[maker-devel] failed to assign putative gene function

[Quanwei Zhang]

Hello:

I am trying to add putative gene function to the predicted gene models.
Firstly, I use uniProt/Swiss-Prot protein sequences to build the database.
I used canonical and isoform proteins of human, mouse and rat with the
script "makeblastdb". Then use "blastp" generated "maker2uni.blastp" whose
context is as below.
maker-CasCan_contig_64815-snap-gene-0.0-mRNA-1    sp|Q6P5S2|LEG1H_HUMAN
 69.97    303    91    0    1    303    1    303    7e-164    464
snap_masked-CasCan_contig_14203-processed-gene-0.10-mRNA-1
 sp|Q91ZA8|NRARP_MOUSE    99.12    114    1    0    1    114    1    114
 3e-80    236

After that, I am trying to add the protein homology data to the Maker gff3
and fasta files with maker_functional_gff and maker_functional_fasta, but
get the reports as below.

Can't parse details from FASTA header: >sp|Q7Z5M8-2|AB12B_HUMAN Isoform 2
of Protein ABHD12B OS=Homo sapiens GN=ABHD12B

Use of uninitialized value $id in hash element at
/public/apps/MAKER/2.31.9/bin/maker_functional_gff line 139, <$IN> line 39.
Use of uninitialized value $id in hash element at
/public/apps/MAKER/2.31.9/bin/maker_functional_gff line 141, <$IN> line 39.
Can't parse details from FASTA header: >sp|Q7Z5M8-4|AB12B_HUMAN Isoform 4
of Protein ABHD12B OS=Homo sapiens GN=ABHD12B

Use of uninitialized value $id in hash element at
/public/apps/MAKER/2.31.9/bin/maker_functional_gff line 139, <$IN> line 45.
Use of uninitialized value $id in hash element at
/public/apps/MAKER/2.31.9/bin/maker_functional_gff line 141, <$IN> line 45.
Can't parse details from FASTA header: >sp|Q7Z5M8-5|AB12B_HUMAN Isoform 5
of Protein ABHD12B OS=Homo sapiens GN=ABHD12B
.....

I am not sure how to deal with this. I followed the command given in the
protocol. Any suggestions?

Thanks

Best
Quanwei
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20170213/bce234f9/attachment-0002.html>