nextgenusfs
funannotate remote
Are you using the latest release? Yes, we used the latest version 1.8.9
Describe the bug when we finished funannotate predict and funannotate iprscan, and begin to funannotate remote, the error happened
What command did you issue? funannotate remote -i ./fun -m all -o ./fun -e [email protected]
Logfiles
$funannotate predict -i Genomic_masked2.fna --species "Phlebopus portentosus" -o ./fun --busco_seed_species anidulans --busco_db dikarya --min_training_models 150 --cpus 80 --name PhPo
[Apr 18 11:43 AM]: OS: CentOS Linux 7, 80 cores, ~ 1584 GB RAM. Python: 3.7.12
[Apr 18 11:43 AM]: Running funannotate v1.8.9
[Apr 18 11:43 AM]: Skipping CodingQuarry as no --rna_bam passed
[Apr 18 11:43 AM]: Parsed training data, run ab-initio gene predictors as follows:
Program Training-Method
augustus busco
genemark selftraining
glimmerhmm busco
snap busco
[Apr 18 11:43 AM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Apr 18 11:43 AM]: Genome loaded: 62 scaffolds; 32,742,503 bp; 13.72% repeats masked
[Apr 18 11:44 AM]: Mapping 553,202 proteins to genome using diamond and exonerate
[Apr 18 12:30 PM]: Found 247,029 preliminary alignments --> aligning with exonerate
[Apr 18 01:00 PM]: Exonerate finished: found 819 alignments
[Apr 18 01:01 PM]: Running GeneMark-ES on assembly
[Apr 18 01:15 PM]: 10,141 predictions from GeneMark
[Apr 18 01:15 PM]: Running BUSCO to find conserved gene models for training ab-initio predictors
[Apr 18 01:20 PM]: 1,062 valid BUSCO predictions found, validating protein sequences
[Apr 18 01:22 PM]: 1,055 BUSCO predictions validated
[Apr 18 01:22 PM]: Training Augustus using BUSCO gene models
[Apr 18 01:23 PM]: Augustus initial training results:
Feature Specificity Sensitivity
nucleotides 97.3% 87.3%
exons 75.3% 70.6%
genes 41.5% 30.6%
[Apr 18 01:23 PM]: Accuracy seems low, you can try to improve by passing the --optimize_augustus option.
[Apr 18 01:23 PM]: Running Augustus gene prediction using phlebopus_portentosus parameters
[Apr 18 01:23 PM]: 6,885 predictions from Augustus
[Apr 18 01:23 PM]: Pulling out high quality Augustus predictions
[Apr 18 01:23 PM]: Found 3 high quality predictions from Augustus (>90% exon evidence)
[Apr 18 01:23 PM]: Running SNAP gene prediction, using training data: ./fun/predict_misc/busco.final.gff3
[Apr 18 01:25 PM]: 50 predictions from SNAP
[Apr 18 01:25 PM]: Running GlimmerHMM gene prediction, using training data: ./fun/predict_misc/busco.final.gff3
[Apr 18 01:37 PM]: 11,194 predictions from GlimmerHMM
[Apr 18 01:37 PM]: Summary of gene models passed to EVM (weights):
Source Weight Count
Augustus 1 6882
Augustus HiQ 2 3
GeneMark 1 10141
GlimmerHMM 1 11194
snap 1 50
Total - 28270
[Apr 18 01:37 PM]: EVM: partitioning input to ~ 35 genes per partition using min 1500 bp interval
[Apr 18 01:39 PM]: Converting to GFF3 and collecting all EVM results
[Apr 18 01:39 PM]: 9,029 total gene models from EVM
[Apr 18 01:39 PM]: Generating protein fasta files from 9,029 EVM models
[Apr 18 01:39 PM]: now filtering out bad gene models (< 50 aa in length, transposable elements, etc).
