[maker-devel] maker_functional_gff Error

[Paul Sheridan]

Dear MAKER Team,

I am running MAKER 2.31.10 a 32 core instance. I followed the Post
Processing of Annotations steps as described in the MAKER Tutorial for GMOD
Online Training 2014 as best I could, but I get an error when I run
maker_functional_gff. The commands in the order of execution and relevant
output are shown below.

Where did I do wrong?

# run blastp command
blastp -query genome.all.maker.proteins.fasta -db uniprot_sprot.fasta
-num_threads 32 -evalue 1e-6 -max_hsps 1 -max_target_seqs 1 -outfmt 6 -out
output.blastp

# run interproscan command
interproscan.sh -appl pfam -dp -f TSV -goterms -iprlookup -pa -t p -i
genome.all.maker.proteins.fasta -o output.iprscan

# create naming table
maker_map_ids --prefix ThuMac --justify 5  genome.all.gff > genome.all.map

# copy files for safe keeping
cp genome.all.gff genome.all.renamed.gff
cp genome.all.noseq.gff genome.all.noseq.renamed.gff
cp genome.all.maker.proteins.fasta genome.all.maker.proteins.renamed.fasta
cp genome.all.maker.proteins.aed.0.50.fasta
genome.all.maker.proteins.aed.0.50.renamed.fasta
cp genome.all.maker.unique.proteins.aed.0.50.fasta
genome.all.maker.unique.proteins.aed.0.50.renamed.fasta
cp genome.all.maker.transcripts.fasta
genome.all.maker.transcripts.renamed.fasta
cp genome.all.maker.transcripts.aed.0.50.fasta
genome.all.maker.transcripts.aed.0.50.renamed.fasta
cp output.iprscan output.renamed.iprscan
cp output.blastp output.renamed.blastp

# replace uninformative MAKER protein/transcript names with useful ones
map_gff_ids genome.all.map genome.all.renamed.gff
map_gff_ids genome.all.map genome.all.noseq.renamed.gff
map_fasta_ids genome.all.map genome.all.maker.proteins.renamed.fasta
map_fasta_ids genome.all.map
genome.all.maker.proteins.aed.0.50.renamed.fasta
map_fasta_ids genome.all.map
genome.all.maker.unique.proteins.aed.0.50.renamed.fasta
map_fasta_ids genome.all.map genome.all.maker.transcripts.renamed.fasta
map_fasta_ids genome.all.map
genome.all.maker.transcripts.aed.0.50.renamed.fasta
map_data_ids genome.all.map output.renamed.iprscan
map_data_ids genome.all.map output.renamed.blastp

# assign annotations
maker_functional_gff uniprot_sprot.db output.renamed.blastp
genome.all.renamed.gff > genome.all.renamed.putative_function.gff

> head output.renamed.blastp
ThuMac30929-RA P20036 41.791 134 77 1 326 458 113 246 9.51e-28 114
ThuMac19623-RA P81018 35.714 168 87 2 1 147 1 168 8.40e-33 117
ThuMac19629-RA Q66I51 68.939 264 79 2 1 263 1 262 1.48e-130 372
ThuMac19628-RA Q61464 55.172 87 37 1 766 852 382 466 4.42e-25 119
ThuMac19627-RA P07898 48.276 58 29 1 13 69 1962 2019 3.60e-13 65.9
ThuMac19626-RA P81018 36.782 174 96 2 21 180 1 174 5.75e-36 127
ThuMac19624-RA P81018 35.057 174 99 2 21 180 1 174 2.19e-33 120
ThuMac19625-RA Q28343 32.520 123 43 2 35 117 2123 2245 7.57e-17 78.6
ThuMac19636-RA Q9QX29 90.909 110 10 0 5 114 458 567 6.45e-65 216
ThuMac19638-RA Q9QX29 57.391 115 35 3 5 114 703 808 3.06e-28 120

> head output.renamed.iprscan
ThuMac08407-RA f1e60af0e3add9ce493bd7a78114da1e 631 Pfam PF00520 Ion
transport protein 154 413 3.8E-21 T 18-04-2019 IPR005821 Ion transport
domain GO:0005216|GO:0006811|GO:0016020|GO:0055085
ThuMac08407-RA f1e60af0e3add9ce493bd7a78114da1e 631 Pfam PF08412 Ion
transport protein N-terminal 109 152 5.1E-19 T 18-04-2019 IPR013621 Ion
transport N-terminal Reactome: R-HSA-1296061
ThuMac08407-RA f1e60af0e3add9ce493bd7a78114da1e 631 Pfam PF00027 Cyclic
nucleotide-binding domain 519 601 1.0E-17 T 18-04-2019 IPR000595 Cyclic
nucleotide-binding domain
ThuMac24094-RA f3c3ae9be61177558ac12f745bd0dd8e 414 Pfam PF13765
SPRY-associated
domain 235 283 8.9E-23 T 18-04-2019 IPR006574 SPRY-associated
ThuMac24094-RA f3c3ae9be61177558ac12f745bd0dd8e 414 Pfam PF00643 B-box zinc
finger 18 56 5.2E-12 T 18-04-2019 IPR000315 B-box-type zinc finger
GO:0008270
ThuMac24094-RA f3c3ae9be61177558ac12f745bd0dd8e 414 Pfam PF00622 SPRY domain
287 391 2.2E-14 T 18-04-2019 IPR003877 SPRY domain GO:0005515
ThuMac08369-RA 7aee1da5a47975ab8e43b68bfd1a117c 139 Pfam PF00076 RNA
recognition motif. (a.k.a. RRM, RBD, or RNP domain) 22 87 1.6E-15 T
18-04-2019 IPR000504 RNA recognition motif domain GO:0003676
ThuMac26054-RA 8f4119609312bd6442f8bb094c104231 462 Pfam PF07565 Band 3
cytoplasmic domain 173 443 7.3E-100 T 18-04-2019 IPR013769 Band 3
cytoplasmic domain GO:0006820|GO:0008509|GO:0016021 Reactome: R-HSA-425381
ThuMac07958-RA d2b749fa573a5e452cadee56090c9588 804 Pfam PF03372
Endonuclease/Exonuclease/phosphatase
family 235 535 7.0E-11 T 18-04-2019 IPR005135
Endonuclease/exonuclease/phosphatase
ThuMac07958-RA d2b749fa573a5e452cadee56090c9588 804 Pfam PF17751 SKICH
domain 555 649 9.8E-23 T 18-04-2019 IPR041611 SKICH domain

> map_data_ids genome.all.map output.renamed.iprscan
WARNING: No mapping available for ThuMac01937-RA
WARNING: No mapping available for ThuMac02226-RA
WARNING: No mapping available for ThuMac20730-RA
WARNING: No mapping available for ThuMac20730-RA
WARNING: No mapping available for ThuMac14750-RA
(Thousands of warnings like these were returned)

> maker_functional_gff uniprot_sprot.db output.renamed.blastp
genome.all.renamed.gff > genome.all.renamed.putative_function.gff
Can't use string ("") as a HASH ref while "strict refs" in use at
/root/maker/bin/maker_functional_gff line 55, <$IN> line 3.

> head genome.all.renamed.putative_function.gff
##gff-version 3
scf7180000008677_pilon_pilon . contig 1 49996 . . .
ID=scf7180000008677_pilon_pilon;Name=scf7180000008677_pilon_pilon

Thanks in Advance,

Paul Sheridan

-- 
CSO at Tupac Bio
Email: paul at tupac.bio
Homepage: www.paulsheridan.net
Mobile: +81 80 7889 0859
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