Funannotate fails to retrieve results from BUSCO

lalalagartija commented 1 year ago

Hi ! I fail to do the functional annotation step when retrieving BUSCO results. It seams like BUSCO annotations are given on the genome but fails to give results for the predicted proteins.

Describe the bug annotations.busco.txt is empty wheter I run funannotate annotate after update or in a blank folder giving the fasta and gff.

What command did you issue? /home/oar-jobs/tools/src/singularity/bin/singularity exec -B ${wdir} funannotate_latest.sif 'funannotate' annotate \ --gff Acast_HiCseq_annot/update_results/Acanthamoeba_castellanii_Neff.gff3 \ --fasta Acanthamoeba_castellanii_HiC-Seq.fasta --species "Acanthamoeba castellanii" --strain Neff \ -o Acast_HiCseq_fun_annotate --cpus ${SLURM_CPUS_PER_TASK} \ --iprscan Acanthamoeba_castellanii_HiC-Seq.update.ipscan.xml \ --busco_db eukaryota -d ./databases

Logfiles ` [Apr 05 04:27 PM]: Annotating proteins with BUSCO eukaryota models

Traceback (most recent call last): File "/venv/bin/funannotate", line 8, in sys.exit(main()) File "/venv/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/venv/lib/python3.8/site-packages/funannotate/annotate.py", line 997, in main lib.runBUSCO(Proteins, buscoDB, args.cpus, os.path.join( File "/venv/lib/python3.8/site-packages/funannotate/library.py", line 5460, in runBUSCO with open(os.path.join(tmpdir, 'run_busco', 'full_table_busco.tsv'), 'r') as busco: FileNotFoundError: [Errno 2] No such file or directory: 'Acast_HiCseq_fun_annotate/annotate_misc/run_busco/full_table_busco.tsv' `

OS/Install Information

output of funannotate check --show-versions `~/Funannotate_annot_Acast_HiCseq$ /home/oar-jobs/tools/src/singularity/bin/singularity exec -B $wdir -B ${wdir}/signalp-5.0b/bin -B /home/oar-jobs/Tools/conda/bin/ /home/oar-jobs/Tools/funannotate_latest.sif 'funannotate' check --show-versions

Checking dependencies for 1.8.14

You are running Python v 3.8.12. Now checking python packages... biopython: 1.80 goatools: 1.2.3 matplotlib: 3.6.3 natsort: 8.2.0 numpy: 1.22.4 pandas: 1.5.3 psutil: 5.9.4 requests: 2.28.2 scikit-learn: 1.1.1 scipy: 1.5.3 seaborn: 0.12.2 All 11 python packages installed

You are running Perl v b'5.026002'. Now checking perl modules... 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 local::lib: 2.000024 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/opt/databases $PASAHOME=/venv/opt/pasa-2.4.1 $TRINITYHOME=/venv/opt/trinity-2.8.5 $EVM_HOME=/venv/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/usr/share/augustus/config $GENEMARK_PATH=gmes_linux_64_4 All 6 environmental variables are set

Checking external dependencies... /home/oar-jobs/rigou/Tools/conda/bin/java: error while loading shared libraries: libjli.so: cannot open shared object file: No such file or directory 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: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.2 bamtools: bamtools 2.5.2 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: 36.3.8g glimmerhmm: 3.0.4 gmap: 2017-11-15 hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 11.0.8-internal kallisto: 0.46.1 mafft: v7.515 (2023/Jan/15) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: 2.6 proteinortho: 6.0.16 salmon: salmon 0.14.1 samtools: samtools 1.12 snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 40 tbl2asn: 25.8 tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] ERROR: emapper.py not installed ERROR: gmes_petap.pl not installed ERROR: pslCDnaFilter not installed ERROR: signalp not installed ERROR: trimmomatic not installed `

alephreish commented 1 year ago

Having the same issue under conda (funannotate=1.8.15) with --busco_db eukaryota.

alephreish commented 1 year ago

I did not attempt much debugging, the workaround that I found was to pre-calculate the busco step with funannotate-BUSCO2.py:

mkdir -p funannotate_results_path/annotate_misc
$CONDA_PREFIX/lib/python*/site-packages/funannotate/aux_scripts/funannotate-BUSCO2.py \
    -i path_to_proteins.faa -m proteins -l funannotate_data_directory/lineage -o busco -c 10 -f
mv run_busco funannotate_results_path/annotate_misc/

nextgenusfs / funannotate