Error with Maker_functional_gff

classic Classic list List threaded Threaded
2 messages Options
Reply | Threaded
Open this post in threaded view
|

Error with Maker_functional_gff

Emmanuel Nnadi
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.

_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
Reply | Threaded
Open this post in threaded view
|

Re: Error with Maker_functional_gff

Daniel Ence-2
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

~Daniel

On Oct 2, 2017, at 10:47 AM, Emmanuel Nnadi <[hidden email]> 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.

On Mon, Oct 2, 2017 at 2:17 PM, Daniel Ence <[hidden email]> 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
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 <[hidden email]> 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.




_______________________________________________
maker-devel mailing list
[hidden email]
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org