[maker-devel] Trouble using custom repeat library w/ Maker v2.31.10

[Martin, John]

Greetings,

     I'm trying to use a custom repeat library in a maker run being
performed on a ~400Mb worm genome.   I've successfully tested my
installation of maker v2.31.10 using a small set of 13 contigs from my
full assembly (~100kb or less) using the 'model_org=all' setting for the
RepeatMasker part of the maker_opts.ctl configuration.  But when I try
to feed maker my repeat library fasta file, maker errors out when trying
to repeatmask because its trying to run hmmpress on the fasta file I set
as 'rmlib=...'

     I've attached the 3 .ctl files I'm using.  I am not setting any
other command line arguments for maker, when I launch the jobs I just type:

maker

in the directory with those .ctl files.   The specific error message I
am getting appears inside each of the subdirectories of the datastore,
inside hmmPress.log files:

Error: File format problem in trying to open HMM file
/gscmnt/gc2732/mitrevalab/
USDA_Zarlenga/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/
SUPERNOVA_assembly/ANNOTATION/MAKER/maker_1/TMP_1/maker_sbWsNX/RM_416.MonJul1522
04492019/consensi.fa.classified.
Format tag is '>rnd-1_family-14#Unknown': unrecognized.
Current H3 format is 'HMMER3/f'. Previous H2/H3 formats also supported.

I am not sure why maker is trying to run hmmpress on the fasta file
entered for the 'rmlib' setting, which the documentation says should be
fasta.   I think hmmpress should be used on hmm files. Can someone help
me troubleshoot this problem?


Thanks,

John Martin


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#-----BLAST and Exonerate Statistics Thresholds
blast_type=ncbi+ #set to 'ncbi+', 'ncbi' or 'wublast'

pcov_blastn=0.8 #Blastn Percent Coverage Threhold EST-Genome Alignments
pid_blastn=0.85 #Blastn Percent Identity Threshold EST-Genome Aligments
eval_blastn=1e-10 #Blastn eval cutoff
bit_blastn=40 #Blastn bit cutoff
depth_blastn=0 #Blastn depth cutoff (0 to disable cutoff)

pcov_blastx=0.5 #Blastx Percent Coverage Threhold Protein-Genome Alignments
pid_blastx=0.4 #Blastx Percent Identity Threshold Protein-Genome Aligments
eval_blastx=1e-06 #Blastx eval cutoff
bit_blastx=30 #Blastx bit cutoff
depth_blastx=0 #Blastx depth cutoff (0 to disable cutoff)

pcov_tblastx=0.8 #tBlastx Percent Coverage Threhold alt-EST-Genome Alignments
pid_tblastx=0.85 #tBlastx Percent Identity Threshold alt-EST-Genome Aligments
eval_tblastx=1e-10 #tBlastx eval cutoff
bit_tblastx=40 #tBlastx bit cutoff
depth_tblastx=0 #tBlastx depth cutoff (0 to disable cutoff)

pcov_rm_blastx=0.5 #Blastx Percent Coverage Threhold For Transposable Element Masking
pid_rm_blastx=0.4 #Blastx Percent Identity Threshold For Transposbale Element Masking
eval_rm_blastx=1e-06 #Blastx eval cutoff for transposable element masking
bit_rm_blastx=30 #Blastx bit cutoff for transposable element masking

ep_score_limit=20 #Exonerate protein percent of maximal score threshold
en_score_limit=20 #Exonerate nucleotide percent of maximal score threshold
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#-----Genome (these are always required)
genome=Tcol_final_assembly.minsize_2000.fna.PART.1 #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= #set of ESTs or assembled mRNA-seq in fasta format
altest= #EST/cDNA sequence file in fasta format from an alternate organism
est_gff=/gscmnt/gc2732/mitrevalab/USDA/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/SUPERNOVA_assembly/ANNOTATION/MAKER/RNAseq_transcript_assembly_w_better_HiSat2_arguments_and_using_stringtie/Merged_StringTie_Transcripts.maker_gff3 #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=/gscmnt/gc2732/mitrevalab/USDA/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/SUPERNOVA_assembly/ANNOTATION/BRAKER2/evidence_protein/All_9_close_nematode.protein.faa  #protein sequence file in fasta format (i.e. from mutiple oransisms)
protein_gff=  #aligned protein homology evidence from an external GFF3 file

