Why does Maker-P output Match-part?

Question

[eennadi]

Hello, I am trying to annotate a genome using Marker-P. I trained SNAP twice. However, I keep getting this output match_part. Please does anyone have any idea why SNAP outputs match_part? How can SNAP be improved to give actual gene prediction and not match_part? This is affecting my downstream processing.

contig_844_pilon_pilon_pilon    maker   three_prime_UTR 78426   78543   .       +       .       ID=maker-contig_844_pilon_pilon_pilon-snap-gene-0.9-mRNA-1:three_prime_utr;Parent=mak
er-contig_844_pilon_pilon_pilon-snap-gene-0.9-mRNA-1
contig_844_pilon_pilon_pilon    snap_masked     match   3034    4761    -11.113 -       .       ID=contig_844_pilon_pilon_pilon:hit:2139958:4.5.0.0;Name=snap_masked-contig_844_pilon
_pilon_pilon-abinit-gene-0.5-mRNA-1;target_length=137831
contig_844_pilon_pilon_pilon    snap_masked     match_part      4756    4761    4.752   -       .       ID=contig_844_pilon_pilon_pilon:hsp:2546570:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139958:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.5-mRNA-1 247 252 +;Gap=M6
contig_844_pilon_pilon_pilon    snap_masked     match_part      3438    3467    -4.056  -       .       ID=contig_844_pilon_pilon_pilon:hsp:2546571:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139958:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.5-mRNA-1 217 246 +;Gap=M30
contig_844_pilon_pilon_pilon    snap_masked     match_part      3034    3249    -11.809 -       .       ID=contig_844_pilon_pilon_pilon:hsp:2546572:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139958:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.5-mRNA-1 1 216 +;Gap=M216
contig_844_pilon_pilon_pilon    snap_masked     match   8277    70209   38.02   +       .       ID=contig_844_pilon_pilon_pilon:hit:2139959:4.5.0.0;Name=snap_masked-contig_844_pilon
_pilon_pilon-abinit-gene-0.0-mRNA-1;target_length=137831
contig_844_pilon_pilon_pilon    snap_masked     match_part      8277    8283    0.381   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546573:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 1 7 +;Gap=M7
contig_844_pilon_pilon_pilon    snap_masked     match_part      10022   10063   22.205  +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546574:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 8 49 +;Gap=M42
contig_844_pilon_pilon_pilon    snap_masked     match_part      10376   10452   8.187   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546575:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 50 126 +;Gap=M77
contig_844_pilon_pilon_pilon    snap_masked     match_part      11500   12132   44.777  +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546576:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 127 759 +;Gap=M633
contig_844_pilon_pilon_pilon    snap_masked     match_part      65704   65857   13.256  +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546577:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 760 913 +;Gap=M154
contig_844_pilon_pilon_pilon    snap_masked     match_part      66366   66479   20.228  +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546578:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 914 1027 +;Gap=M114
contig_844_pilon_pilon_pilon    snap_masked     match_part      67420   67468   1.301   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546579:4.5.0.0;Parent=contig_844_pilon_p
ilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 1028 1076 +;Gap=M49
contig_844_pilon_pilon_pilon    snap_masked     match_part      68142   68984   -81.985 +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546580:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 1077 1919 +;Gap=M843
contig_844_pilon_pilon_pilon    snap_masked     match_part      70197   70209   9.670   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546581:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2139959:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.0-mRNA-1 1920 1932 +;Gap=M13
contig_844_pilon_pilon_pilon    snap_masked     match   73499   74007   16.582  +       .       ID=contig_844_pilon_pilon_pilon:hit:2139960:4.5.0.0;Name=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1;target_length=137831
contig_844_pilon_pilon_pilon    snap_masked     match_part      73499   73503   5.483   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546582:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2139960:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 1 5 +;Gap=M5
contig_844_pilon_pilon_pilon    snap_masked     match_part      73517   73898   4.058   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546583:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2139960:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 6 387 +;Gap=M382
contig_844_pilon_pilon_pilon    snap_masked     match_part      73993   74007   7.041   +       .       ID=contig_844_pilon_pilon_pilon:hsp:2546584:4.5.0.0;Parent=contig_844_pilon_pilon_pilon:hit:2139960:4.5.0.0;Target=snap_masked-contig_844_pilon_pilon_pilon-abinit-gene-0.1-mRNA-1 388 402 +;Gap=M15

[liorglic]

Can you please reformat your MAKER output as blockquote or code? it's impossible to read as it is now...

