I am trying to do a second round of maker genome annotation with ab initio prediction by snap.
The error I am getting is as follows:
error: unknown command "genome.hmm", see 'snap help'.
ERROR: Snap failed
--> rank=NA, hostname=bioinformatics
ERROR: Failed while preparing ab-inits
ERROR: Chunk failed at level:0, tier_type:2
FAILED CONTIG:tig00000009
For every single contig.
Running snap standalone with the same hmm file works fine, with this command:
snap genome.hmm genome.fa
I made the hmm file with the following commands:
../maker2zff -d genome_index.log
fathom genome.ann genome.dna -gene-stats > gene-stats.log 2>&1
fathom genome.ann genome.dna -validate > validate.log 2>&1
fathom genome.ann genome.dna -categorize 1000 > categorize.log 2>&1
fathom uni.ann uni.dna -export 1000 -plus > uni-plus.log 2>&1
mkdir params/
cd params/
forge ../export.ann ../export.dna > ../forge.log 2>&1
cd ..
../snap/SNAP/hmm-assembler.pl genome params > genome.hmm
This is what the top of the hmm file looks like:
zoeHMM genome.all 6 8 6 7
<STATES>
Einit 0 0 3 -1 explicit
Esngl 0 0 150 -1 explicit
Eterm 0 0 3 -1 explicit
Exon 0 0 6 -1 explicit
Inter 0.9 0.9 0 0 geometric
Intron 0.1 0.1 0 0 geometric
<STATE_TRANSITIONS>
Einit Intron 1
Esngl Inter 1
Eterm Inter 1
Exon Intron 1
Inter Einit 0.949186
Inter Esngl 0.050814
Intron Eterm 0.256243
Intron Exon 0.743757
<PHASE_PREFERENCES>
0.431103
0.338360
0.230537
0.626318
0.196158
0.177524
0.584598
0.233223
0.182178
0.611959
0.195929
0.192112
0.740282
0.259718
0.747634
0.252366
0.745197
0.254803
<STATE_DURATIONS>
Einit 2
DEFINED 0 249
-8.559 -8.500 -8.444 -8.389 -8.337
-8.286 -8.237 -8.189 -8.144 -8.099
-8.056 -8.024 -7.992 -7.962 -7.932
-7.902 -7.873 -7.845 -7.817 -7.790
-7.763 -7.760 -7.757 -7.754 -7.751
-7.748 -7.745 -7.741 -7.738 -7.735
-7.732 -7.729 -7.726 -7.722 -7.719
-7.716 -7.712 -7.709 -7.706 -7.702
-7.699 -7.699 -7.699 -7.699 -7.699
-7.699 -7.699 -7.699 -7.699 -7.699
-7.699 -7.698 -7.697 -7.697 -7.696
-7.695 -7.694 -7.693 -7.692 -7.691
-7.691 -7.694 -7.698 -7.701 -7.705
-7.708 -7.712 -7.716 -7.719 -7.723
-7.726 -7.731 -7.736 -7.741 -7.746
-7.751 -7.755 -7.760 -7.765 -7.770
-7.775 -7.780 -7.784 -7.789 -7.793
-7.798 -7.802 -7.807 -7.812 -7.816
-7.821 -7.828 -7.835 -7.842 -7.850
The maker_opts file:
genome= genome.fa
organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic
maker_gff= genome.all.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=
altest= #EST/cDNA sequence file in fasta format from an alternate organism
est_gff= genome_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=
protein_gff=genome_protein2genome.gff #aligned protein homology evid$
model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib= #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= genome_repeat.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)
snaphmm=genome.hmm
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=0 #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)
other_gff= #extra features to pass-through to final MAKER generated GFF3 file
I’m honestly losing my mind I’ve been struggling with this error for two days.