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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Protein FASTA file not found, exiting - annotate_misc genome.protein.fa has no data #1019

Closed stachyris closed 1 month ago

stachyris commented 2 months ago

Are you using the latest release? If you are not using the latest release of funannotate, please upgrade, if bug persists then report here.

Running Running 1.8.15 as a container

Describe the bug A clear and concise description of what the bug is.

Not sure where the issue coming from but the error file indicate "Protein FASTA file not found, exiting". Both eggnog and InterPro Scan was run outside of Funannotate after Braker3 (All containersized)

What command did you issue? Copy/paste the command used.

singularity exec -B /work,/project /project/brant/containers/funannotate.sif funannotate annotate --fasta ../01_repeat_masking/bShoAlb1.1.fasta.masked --gff ./braker/braker-transcript-removed.gff --iprscan ./braker/braker-star-removed.aa.fasta.xml --out funannotate --species "Sholicola albiventris" --eggnog ./braker/eggnog/Sholicola_albiventris.emapper.annotation --busco_db aves -d /project/brant/reference-databases/funannotate/ --cpus 64

Logfiles Please provide relavent log files of the error.

[04/02/24 14:27:13]: /venv/bin/funannotate annotate --fasta ../01_repeat_masking/bShoAlb1.1.fasta.masked --gff ./braker/braker-transcript-removed.gff --iprscan ./braker/braker-star-removed.aa.fasta.xml --out funannotate --species Sholicola albiventris --eggnog ./braker/eggnog/Sholicola_albiventris.emapper.annotation --busco_db aves -d /project/brant/reference-databases/funannotate/ --cpus 64

[04/02/24 14:27:13]: OS: Debian GNU/Linux 10, 64 cores, ~ 263 GB RAM. Python: 3.8.12 [04/02/24 14:27:13]: Running 1.8.15 [04/02/24 14:27:13]: hmmscan version=HMMER 3.3.2 (Nov 2020) path=/venv/bin/hmmscan [04/02/24 14:27:13]: hmmsearch version=HMMER 3.3.2 (Nov 2020) path=/venv/bin/hmmsearch [04/02/24 14:27:13]: diamond version=2.1.7 path=/venv/bin/diamond [04/02/24 14:27:13]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt' [04/02/24 14:27:13]: Parsing annotation and preparing annotation files. [04/02/24 14:27:28]: Found 38,177 gene models from GFF3 annotation [04/02/24 14:27:31]: TBL file: funannotate/annotate_misc/genome.tbl [04/02/24 14:27:31]: GFF3 file: ./braker/braker-transcript-removed.gff [04/02/24 14:27:31]: Protein FASTA file not found, exiting

OS/Install Information

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 ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir

Checking external dependencies... PASA: 2.4.1 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.3.2 bamtools: bamtools 2.5.2 bedtools: bedtools v2.31.0 blat: BLAT v35 diamond: 2.1.7 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: v7.520 (2023/Mar/22) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.26-r1175 pigz: 2.6 proteinortho: 6.0.16 pslCDnaFilter: no way to determine 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] trimmomatic: 0.39 ERROR: emapper.py not installed ERROR: gmes_petap.pl not installed ERROR: signalp not installed

ydanylko commented 1 month ago

Having the same error, with all installed except gmes_petap. Downgrading biopython not the solution because I am using 1.79 and it is not working all the same.

stachyris commented 1 month ago

Closing this issue as Funannotate worked after sanitizing the gff with gfftk.