funannotate compare fails at proteinortho

[xvazquezc]

Are you using the latest release? 1.8.15

Describe the bug funannotate compare crashes at ProteinOrtho step, wether if you provide the file or if it's run internally. ProteinOrtho output is generated normally but it crashes right after. The issue seems to be something to do with this section of compare.py.

Also, it may relate to #180, or at least the log is similar to the one in the last comment of that issue.

What command did you issue?

funannotate compare -i input/*gbk \
--ml_method iqtree \
--run_dnds full \
--cpus $NCPUS

Logfiles funannotate-compare.log

OS/Install Information

$ funannotate check --show-versions
-------------------------------------------------------
Checking dependencies for 1.8.15
-------------------------------------------------------
You are running Python v 3.7.12. Now checking python packages...
biopython: 1.79
goatools: 1.2.3
matplotlib: 3.3.4
natsort: 8.3.1
numpy: 1.21.6
pandas: 1.2.3
psutil: 5.9.3
requests: 2.28.2
scikit-learn: 0.24.1
scipy: 1.5.3
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: 1.855
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=/srv/scratch/z3382651/funannotate_db
$PASAHOME=/srv/scratch/z3382651/miniconda3/envs/funannotate/opt/pasa-2.5.2
$TRINITY_HOME=/srv/scratch/z3382651/miniconda3/envs/funannotate/opt/trinity-2.8.5
$EVM_HOME=/srv/scratch/z3382651/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/apps/z_install_tree/linux-rocky8-ivybridge/gcc-12.2.0/augustus-3.4.0-duwzji3wkoy43fsbfld4uedt7jxrojr5/config
    ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
-------------------------------------------------------
Checking external dependencies...
  File "/srv/scratch/z3382651/eggnog-mapper/emapper.py", line 59
    print dbpath
               ^
SyntaxError: Missing parentheses in call to 'print'. Did you mean print(dbpath)?
PASA: 2.5.2
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.4.0
bamtools: bamtools 2.5.2
bedtools: bedtools v2.30.0
blat: BLAT v35
diamond: 2.1.6
ete3: 3.1.2
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2021-08-25
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: 2.24-r1122
pigz: 2.4
proteinortho: 6.0.29
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.12
signalp: 6.0
snap: 2006-07-28
stringtie: 2.2.1
tRNAscan-SE: 2.0.11 (Oct 2022)
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

[aldendirks]

I'm getting the same issue.

[hyphaltip]

I really feel that a lot of the functionality in compare needs to be factored out - I have other standalone tools which generate protein domain profiles and aggregates. If you want a tree of species I'd encourage using OrthoFinder or PHYling or other tools more simply.