danielabermeo8
commented
1 month ago Hi, I notice that your gmes_petap.pl is working, and I am having soe issues with that. Please can you explain me how do you download it, because I already have the PATH for GENEMARK but I got this error in funannotate check --show-versions: ERROR: gmes_petap.pl not installed I hope you can help me please
Are you using the latest release? yes.
Describe the bug augustus.training.proteins.fa is empty. I tried different pasa gff3 file and used the soft masked genome as reference, but it was not work.
ls -ll /tmp total 16 -rwxrwxrwx 1 ding ding 0 May 10 11:51 augustus.training.proteins.faWhat command did you issue?
funannotate predict -i /mnt/e/linux/ding/data/annotate/00clean/nd.mx2.np2.clean.sort.mask.fa --species "Trichoderma asperellum" --isolate MX2 --transcript_evidence /mnt/f/lab/ann/trinity_out_dir2/Trinity-GG.fasta --rna_bam /mnt/e/linux/ding/data/annotate/bam/123mx2_merged.bam --pasa_gff /mnt/e/linux/ding/data/annotate/02PASA/mx2.sqlite.assemblies.fasta.transdecoder.gff3 --out /mnt/e/linu x/ding/data/annotate/03funannotate_1/Logfiles
[May 10 10:55 AM]: OS: Ubuntu 22.04, 12 cores, ~ 16 GB RAM. Python: 3.8.15 [May 10 10:55 AM]: Running funannotate v1.8.15 [May 10 10:55 AM]: Parsed training data, run ab-initio gene predictors as follows: Program Training-Method augustus pasa codingquarry rna-bam genemark selftraining glimmerhmm pasa snap pasa [May 10 11:00 AM]: Loading genome assembly and parsing soft-masked repetitive sequences [May 10 11:00 AM]: Genome loaded: 8 scaffolds; 37,465,576 bp; 6.61% repeats masked [May 10 11:00 AM]: Existing transcript alignments found: /mnt/e/linux/ding/data/annotate/03funannotate_1/predict_misc/transcript_alignments.gff3 [May 10 11:00 AM]: Existing RNA-seq BAM hints found: /mnt/e/linux/ding/data/annotate/03funannotate_1/predict_misc/hints.BAM.gff [May 10 11:00 AM]: Existing protein alignments found: /mnt/e/linux/ding/data/annotate/03funannotate_1/predict_misc/protein_alignments.gff3 [May 10 11:00 AM]: Existing GeneMark annotation found: /mnt/e/linux/ding/data/annotate/03funannotate_1/predict_misc/genemark.gff [May 10 11:00 AM]: 10,730 predictions from GeneMark [May 10 11:00 AM]: Filtering PASA data for suitable training set [May 10 11:00 AM]: CMD ERROR: diamond makedb --in /tmp/augustus.training.proteins.fa --db /tmp/aug_training.dmnd [May 10 11:00 AM]: diamond v2.1.8.162 (C) Max Planck Society for the Advancement of Science, Benjamin Buchfink, University of Tuebingen Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)
CPU threads: 12
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1) Database input file: /tmp/augustus.training.proteins.fa Opening the database file... Error: Error detecting input file format. First line seems to be blank.
OS/Install Information `funannotate check --show-versions
Checking dependencies for 1.8.15
You are running Python v 3.8.15. Now checking python packages... biopython: 1.76 goatools: 1.3.11 matplotlib: 3.7.5 natsort: 8.4.0 numpy: 1.24.4 pandas: 1.5.3 psutil: 5.9.8 requests: 2.31.0 scikit-learn: 1.3.2 scipy: 1.10.1 seaborn: 0.13.1 All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules... Carp: 1.50 Clone: 0.46 DBD::SQLite: 1.72 DBD::mysql: 4.046 DBI: 1.643 DB_File: 1.858 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.54 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05 Thread::Queue: 3.14 Tie::File: 1.06 URI::Escape: 5.17 YAML: 1.31 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed
Checking Environmental Variables... $FUNANNOTATE_DB=/mnt/f/database/2024/funannotate/funannotate_db $PASAHOME=/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/opt/pasa-2.5.3 $TRINITY_HOME=/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/config/ $GENEMARK_PATH=/mnt/e/linux/ding/soft/gmes_linux_64_4/gmes_linux_64_4/gmes_petap.pl/mnt/e/linux/ding/soft/gmes_linux_64_4/gmes_linux_64_4/gmes_petap.pl All 6 environmental variables are set
Checking external dependencies... Traceback (most recent call last): File "/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/bin/ete3", line 5, in
from ete3.tools.ete import main
File "/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/lib/python3.8/site-packages/ete3/tools/ete.py", line 55, in
from . import (ete_split, ete_expand, ete_annotate, ete_ncbiquery, ete_view,
File "/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/lib/python3.8/site-packages/ete3/tools/ete_view.py", line 48, in
from .. import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle, CircleFace, AttrFace,
ImportError: cannot import name 'TextFace' from 'ete3' (/mnt/e/linux/ding/soft/miniconda3/envs/funannotate/lib/python3.8/site-packages/ete3/init.py)
PASA: 2.5.3 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.31.1 blat: BLAT v37x1 diamond: 2.1.8 emapper.py: 2.1.12 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2023-10-10 gmes_petap.pl: 4.71_lic hisat2: 2.2.1 hmmscan: HMMER 3.4 (Aug 2023) hmmsearch: HMMER 3.4 (Aug 2023) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.14.1+ minimap2: 2.26-r1175 pigz: 2.8 proteinortho: 6.3.1 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.18 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.12 (Nov 2022) tantan: tantan 49 tbl2asn: 25.8 tblastn: tblastn 2.14.1+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: ete3 not installed`