[Apr 18 01:40 PM]: Found 271 gene models to remove: 5 too short; 0 span gaps; 266 transposable elements
[Apr 18 01:40 PM]: 8,758 gene models remaining
[Apr 18 01:40 PM]: Predicting tRNAs
[Apr 18 01:42 PM]: 100 tRNAscan models are valid (non-overlapping)
[Apr 18 01:42 PM]: Generating GenBank tbl annotation file
[Apr 18 01:42 PM]: Collecting final annotation files for 8,858 total gene models
[Apr 18 01:42 PM]: Converting to final Genbank format
[Apr 18 01:43 PM]: Funannotate predict is finished, output files are in the ./fun/predict_results folder
[Apr 18 01:43 PM]: Your next step might be functional annotation, suggested commands:
Run InterProScan (manual install): funannotate iprscan -i ./fun -c 80
Run antiSMASH (optional): funannotate remote -i ./fun -m antismash -e [email protected]
Annotate Genome: funannotate annotate -i ./fun --cpus 80 --sbt yourSBTfile.txt
[Apr 18 01:43 PM]: Training parameters file saved: ./fun/predict_results/phlebopus_portentosus.parameters.json [Apr 18 01:43 PM]: Add species parameters to database:
funannotate species -s phlebopus_portentosus -a ./fun/predict_results/phlebopus_portentosus.parameters.json
$funannotate iprscan -i ./fun -m local --iprscan_path /public/home/liuyuanchao/software/InterProScan/interproscan-5.53-87.0/interproscan.sh --cpus 100 Running InterProScan5 on 8758 proteins Important: you need to manually configure your interproscan.properties file for embedded workers. Will try to launch 100 interproscan processes, adjust -c,--cpus for your system InterProScan5 search has completed successfully! Results are here: ./fun/annotate_misc/iprscan.xml
$funannotate remote -i ./fun -m all -o ./fun -e [email protected]
[Apr 18 04:26 PM]: OS: CentOS Linux 7, 20 cores, ~ 131 GB RAM. Python: 3.7.12
[Apr 18 04:26 PM]: Running 1.8.9
[Apr 18 04:26 PM]: Output directory ./fun already exists, will use any existing data. If this is not what you want, exit, and provide a unique name for output folder
[Apr 18 04:26 PM]: Parsing input files
[Apr 18 04:26 PM]: Predicting secreted and transmembrane proteins using Phobius
[Apr 18 04:28 PM]: Connecting to antiSMASH fungi v6 webserver
[Apr 18 04:28 PM]: Queue Length: 0; Jobs Running: 31
[Apr 18 04:28 PM]: PLEASE to not abuse the webserver, be considerate!
[Apr 18 04:28 PM]: Uploading /public/home/liuyuanchao/funannotate_analysis/Phlebopus_portentosus/fun/predict_results/Phlebopus_portentosus.gbk to webserver
Traceback (most recent call last):
File "/public/home/liuyuanchao/software/anaconda3/envs/funannotate/bin/funannotate", line 10, in
OS/Install Information
- output of
funannotate check --show-versions$funannotate check --show-versions
Checking dependencies for 1.8.9
You are running Python v 3.7.12. Now checking python packages... biopython: 1.77 goatools: 1.1.6 matplotlib: 3.4.3 natsort: 8.0.0 numpy: 1.21.4 pandas: 1.3.4 psutil: 5.8.0 requests: 2.26.0 scikit-learn: 1.0.1 scipy: 1.7.0 seaborn: 0.11.2 All 11 python packages installed
You are running Perl v b'5.026002'. Now checking perl modules... Bio::Perl: 1.007002 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 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/public/home/liuyuanchao/software/funannotate/database $PASAHOME=/public/home/liuyuanchao/software/anaconda3/envs/funannotate/opt/pasa-2.4.1 $TRINITY_HOME=/public/home/liuyuanchao/software/anaconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/public/home/liuyuanchao/software/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/public/home/liuyuanchao/software/anaconda3/envs/funannotate/config/ ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v36 diamond: 2.0.13 emapper.py: 2.1.3 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.68_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.490 (2021/Oct/30) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.22-r1101 proteinortho: 6.0.31 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.12 signalp: 5.0b snap: 2006-07-28 stringtie: 2.1.7 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 26 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 36 external dependencies are installed
