# 可能需要花一些时间,数据集太多funannotate setup -d funannotate_db --install all 配置环境变量, 在激活funannotate环境的同时,启用这部分环境变量,方法参考 #在conda环境下,进行如下配置,即可在激活环境的同时,激活这些环境变脸变量cat /home/user222/miniconda3/envs/funannotate/etc/conda/activate.d/env_vars....
Checking Environmental Variables... $FUNANNOTATE_DB=/media/funannotate_db $PASAHOME=/home/anaconda3/envs/funannotate/opt/pasa-2.5.3 $TRINITY_HOME=/home/anaconda3/envs/funannotate/opt/trinity-2.15.2 $EVM_HOME=/home/anaconda3/envs/funannotate/opt/evidencemodeler-2.1.0 $AUGUSTUS_CONFIG_PATH=/home...
fix update bug where PASA db not found if using --gff and --fasta Jan 20, 2020 scripts allow --debug in iprscan Jan 13, 2020 .gitignore parse gaps (Ns) with softmasked and use for tRNA intersection Oct 30, 2019 LICENSE.md
--memory 100G --stranded no --pasa_db sqlite --species "$SPECIES" --max_intronlen 10000 --pasa_alignment_overlap 30.0 --coverage 50 --name "$FUNNAME" --trinity $TRINITY ) Terminal ouput: [01:38 AM]: Writing 17,671 loci to TBL format: dropped 0 overlapping, 2 too short, an...
DB_File: 1.852 Data::Dumper: 2.173 File::Basename: 2.85 File::Which: 1.23 Getopt::Long: 2.5 Hash::Merge: 0.300 JSON: 4.02 LWP::UserAgent: 6.39 Logger::Simple: 2.0 POSIX: 1.76 Parallel::ForkManager: 2.02 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 ...
Hi, I have installed funannotate with the docker option, as I could not make the Hombrew installation correctly. All databases were installed correctly with "funannotate setup" except for dbCAN because the website was down. I ended up do...
"dbCAN-log": "https://bcb.unl.edu/dbCAN2/download/Databases/V11/readme.txt", "pfam": "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz", "pfam-tsv": "http://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pfam-A.clans.tsv.gz", "pfam-log": "http:/...
@03f7b3ce6426:/mnt/OneTB/annotation/funannotate$ diamond makedb --in NbenthamianaGenbankAA.fasta --db diamond -p 8 diamond v2.0.13.151 (C) Max Planck Society for the Advancement of Science Documentation, support and updates available at http://www.diamondsearch.org Please cite: http://dx...
DB_File: 1.858 Data::Dumper: 2.183 File::Basename: 2.85 File::Which: 1.24 Getopt::Long: 2.58 Hash::Merge: 0.302 JSON: 4.10 LWP::UserAgent: 6.67 Logger::Simple: 2.0 POSIX: 1.94 Parallel::ForkManager: 2.03 Pod::Usage: 1.69 Scalar::Util::Numeric: 0.40 Storable: 3.15 Text::Soundex: 3.05...
explicit number of threads for tRNAscan-SE runs#411* force to string for cpu arg * fix trnascan cpus * update dbCAN to v8 * filter cazy subdomains out if exist * update EVM script to try to partition in between putative gene loci * EVM update; PASA updated options; predict simplified ...