Open wangpeng-design opened 2 weeks ago
thats an augustus parameter not a funannotate parameter so you should not provide it.
The directions which mention that cmdline parameter are telling you how to run augustus OUTSIDE of funannotate and then provide a GFF file to funannotate if you want to do it in your own way. However if you are running funannotate normally where it will train and run augustus for your automatically then this parameter is already sent to augustus.
here are all the cmdline options to predict:
funannotate predict
Usage: funannotate predict <arguments>
version: 1.8.17
Description: Script takes genome multi-fasta file and a variety of inputs to do a comprehensive whole
genome gene prediction. Uses AUGUSTUS, GeneMark, Snap, GlimmerHMM, BUSCO, EVidence Modeler,
tbl2asn, tRNAScan-SE, Exonerate, minimap2.
Required:
-i, --input Genome multi-FASTA file (softmasked repeats)
-o, --out Output folder name
-s, --species Species name, use quotes for binomial, e.g. "Aspergillus fumigatus"
Optional:
-p, --parameters Ab intio parameters JSON file to use for gene predictors
--isolate Isolate name, e.g. Af293
--strain Strain name, e.g. FGSCA4
--name Locus tag name (assigned by NCBI?). Default: FUN_
--numbering Specify where gene numbering starts. Default: 1
--maker_gff MAKER2 GFF file. Parse results directly to EVM.
--pasa_gff PASA generated gene models. filename:weight
--other_gff Annotation pass-through to EVM. filename:weight
--rna_bam RNA-seq mapped to genome to train Augustus/GeneMark-ET
--stringtie StringTie GTF result
-w, --weights Ab-initio predictor and EVM weight. Example: augustus:2 or pasa:10
--augustus_species Augustus species config. Default: uses species name
--min_training_models Minimum number of models to train Augustus. Default: 200
--genemark_mode GeneMark mode. Default: ES [ES,ET]
--genemark_mod GeneMark ini mod file
--busco_seed_species Augustus pre-trained species to start BUSCO. Default: anidulans
--optimize_augustus Run 'optimze_augustus.pl' to refine training (long runtime)
--busco_db BUSCO models. Default: dikarya. `funannotate outgroups --show_buscos`
--organism Fungal-specific options. Default: fungus. [fungus,other]
--ploidy Ploidy of assembly. Default: 1
-t, --tbl2asn Assembly parameters for tbl2asn. Default: "-l paired-ends"
-d, --database Path to funannotate database. Default: $FUNANNOTATE_DB
--protein_evidence Proteins to map to genome (prot1.fa prot2.fa uniprot.fa). Default: uniprot.fa
--protein_alignments Pre-computed protein alignments in GFF3 format
--p2g_pident Exonerate percent identity. Default: 80
--p2g_diamond_db Premade diamond genome database for protein2genome mapping
--p2g_prefilter Pre-filter hits software selection. Default: diamond [tblastn]
--transcript_evidence mRNA/ESTs to align to genome (trans1.fa ests.fa trinity.fa). Default: none
--transcript_alignments Pre-computed transcript alignments in GFF3 format
--augustus_gff Pre-computed AUGUSTUS GFF3 results (must use --stopCodonExcludedFromCDS=False)
--genemark_gtf Pre-computed GeneMark GTF results
--trnascan Pre-computed tRNAscanSE results
--min_intronlen Minimum intron length. Default: 10
--max_intronlen Maximum intron length. Default: 3000
--soft_mask Softmasked length threshold for GeneMark. Default: 2000
--min_protlen Minimum protein length. Default: 50
--repeats2evm Use repeats in EVM consensus model building
--keep_evm Keep existing EVM results (for rerunning pipeline)
--evm-partition-interval Min length between genes to make a partition: Default: 1500
--no-evm-partitions Do not split contigs into partitions
--repeat_filter Repetitive gene model filtering. Default: overlap blast [overlap,blast,none]
--keep_no_stops Keep gene models without valid stops
--SeqCenter Sequencing facilty for NCBI tbl file. Default: CFMR
--SeqAccession Sequence accession number for NCBI tbl file. Default: 12345
--force Annotated unmasked genome
--cpus Number of CPUs to use. Default: 2
--no-progress Do not print progress to stdout for long sub jobs
--tmpdir Volume/location to write temporary files. Default: /tmp
--header_length Maximum length of FASTA headers. Default: 16
ENV Vars: If not specified at runtime, will be loaded from your $PATH
--EVM_HOME
--AUGUSTUS_CONFIG_PATH
--GENEMARK_PATH
--BAMTOOLS_PATH
Thank you!
Are you using the latest release? If you are not using the latest release of funannotate, please upgrade, if bug persists then report here. v1.8.13 Describe the bug A clear and concise description of what the bug is. funannotate-predict.py: error: unrecognized arguments: --stopCodonExcludedFromCDS=False What command did you issue? Copy/paste the command used. funannotate predict -i PGChrGenome.softmask.fasta --species "Pleurotus ostreatus" --transcript_alignments transcript_alignments.gff3:8 --protein_alignments protein_alignments.gff:4 --augustus_gff gene_predictions.gff:1 --trnascan tRNA.out -o output_folder --stopCodonExcludedFromCDS=False Logfiles Please provide relavent log files of the error.
OS/Install Information
output of
funannotate check --show-versions
Checking dependencies for 1.8.13
You are running Python v 3.8.15. Now checking python packages... biopython: 1.83 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.4.0 numpy: 1.24.3 pandas: 1.4.2 psutil: 6.0.0 requests: 2.32.3 scikit-learn: 1.1.1 scipy: 1.10.1 seaborn: 0.13.2 All 11 python packages installed
You are running Perl v b'5.026002'. Now checking perl modules... Carp: 1.38 Clone: 0.42 DBD::SQLite: 1.64 DBD::mysql: 4.046 DBI: 1.642 DB_File: 1.855 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.300 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.12 Tie::File: 1.02 URI::Escape: 3.31 YAML: 1.29 threads: 2.15 threads::shared: 1.56 ERROR: local::lib not installed, install with cpanm local::lib
Checking Environmental Variables... $FUNANNOTATE_DB=/public/home/bs20233171040/Genomic_data/funannotate_db $PASAHOME=/public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/opt/pasa-2.4.1 $TRINITY_HOME=/public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/config/ $GENEMARK_PATH=/public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/bin/gmes_petap.pl All 6 environmental variables are set
Checking external dependencies... samtools: /public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/bin/../lib/libtinfow.so.6: no version information available (required by samtools) samtools: /public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/bin/../lib/libncursesw.so.6: no version information available (required by samtools) samtools: /public/home/bs20233171040/$/public/home/bs20233171040/software/anaconda3/envs/funannotate/bin/../lib/libncursesw.so.6: no version information available (required by samtools) PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.4.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.1.8 emapper.py: 2.1.12 ete3: 3.1.3 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 gmes_petap.pl: 4.33 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.9.1-internal kallisto: 0.46.1 mafft: v7.525 (2024/Mar/13) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.28-r1209 pigz: pigz 2.8 proteinortho: 6.0.34 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.15.1 signalp: environment. snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 31 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 All 37 external dependencies are installed