MAKER genome annotation error with SNAP ab initio prediction
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Entering edit mode
9 weeks ago
sorrymouse ▴ 110

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 (these are always required)

genome= genome.fa organism_type=eukaryotic #eukaryotic or prokaryotic. Default is eukaryotic

-----Re-annotation Using MAKER Derived GFF3

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 Evidence (for best results provide a file for at least one)

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 Homology Evidence (for best results provide a file for at least one)

protein= protein_gff=genome_protein2genome.gff #aligned protein homology evid$

-----Repeat Masking (leave values blank to skip repeat masking)

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)

-----Gene Prediction

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 Annotation Feature Types (features MAKER doesn't recognize)

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.

SNAP annotation genome MAKER • 476 views
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What does your maker_exe.ctl look like? It could be that the path to SNAP isn't set correctly

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-----Location of Executables Used by MAKER/EVALUATOR

makeblastdb=/usr/bin/makeblastdb #location of NCBI+ makeblastdb executable blastn=/usr/bin/blastn #location of NCBI+ blastn executable blastx=/usr/bin/blastx #location of NCBI+ blastx executable tblastx=/usr/bin/tblastx #location of NCBI+ tblastx executable formatdb=/usr/bin/formatdb #location of NCBI formatdb executable blastall=/usr/bin/blastall #location of NCBI blastall executable xdformat= #location of WUBLAST xdformat executable blasta= #location of WUBLAST blasta executable prerapsearch= #location of prerapsearch executable rapsearch= #location of rapsearch executable RepeatMasker=/RepeatMasker/RepeatMasker #location of RepeatMasker executable exonerate=/usr/bin/exonerate #location of exonerate executable

-----Ab-initio Gene Prediction Algorithms

snap=snap/SNAP/snap #location of snap executable gmhmme3= #location of eukaryotic genemark executable gmhmmp= #location of prokaryotic genemark executable augustus=/usr/local/bin/augustus #location of augustus executable fgenesh= #location of fgenesh executable evm= #location of EvidenceModeler executable tRNAscan-SE= #location of trnascan executable snoscan= #location of snoscan executable

-----Other Algorithms

probuild= #location of probuild executable (required for genemark)

This is the location of the snap executable

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9 weeks ago
snap=snap/SNAP/snap

I think this is your problem in maker_exe.ctl - try setting this to the absolute path of snap, something like /usr/bin/snap, not snap/SNAP/snap. It could be that the error you're seeing in SNAP is not due to your hmm file being wrong, but due to MAKER failing to start SNAP in the first place.

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Amazingly when I tried this last night it did not work, yet as I desperately tried again this morning it appears to be running smoothly. Thank you!

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Great to hear :)

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