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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
300 stars 82 forks source link

ERROR: dependencies not installed #915

Closed lukaskon closed 1 year ago

lukaskon commented 1 year ago

I just installed the latest version of funannote via conda and have dependency issues below. Any advice?

Checking dependencies for 1.8.15

You are running Python v 3.8.13. Now checking python packages... biopython: 1.79 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.2.0 numpy: 1.23.4 pandas: 1.5.1 psutil: 5.9.4 requests: 2.28.1 scikit-learn: 1.1.3 scipy: 1.9.3 seaborn: 0.12.1 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: 5.12 YAML: 1.30 local::lib: 2.000029 threads: 2.25 threads::shared: 1.61 All 27 Perl modules installed

Checking Environmental Variables... $PASAHOME=/mnt/home/lukaskon/anaconda2/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/mnt/home/lukaskon/anaconda2/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/mnt/home/lukaskon/anaconda2/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/mnt/home/lukaskon/anaconda2/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: pslDnaFiler found but error running: pslCDnaFilter: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.5.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.31.0 blat: BLAT v36x2 diamond: 2.1.6 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2023-03-24 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 17.0.3-internal kallisto: 0.46.1 mafft: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.13.0+ minimap2: 2.26-r1175 pigz: 2.6 proteinortho: 6.2.3 salmon: salmon 0.14.1 samtools: samtools 1.16.1 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.11 (Oct 2022) tantan: tantan 40 tbl2asn: 25.8 tblastn: tblastn 2.13.0+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 ERROR: emapper.py not installed ERROR: gmes_petap.pl not installed ERROR: pslCDnaFilter not installed ERROR: signalp not installed

lukaskon commented 1 year ago

(funannotate) funannotate$ funannotate test -t all --cpus 12 ######################################################### Running funannotate clean unit testing: minimap2 mediated assembly duplications Downloading: https://osf.io/8pjbe/download?version=1 Bytes: 252076 CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive ######################################################### minimap2 version=2.26-r1175 path=/mnt/home/lukaskon/anaconda2/envs/funannotate/bin/minimap2

6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp Checking duplication of 6 contigs

scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153 scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858 scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039

6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file ######################################################### SUCCESS: funannotate clean test complete. #########################################################

######################################################### Running funannotate mask unit testing: RepeatModeler --> RepeatMasker Downloading: https://osf.io/hbryz/download?version=1 Bytes: 375687 CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 12 #########################################################

[May 15 05:17 PM]: OS: CentOS Linux 7, 128 cores, ~ 1056 GB RAM. Python: 3.8.13 [May 15 05:17 PM]: Running funanotate v1.8.15 [May 15 05:17 PM]: Soft-masking simple repeats with tantan [May 15 05:17 PM]: Repeat soft-masking finished: Masked genome: /mnt/ufs18/home-054/lukaskon/anaconda2/envs/funannotate/test-mask_87413c55-a7bb-4bf9-94f3-6eeb6c32a2d5/test.masked.fa num scaffolds: 2 assembly size: 1,216,048 bp masked repeats: 50,965 bp (4.19%)

######################################################### SUCCESS: funannotate mask test complete. #########################################################

######################################################### Running funannotate predict unit testing CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 12 --species Awesome testicus]]]]]]]]]]]]#########################################################

[May 15 05:17 PM]: OS: CentOS Linux 7, 128 cores, ~ 1056 GB RAM. Python: 3.8.13 [May 15 05:17 PM]: Running funannotate v1.8.15 [May 15 05:17 PM]: Funannotate database not properly configured, run funannotate setup. ######################################################### Traceback (most recent call last): File "/mnt/home/lukaskon/anaconda2/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/mnt/home/lukaskon/anaconda2/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/mnt/home/lukaskon/anaconda2/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 405, in main runPredictTest(args) File "/mnt/home/lukaskon/anaconda2/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 160, in runPredictTest assert 1500 <= countGFFgenes(os.path.join( File "/mnt/home/lukaskon/anaconda2/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 45, in countGFFgenes with open(input, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'test-predict_87413c55-a7bb-4bf9-94f3-6eeb6c32a2d5/annotate/predict_results/Awesome_testicus.gff3'

nextgenusfs commented 1 year ago

Should be obvious from the error no? 

[May 15 05:17 PM]: Funannotate database not properly configured, run funannotate setup.

You have to install databases, the conda install message should have told you that. https://github.com/bioconda/bioconda-recipes/blob/master/recipes/funannotate/post-link.sh

And read the docs for more help. https://funannotate.readthedocs.io/en/latest/install.html#install

lukaskon commented 1 year ago

Ran setup again and all good now, sorry about confusion.