061-RA	sp|P10978|POLX_TOBAC	49.315	73	37	0	43	115	874	946	2.95e-14	71.6
> MUCPR_026643-RA	sp|Q00451|PRF1_SOLLC	86.207	87	11	1	243	328	257	343	3.65e-32	126
> 
> Is it ok?
> 
> I wish to ask, I did not assemble my contigs into scaffold before annotating would it affect the end result?
> 
> I wish to assemble my sequence into scaffold can you advice on the best software to use?
> 
> I attempted using SSPACE: a new stand-alone scaffolding tool for small and large genomes
> but am having problem with the library. Funny enough the software does not have support to solve problems
> 
> Thanks
> 
> 
> 
> 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://www.researchgate.net/profile/Emmanuel_Nnadi/publications>
> On Mon, Oct 2, 2017 at 2:17 PM, Daniel Ence <dandence at gmail.com <mailto:dandence at gmail.com>> wrote:
> 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 <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 <mailto: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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