#-----Repeat Masking (leave values blank to skip repeat masking)
model_org=all #select a model organism for RepBase masking in RepeatMasker
rmlib=/gscmnt/gc2732/mitrevalab/USDA/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/SUPERNOVA_assembly/ANNOTATION/REPEAT_LIBRARY_std_RepeatModeler_install_bsub_pa4_spanhosts1_n5_249Gb/RM_1.TueMay281756062019/consensi.fa.classified #provide an organism specific repeat library in fasta format for RepeatMasker
repeat_protein=/usr/local/maker/data/te_proteins.fasta #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= #SNAP HMM file
gmhmm= #GeneMark HMM file
augustus_species=Trichostrongylus_colubriformis_assembly_rnaseq-train #Augustus gene prediction species model
fgenesh_par_file= #FGENESH parameter file
pred_gff=/gscmnt/gc2732/mitrevalab/USDA/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/SUPERNOVA_assembly/ANNOTATION/BRAKER2/braker2_run_rnaseq_only/braker/Trichostrongylus_colubriformis_assembly_rnaseq-train/augustus.hints.gff3 #ab-initio predictions from an external GFF3 file
model_gff= #annotated gene models from an external GFF3 file (annotation pass-through)
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
unmask=0 #also run ab-initio prediction programs on unmasked sequence, 1 = yes, 0 = no

#-----Other Annotation Feature Types (features MAKER doesn't recognize)
other_gff= #extra features to pass-through to final MAKER generated GFF3 file

#-----External Application Behavior Options
alt_peptide=C #amino acid used to replace non-standard amino acids in BLAST databases
cpus=1 #max number of cpus to use in BLAST and RepeatMasker (not for MPI, leave 1 when using MPI)

#-----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=25 #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)

split_hit=10000 #length for the splitting of hits (expected max intron size for evidence alignments)
single_exon=0 #consider single exon EST evidence when generating annotations, 1 = yes, 0 = no
single_length=250 #min length required for single exon ESTs if 'single_exon is enabled'
correct_est_fusion=0 #limits use of ESTs in annotation to avoid fusion genes

tries=2 #number of times to try a contig if there is a failure for some reason
clean_try=0 #remove all data from previous run before retrying, 1 = yes, 0 = no
clean_up=0 #removes theVoid directory with individual analysis files, 1 = yes, 0 = no
TMP=/gscmnt/gc2732/mitrevalab/USDA/t_colubriformis/180530_assembly_and_annotation_PacBio_sequel_data/SUPERNOVA_assembly/ANNOTATION/MAKER/maker_1/TMP_1 #specify a directory other than the system default temporary directory for temporary files
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#-----Location of Executables Used by MAKER/EVALUATOR
makeblastdb=/usr/local/rmblast-2.9.0/makeblastdb #location of NCBI+ makeblastdb executable
blastn=/usr/local/ncbi-blast-2.9.0+/bin/blastn #location of NCBI+ blastn executable
blastx=/usr/local/rmblast-2.9.0/blastx #location of NCBI+ blastx executable
tblastx=/usr/local/ncbi-blast-2.9.0+/bin/tblastx #location of NCBI+ tblastx executable
formatdb=/gsc/pkg/bio/blast/blast-2.2.26/bin/formatdb #location of NCBI formatdb executable
blastall=/gsc/pkg/bio/blast/blast-2.2.26/bin/blastall #location of NCBI blastall executable
xdformat=/gsc/pkg/bio/wu-blast/blast2_2006-05-04/xdformat #location of WUBLAST xdformat executable
blasta=/gsc/pkg/bio/wu-blast/blast2_2006-05-04/blasta #location of WUBLAST blasta executable
RepeatMasker=/usr/local/RepeatMasker/RepeatMasker #location of RepeatMasker executable
exonerate=/usr/local/exonerate-2.2.0-x86_64/bin/exonerate #location of exonerate executable

#-----Ab-initio Gene Prediction Algorithms
snap=/usr/local/snap/snap #location of snap executable
gmhmme3=/usr/local/gm_et_linux_64/gmes_petap/gmhmme3 #location of eukaryotic genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus=/usr/local/augustus.2.5.5/bin/augustus #location of augustus executable
fgenesh= #location of fgenesh executable
tRNAscan-SE= #location of trnascan executable
snoscan= #location of snoscan executable

#-----Other Algorithms
probuild=/usr/local/gm_et_linux_64/gmes_petap/probuild #location of probuild executable (required for genemark)