nextgenusfs
commented
2 months ago Either set the GENEMARK_PATH environmental variable or add the genemark folder to your PATH so that gmes_petap.pl is callable from the funannotate environment. All this script is doing is seeing if these command line tools are in your PATH.
When installing funannotate via conda I need to add a couple of dependencies, such as
signalpandgmes_petap.pl. After doing so and making sure that they are installed, I dofunannotate check --show-versionsand recieve:ERROR: gmes_petap.pl not installed ERROR: signalp not installedOS/Install Information
output of
funannotate check --show-versions`------------------------------------------------------- Checking dependencies for 1.8.1You are running Python v 3.7.8. Now checking python packages... biopython: 1.76 goatools: 1.0.11 matplotlib: 3.3.3 natsort: 7.0.1 numpy: 1.19.4 pandas: 1.1.4 psutil: 5.7.0 requests: 2.25.0 scikit-learn: 0.23.2 scipy: 1.5.3 seaborn: 0.11.0 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... $PASAHOME=/home/lebi_kimura/miniconda3/envs/funannotate/opt/pasa-2.4.1 $TRINITY_HOME=/home/lebi_kimura/miniconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/home/lebi_kimura/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/home/lebi_kimura/miniconda3/envs/funannotate/config/ ERROR: FUNANNOTATE_DB not set. export FUNANNOTATE_DB=/path/to/dir ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
Checking external dependencies... ERROR: signalp found but error running signalp PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.3 bamtools: bamtools 2.5.1 bedtools: bedtools v2.29.2 blat: BLAT v36 diamond: 2.0.4 emapper.py: There was an error retrieving eggnog-mapper DB data: not a valid file "/home/lebi_kimura/miniconda3/envs/funannotate/lib/python3.7/site-packages/data/eggnog.db" Maybe you need to run download_eggnog_data.py emapper-2.1.12 / Expected eggNOG DB version: 5.0.2 / Installed eggNOG DB version: unknown / Diamond found: diamond 2.0.4 / MMseqs2 found: 113e3212c137d026e297c7540e1fcd039f6812b1 / Compatible novel families DB version: 1.0.1
ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2017-11-15 hisat2: 2.2.1 hmmscan: HMMER 3.3.1 (Jul 2020) hmmsearch: HMMER 3.3.1 (Jul 2020) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.471 (2020/Jul/3) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.17-r941 proteinortho: 6.0.24 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.10 snap: 2006-07-28 stringtie: 2.1.4 tRNAscan-SE: 2.0.6 (May 2020) tantan: tantan 13 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: gmes_petap.pl not installed ERROR: signalp not installed `
How should I fix this?