funannotate test fails at signalp step #1120
Description
This is essentially the same error reported in #939
I see the following:
[Jul 28 12:10 PM]: Predicting secreted proteins with SignalP
Traceback (most recent call last):
File "/home/kodalivk/.conda/envs/funannotate/bin/funannotate", line 10, in <module>
sys.exit(main())
^^^^^^
File "/home/kodalivk/.conda/envs/funannotate/lib/python3.11/site-packages/funannotate/funannotate.py", line 717, in main
mod.main(arguments)
File "/home/kodalivk/.conda/envs/funannotate/lib/python3.11/site-packages/funannotate/annotate.py", line 1340, in main
lib.signalP(
File "/home/kodalivk/.conda/envs/funannotate/lib/python3.11/site-packages/funannotate/library.py", line 7223, in signalP
if "." in version:
^^^^^^^^^^^^^^
TypeError: argument of type 'bool' is not iterable
The output of funannotate check --show-versions is show below:
funannotate check --show-versions
/home/kodalivk/.conda/envs/funannotate/lib/python3.11/site-packages/funannotate/funannotate.py:11: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.
from pkg_resources import get_distribution
-------------------------------------------------------
Checking dependencies for 1.8.17
-------------------------------------------------------
You are running Python v 3.11.13. Now checking python packages...
biopython: 1.79
goatools: 1.4.12
matplotlib: 3.10.3
natsort: 8.4.0
numpy: 2.3.2
pandas: 2.3.1
psutil: 7.0.0
requests: 2.32.4
scikit-learn: 1.7.1
scipy: 1.16.0
seaborn: 0.13.2
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: 1.76
DBD::mysql: 4.050
DBI: 1.643
DB_File: 1.858
Data::Dumper: 2.183
File::Basename: 2.85
File::Which: 1.24
Getopt::Long: 2.58
Hash::Merge: 0.302
JSON: 4.10
LWP::UserAgent: 6.68
Logger::Simple: 2.0
POSIX: 1.94
Parallel::ForkManager: 2.03
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: 5.17
YAML: 1.30
local::lib: 2.000029
threads: 2.25
threads::shared: 1.61
All 27 Perl modules installed
Checking Environmental Variables...
$FUNANNOTATE_DB=/home/kodalivk/funannotate_db
$PASAHOME=/home/kodalivk/.conda/envs/funannotate/opt/pasa-2.5.3
$TRINITY_HOME=/home/kodalivk/.conda/envs/funannotate/bin
$EVM_HOME=/home/kodalivk/.conda/envs/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/home/kodalivk/.conda/envs/funannotate/config/
ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
-------------------------------------------------------
Checking external dependencies...
ERROR: gmap found but error running gmap
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.15.2
augustus: 3.5.0
bamtools: bamtools 2.5.3
bedtools: bedtools v2.31.1
blat: BLAT v39x1
diamond: 2.1.13
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
hisat2: 2.2.1
hmmscan: HMMER 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
java: 23.0.2-internal
kallisto: 0.46.1
mafft: v7.526 (2024/Apr/26)
makeblastdb: makeblastdb 2.16.0+
minimap2: 2.30-r1287
pigz: 2.8
proteinortho: 6.3.6
pslCDnaFilter: no way to determine
salmon: salmon 1.10.3
samtools: samtools 1.22
snap: 2006-07-28
stringtie: 3.0.0
tRNAscan-SE: 2.0.12 (Nov 2022)
tantan: tantan 51
tbl2asn: 25.8
tblastn: tblastn 2.16.0+
trimal: trimAl v1.5.rev0 build[2024-05-27]
trimmomatic: 0.39
ERROR: emapper.py not installed
ERROR: gmap not installed
ERROR: gmes_petap.pl not installed
ERROR: signalp not installed
And I don't have signalp in my PATH:
which signalp
/usr/bin/which: no signalp in (...
which signalp6
/usr/bin/which: no signalp6 in (...
How can I get past this error?