Can I skip signalP prediction step in functional annotation?

[kushalsuryamohan]

Are you using the latest release? If you are not using the latest release of funannotate, please upgrade, if bug persists then report here. Yes Describe the bug A clear and concise description of what the bug is. I do have SignalP not installed because I cannot download the academic version (not working in academia). Can I skip this part in functional annotation?

What command did you issue? Copy/paste the command used. funannotate annotate -i funannotate_train --busco_db vertebrata --cpus 12 --no-progress

Logfiles Please provide relevant log files of the error.

[Jul 24 09:33 PM]: OS: CentOS Linux 7, 80 cores, ~ 264 GB RAM. Python: 3.8.15 [Jul 24 09:33 PM]: Running 1.8.15 [Jul 24 09:33 PM]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt' [Jul 24 09:33 PM]: Found existing output directory funannotate_train. Warning, will re-use any intermediate files found. [Jul 24 09:33 PM]: Parsing input files [Jul 24 09:33 PM]: Existing tbl found: funannotate_train/update_results/Dendroaspis_angusticeps.tbl [Jul 24 09:44 PM]: Adding Functional Annotation to Dendroaspis angusticeps, NCBI accession: None [Jul 24 09:44 PM]: Annotation consists of: 38,599 gene models [Jul 24 09:44 PM]: 41,870 protein records loaded [Jul 24 09:44 PM]: Existing Pfam-A results found: funannotate_train/annotate_misc/annotations.pfam.txt [Jul 24 09:44 PM]: 38,194 annotations added [Jul 24 09:44 PM]: Running Diamond blastp search of UniProt DB version 2023_02 [Jul 24 09:44 PM]: 11,670 valid gene/product annotations from 15,237 total [Jul 24 09:44 PM]: Existing Eggnog-mapper results found: funannotate_train/annotate_misc/eggnog.emapper.annotations [Jul 24 09:44 PM]: Parsing EggNog Annotations [Jul 24 09:44 PM]: EggNog version parsed as 2.1.10 [Jul 24 09:44 PM]: 62,872 COG and EggNog annotations added [Jul 24 09:44 PM]: Combining UniProt/EggNog gene and product names using Gene2Product version 1.88 [Jul 24 09:44 PM]: 19,037 gene name and product description annotations added [Jul 24 09:44 PM]: Existing MEROPS results found: funannotate_train/annotate_misc/annotations.merops.txt [Jul 24 09:44 PM]: 1,165 annotations added [Jul 24 09:44 PM]: Existing CAZYme results found: funannotate_train/annotate_misc/annotations.dbCAN.txt [Jul 24 09:44 PM]: 322 annotations added [Jul 24 09:44 PM]: Existing BUSCO2 results found: funannotate_train/annotate_misc/annotations.busco.txt [Jul 24 09:44 PM]: 2,542 annotations added [Jul 24 09:44 PM]: Existing Phobius results found: funannotate_train/annotate_misc/phobius.results.txt [Jul 24 09:44 PM]: Predicting secreted proteins with SignalP Traceback (most recent call last): File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/lib/python3.8/site-packages/funannotate/annotate.py", line 1331, in main lib.signalP( File "/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py", line 7204, in signalP if "." in version: TypeError: argument of type 'bool' is not iterable

OS/Install Information

• output of funannotate check --show-versions

---

Checking dependencies for 1.8.15

You are running Python v 3.8.15. Now checking python packages... biopython: 1.81 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.3.1 numpy: 1.24.3 pandas: 1.5.3 psutil: 5.9.5 requests: 2.29.0 scikit-learn: 1.2.2 scipy: 1.10.1 seaborn: 0.12.2 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...
$FUNANNOTATE_DB=/MG/SHARED/APPS/FUNANNOTATE_DB
$PASAHOME=/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/opt/pasa-2.5.2
$TRINITY_HOME=/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/opt/trinity-2.8.5
$EVM_HOME=/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/MG/SHARED/APPS/ANACONDA_DIR/anaconda/envs/funannotate/config/
$GENEMARK_PATH=/MG/SHARED/APPS/GENEMARK_LISCENCE/gmes_linux_64_4/

```All 6 environmental variables are set
-------------------------------------------------------
Checking external dependencies...
PASA: 2.5.2
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.5.0
bamtools: bamtools 2.5.1
bedtools: bedtools v2.30.0
blat: BLAT v36x2
diamond: 2.1.6
emapper.py: 2.1.10
ete3: 3.1.2
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2023-03-24
gmes_petap.pl: 4.71_lic
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
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.17
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: signalp not installed

[nextgenusfs]

Yes, it will skip if signalp is not found, so it must have found signalp in the PATH and tried to run it.

https://github.com/nextgenusfs/funannotate/blob/master/funannotate/annotate.py#L1314-L1322

[Nitin123-4]

funannotate check shows ERROR: signalp not installed.

Not sure how it is still taking signalp.

is there any way to avoid running signalp?

[Okompath]

was this ever resolved? having the same issue.

[nextgenusfs]

I can't say it was ever a problem. Funannotate just looks in the path for signalp, if it finds it then it tries to run it. If it doesn't than it skips it.