[eennadi]

Thanks @juke34

Here is the maker control option is used

#-----Genome (these are always required)
genome= ~/Flye_racon3_pilon3.fasta #genome sequence (fasta file or fasta embeded in GFF3 file)
organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

#-----Re-annotation Using MAKER Derived GFF3
maker_gff= #MAKER derived GFF3 file
est_pass=0 #use ESTs in maker_gff: 1 = yes, 0 = no
altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no
protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no
rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no
model_pass=0 #use gene models in maker_gff: 1 = yes, 0 = no
pred_pass=0 #use ab-initio predictions in maker_gff: 1 = yes, 0 = no
other_pass=0 #passthrough anyything else in maker_gff: 1 = yes, 0 = no

#-----EST Evidence (for best results provide a file for at least one)
est=~/maker/EST_Fabaceae.fasta,~/emmanuel/maker/GENV01.1_transcrptomedata.fa  #set of ESTs or assembled mRNA-seq in fasta format
altest= #EST/cDNA sequence file in fasta format from an alternate organism
est_gff= #aligned ESTs or mRNA-seq from an external GFF3 file
altest_gff= #aligned ESTs from a closly relate species in GFF3 format

#-----Protein Homology Evidence (for best results provide a file for at least one)
protein=~/Makersupport/uniprot-fabaceae-filtered-reviewed_18_05_2020.fasta  #protein sequence file in fasta format (i.e. from mutiple organisms)
protein_gff=  #aligned protein homology evidence from an external GFF3 file

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org= #select a model organism for RepBase masking in RepeatMasker
rmlib=~/maker/Fabacae_repeat.fa #provide an organism specific repeat library in fasta format for RepeatMasker
repeat_protein=  #provide a fasta file of transposable element proteins for RepeatRunner
rm_gff= #pre-identified repeat elements from an external GFF3 file
prok_rm=0 #forces MAKER to repeatmask prokaryotes (no reason to change this), 1 = yes, 0 = no
softmask=1 #use soft-masking rather than hard-masking in BLAST (i.e. seg and dust filtering)

#-----Gene Prediction
snaphmm=~/maker/Mucuna_2020_05_18/annotation_combined_repeats/mucuna_snap_2/mucuna_snap2.hmm  #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=  #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff= #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
run_evm=0 #run EvidenceModeler, 1 = yes, 0 = no
est2genome=0 #infer gene predictions directly from ESTs, 1 = yes, 0 = no
protein2genome=0 #infer predictions from protein homology, 1 = yes, 0 = no
trna=1 #find tRNAs with tRNAscan, 1 = yes, 0 = no
snoscan_rrna= #rRNA file to have Snoscan find snoRNAs
snoscan_meth= #-O-methylation site fileto have Snoscan find snoRNAs
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no
allow_overlap= #allowed gene overlap fraction (value from 0 to 1, blank for default)

#-----MAKER Behavior Options
max_dna_len=100000 #length for dividing up contigs into chunks (increases/decreases memory usage)
min_contig=1 #skip genome contigs below this length (under 10kb are often useless)

pred_flank=200 #flank for extending evidence clusters sent to gene predictors
pred_stats=0 #report AED and QI statistics for all predictions as well as models
AED_threshold=1 #Maximum Annotation Edit Distance allowed (bound by 0 and 1)
min_protein=0 #require at least this many amino acids in predicted proteins
alt_splice=0 #Take extra steps to try and find alternative splicing, 1 = yes, 0 = no
always_complete=0 #extra steps to force start and stop codons, 1 = yes, 0 = no
map_forward=0 #map names and attributes forward from old GFF3 genes, 1 = yes, 0 = no
keep_preds=0 #Concordance threshold to add unsupported gene prediction (bound by 0 and 1)

[GenoMax]

eennadi : Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is for new answers to original question

[Juke34]

check your output to see if you have any gene model:

awk '{if($3 == "gene") print $0}' maker_file.gff | wc -l

Answer 1

[Juke34]

match / match_part from SNAP are the pure snap prediction not yet processed by MAKER. MAKER will make gene models from it according to parameters you have set. E.g. if keep_preds option is set to 0, MAKER will select the gene models in agreement with the available extrinsic evidence (protein / transcript alignments). In this case if you didn't provide any extrinsic evidence then no gene models will be selected/created by MAKER.

I might suggest to use maker_merge_outputs_from_datastore.pl from GAAS to collect the MAKER output. Here is explained the MAKER output.

Answer 2

[liorglic]

There is nothing wrong with having match and match_part features in your output gff - these are simply the "evidence" from which MAKER synthesizes gene models. In many cases they are not needed, so to get a gff containing only gene models you can use: gff3_merge -d <data store index> -n -g.