When running funannotate compare, comparison of 2 species succeeds but comparison of 3 species fails

[liuyca1]

Are you using the latest release?
yes V1.8.17

Describe the bug
When I run funannotate compare, I enter the annotation results of 2 species for comparison, and it can run successfully, but when I enter the annotation results of 3 species, an error occurs.

What command did you issue?
funannotate-docker compare -i GLeI1521_XWZ.gbk GLeI1615_BMK.gbk --cpus 80
funannotate-docker compare -i GLeI1521_BMK.gbk GLeI1521_XWZ.gbk GLeI1615_BMK.gbk --cpus 80

Logfiles
$cat compare2.pbs.e168371
logname: no login name
logname: no login name
[May 16 10:00 AM]: OS: Debian GNU/Linux 10, 80 cores, ~ 1584 GB RAM. Python: 3.8.12
[May 16 10:00 AM]: Running 1.8.17
[May 16 10:00 AM]: Now parsing 2 genomes
[May 16 10:00 AM]: working on Ganoderma leucocontextum
[May 16 10:01 AM]: working on Ganoderma leucocontextum
[May 16 10:01 AM]: No secondary metabolite annotations found
[May 16 10:01 AM]: Summarizing PFAM domain results
Fontconfig error: No writable cache directories
[May 16 10:01 AM]: Summarizing InterProScan results
[May 16 10:01 AM]: Loading InterPro descriptions
[May 16 10:01 AM]: Summarizing MEROPS protease results
[May 16 10:01 AM]: found 12/87 MEROPS familes with stdev >= 1.000000
[May 16 10:01 AM]: Summarizing CAZyme results
[May 16 10:01 AM]: found 11/105 CAZy familes with stdev >= 1.000000
[May 16 10:01 AM]: Summarizing COG results
[May 16 10:01 AM]: Summarizing secreted protein results
[May 16 10:01 AM]: Summarizing fungal transcription factors
[May 16 10:01 AM]: Running GO enrichment for each genome
[May 16 11:47 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile...
[May 16 11:48 AM]: Compiling all annotations for each genome
[May 16 11:48 AM]: Skipping RAxML phylogeny as at least 4 taxa are required
[May 16 11:48 AM]: Compressing results to output file: funannotate_compare.tar.gz
[May 16 11:49 AM]: Funannotate compare completed successfully!

---

$cat compare1.pbs.e168370
logname: no login name
logname: no login name
[May 16 09:00 AM]: OS: Debian GNU/Linux 10, 80 cores, ~ 1584 GB RAM. Python: 3.8.12
[May 16 09:00 AM]: Running 1.8.17
[May 16 09:00 AM]: Now parsing 3 genomes
[May 16 09:00 AM]: working on Ganoderma leucocontextum
[May 16 09:00 AM]: working on Ganoderma leucocontextum
[May 16 09:01 AM]: working on Ganoderma leucocontextum
[May 16 09:01 AM]: No secondary metabolite annotations found
[May 16 09:01 AM]: Summarizing PFAM domain results
Fontconfig error: No writable cache directories
[May 16 09:01 AM]: Summarizing InterProScan results
[May 16 09:01 AM]: Loading InterPro descriptions
[May 16 09:01 AM]: Summarizing MEROPS protease results
[May 16 09:01 AM]: found 14/87 MEROPS familes with stdev >= 1.000000
[May 16 09:01 AM]: Summarizing CAZyme results
[May 16 09:01 AM]: found 16/105 CAZy familes with stdev >= 1.000000
[May 16 09:01 AM]: Summarizing COG results
[May 16 09:01 AM]: Summarizing secreted protein results
[May 16 09:01 AM]: Summarizing fungal transcription factors
[May 16 09:01 AM]: Running GO enrichment for each genome
[May 16 10:35 AM]: Running orthologous clustering tool, ProteinOrtho. This may take awhile...
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 717, in main
mod.main(arguments)
File "/venv/lib/python3.8/site-packages/funannotate/compare.py", line 1254, in main
if row != "*":
File "/venv/lib/python3.8/site-packages/pandas/core/generic.py", line 1466, in nonzero
raise ValueError(
ValueError: The truth value of a Series is ambiguous. Use a.empty, a.bool(), a.item(), a.any() or a.all().

OS/Install Information

• output of funannotate check --show-versions
  $funannotate-docker check --show-versions

---

Checking dependencies for 1.8.17

You are running Python v 3.8.12. Now checking python packages...
biopython: 1.79
goatools: 1.3.11
matplotlib: 3.7.3
natsort: 8.4.0
numpy: 1.22.4
pandas: 2.0.3
psutil: 5.9.8
requests: 2.31.0
scikit-learn: 0.24.2
scipy: 1.5.3
seaborn: 0.13.0
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
threads: 2.15
threads::shared: 1.56
ERROR: local::lib not installed, install with cpanm local::lib

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 v2.31.1
blat: BLAT v35
diamond: 2.1.8
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 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
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: 2.8
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 49
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