funannotate predict failed

[gengce]

---

Checking dependencies for 1.8.9

You are running Python v 3.7.10. Now checking python packages... biopython: 1.76 goatools: 1.0.15 matplotlib: 3.4.1 natsort: 7.1.1 numpy: 1.20.2 pandas: 1.2.4 psutil: 5.7.0 requests: 2.25.1 scikit-learn: 0.24.1 scipy: 1.6.2 seaborn: 0.11.1 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=/home/train/DATA/funDB $PASAHOME=/opt/biosoft/miniconda/envs/funannotate/fun3/opt/pasa-2.4.1 $TRINITY_HOME=/opt/biosoft/miniconda/envs/funannotate/fun3/opt/trinity-2.8.5 $EVM_HOME=/opt/biosoft/miniconda/envs/funannotate/fun3/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/opt/biosoft/miniconda/envs/funannotate/fun3/config/ $GENEMARK_PATH=/opt/biosoft/gm_et_linux_64/gmes_linux_64:/opt/biosoft/eggnog-mapper:/opt/biosoft/miniconda/envs/funannotate/fun3/bin:/opt/biosoft/eggnog-mapper:/opt/biosoft/eggnog-mapper:/home/miniconda3/condabin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/bin:/bin:/opt/biosoft/gm_et_linux_64/gmes_linux_64:/root/bin All 6 environmental variables are set

Checking external dependencies... File "/opt/biosoft/eggnog-mapper/emapper.py", line 64 print dbpath ^ SyntaxError: Missing parentheses in call to 'print'. Did you mean print(dbpath)? 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 v36 diamond: 2.0.11 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 gmes_petap.pl: 4.65_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.1 kallisto: 0.46.1 mafft: v7.475 (2020/Nov/23) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.18-r1015 proteinortho: 6.0.30 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.12 signalp: 4.1 snap: 2006-07-28 stringtie: 2.1.5 tRNAscan-SE: 2.0.7 (Oct 2020) 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 ERROR: emapper.py not installed

[08/24/21 08:11:23]: /opt/biosoft/miniconda/envs/funannotate/fun3/bin/funannotate predict -i Aspcad1mask -o Aspcad1predict --busco_seed_species=aspergillus_oryzae -s Aspergillus candidus --name ASPcad1 --genemark_gtf genemark.gtf --cpus 30

[08/24/21 08:11:23]: OS: CentOS 6.10, 80 cores, ~ 529 GB RAM. Python: 3.7.10 [08/24/21 08:11:23]: Running funannotate v1.8.9 [08/24/21 08:11:24]: GeneMark path: /opt/biosoft/gm_et_linux_64/gmes_linux_64:/opt/biosoft/eggnog-mapper:/opt/biosoft/miniconda/envs/funannotate/fun3/bin:/opt/biosoft/eggnog-mapper:/opt/biosoft/eggnog-mapper:/home/miniconda3/condabin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/bin:/bin:/opt/biosoft/gm_et_linux_64/gmes_linux_64:/root/bin [08/24/21 08:11:24]: Full path to gmes_petap.pl: /opt/biosoft/gm_et_linux_64/gmes_linux_64:/opt/biosoft/eggnog-mapper:/opt/biosoft/miniconda/envs/funannotate/fun3/bin:/opt/biosoft/eggnog-mapper:/opt/biosoft/eggnog-mapper:/home/miniconda3/condabin:/usr/lib64/qt-3.3/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/bin:/bin:/opt/biosoft/gm_et_linux_64/gmes_linux_64:/root/bin/gmes_petap.pl [08/24/21 08:11:24]: GeneMark appears to be functional? False [08/24/21 08:11:24]: {'augustus': 1, 'hiq': 2, 'genemark': 0, 'pasa': 6, 'codingquarry': 0, 'snap': 1, 'glimmerhmm': 1, 'proteins': 1, 'transcripts': 1} [08/24/21 08:11:24]: Skipping CodingQuarry as no --rna_bam passed [08/24/21 08:11:24]: {'augustus': 'busco', 'snap': 'busco', 'glimmerhmm': 'busco'} [08/24/21 08:11:24]: Parsed training data, run ab-initio gene predictors as follows: [08/24/21 08:11:26]: {'augustus': 1, 'hiq': 2, 'genemark': 0, 'pasa': 6, 'codingquarry': 0, 'snap': 1, 'glimmerhmm': 1, 'proteins': 1, 'transcripts': 1} [08/24/21 08:11:34]: Loading genome assembly and parsing soft-masked repetitive sequences [08/24/21 08:11:36]: Genome loaded: 268 scaffolds; 27,317,772 bp; 5.38% repeats masked [08/24/21 08:11:47]: Existing protein alignments found: Aspcad1predict/predict_misc/protein_alignments.gff3 [08/24/21 08:11:48]: join_mult_hints.pl [08/24/21 08:11:48]: /opt/biosoft/miniconda/envs/funannotate/fun3/lib/python3.7/site-packages/funannotate/aux_scripts/genemark_gtf2gff3.pl genemark.gtf [08/24/21 08:11:49]: perl /opt/biosoft/miniconda/envs/funannotate/fun3/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl Aspcad1predict/predict_misc/genemark.gff [08/24/21 08:11:52]: Existing BUSCO results found: Aspcad1predict/predict_misc/busco.final.gff3 containing 1 predictions [08/24/21 08:11:52]: Not enough gene models 1 to train Augustus (200 required), exiting

can you help me to find why "No enough gene model happen",

[nextgenusfs]

Likely a few things.

1. GeneMark is not installed properly
2. Augustus 3.4 does not work with BUSCO in funannotate, use v3.3.3

[nhungdoan1905]

[Mar 25 12:25 PM]: Mapping 557,938 proteins to genome using diamond and exonerate [Mar 25 12:35 PM]: Found 281,811 preliminary alignments with diamond in 0:08:18 --> generated FASTA files for exonerate in 0:01:04 Progress: 281811 complete, 0 failed, 0 remaining [Mar 25 03:08 PM]: Exonerate finished in 2:33:17: found 2,006 alignments [Mar 25 03:08 PM]: Running BUSCO to find conserved gene models for training ab-initio predictors [Mar 25 03:56 PM]: 1,285 valid BUSCO predictions found, validating protein sequences [Mar 25 03:58 PM]: 1,283 BUSCO predictions validated [Mar 25 03:58 PM]: Training Augustus using BUSCO gene models [Mar 25 03:58 PM]: Augustus initial training results: Feature Specificity Sensitivity nucleotides 99.1% 95.5% exons 90.0% 83.3% genes 81.2% 67.1% [Mar 25 03:58 PM]: Running Augustus gene prediction using penicillin_herquei parameters Traceback (most recent call last): File "/datausers2/ibt/pbngoc/.local/lib/python3.8/site-packages/funannotate/aux_scripts/augustus_parallel.py", line 9, in from Bio import SeqIO ImportError: No module named Bio [Mar 25 03:58 PM]: CMD ERROR: perl /datausers2/ibt/pbngoc/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl /datausers2/ibt/pbngoc/data/12C_funannotate/predict_misc/augustus.gff3 [Mar 25 03:58 PM]: Error, cannot open file /datausers2/ibt/pbngoc/data/12C_funannotate/predict_misc/augustus.gff3 at /datausers2/ibt/pbngoc/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl line 23.

i got these err when running funannotate, how can i solve it