Are you using the latest release?
Yes, 1.8.17.
Describe the bug
GeneMark-ES is failing without much information, so I'm wondering if you could give me some clue for going about debugging this. Thanks in advance!
What command did you issue?
export GENEMARK_PATH="/scratch3/jasons/protist_gene_prediction/software/gmes_linux_64_4"
export FUNANNOTATE_DB="/scratch3/jasons/protist_gene_prediction/software/funannotate_db"
/scratch2/software/anaconda/envs/funannotate/bin/funannotate predict \
--input S2_hifi_anvio_mmap02_np2_fun_mask.fa \
--out funannotate_out \
--species Trimyema koreanum \
--strain TK \
--cpus 40 \
--organism other \
--busco_db eukaryota Logfiles
funannotate-predict.log
...
[03/19/26 01:07:29]: Running GeneMark-ES on assembly
[03/19/26 01:07:29]: /scratch2/software/gmes_linux_64-aug-2020/gmes_petap.pl --ES --max_intron 3000 --soft_mask 2000 -- cores 40 --sequence /scratch3/hbeen/TK/Genome/Strategy2/EukFinder/hifiasm_meta/Anvio/Funannotate/np/funannotate_out/ predict_misc/genome.softmasked.fa
[03/19/26 01:07:58]: CMD ERROR: /scratch2/software/gmes_linux_64-aug-2020/gmes_petap.pl --ES --max_intron 3000 -- soft_mask 2000 --cores 40 --sequence /scratch3/hbeen/TK/Genome/Strategy2/EukFinder/hifiasm_meta/Anvio/Funannotate/np/ funannotate_out/predict_misc/genome.softmasked.fa
gmes.log
...
/scratch2/software/gmes_linux_64-aug-2020/gmes_petap.pl : [Thu Mar 19 01:07:57 2026] /scratch2/software/gmes_linux_64- aug-2020/workaround/link.sh /scratch3/hbeen/TK/Genome/Strategy2/EukFinder/hifiasm_meta/Anvio/Funannotate/np/ funannotate_out/predict_misc/genemark/run/ES_ini/es_ini.mod /scratch3/hbeen/TK/Genome/Strategy2/EukFinder/hifiasm_meta/Anvio/Funannotate/np/funannotate_out/predict_misc/genemark/run/ES_A_1/prev.mod
/scratch2/software/gmes_linux_64-aug-2020/gmes_petap.pl : [Thu Mar 19 01:07:58 2026] /scratch2/software/gmes_linux_64- aug-2020/parse_set.pl --section ES_A --cfg /scratch3/hbeen/TK/Genome/Strategy2/EukFinder/hifiasm_meta/Anvio/ Funannotate/np/funannotate_out/predict_misc/genemark/run.cfg --v
/scratch2/software/gmes_linux_64-aug-2020/gmes_petap.pl : [Thu Mar 19 01:07:58 2026] error
OS/Install Information
-------------------------------------------------------
Checking dependencies for 1.8.17
-------------------------------------------------------
You are running Python v 3.9.19. Now checking python packages...
biopython: 1.79
goatools: 1.2.3
matplotlib: 3.9.2
natsort: 8.4.0
numpy: 1.26.4
pandas: 2.2.3
psutil: 6.1.0
requests: 2.32.3
scikit-learn: 1.5.2
scipy: 1.13.1
seaborn: 0.13.2
All 11 python packages installed
You are running Perl v b'5.032001'. Now checking perl modules...
Carp: 1.38
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: 6.67
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: 5.12
YAML: 1.30
local::lib: 2.000029
threads: 2.25
threads::shared: 1.61
All 27 Perl modules installed
Checking Environmental Variables...
$FUNANNOTATE_DB=/db1/funannotate/
$PASAHOME=/scratch5/software/miniconda3/envs/funannotate-latest/opt/pasa-2.5.3
$TRINITY_HOME=/scratch5/software/miniconda3/envs/funannotate-latest/opt/trinity-2.15.2
$EVM_HOME=/scratch5/software/miniconda3/envs/funannotate-latest/opt/evidencemodeler-2.1.0
$AUGUSTUS_CONFIG_PATH=/scratch5/software/miniconda3/envs/funannotate-latest/config/
ERROR: GENEMARK_PATH not set. export GENEMARK_PATH=/path/to/dir
-------------------------------------------------------
Checking external dependencies...
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.15.2
augustus: 3.5.0
bamtools: bamtools 2.5.2
bedtools: bedtools v2.31.1
blat: BLAT v39x1
diamond: 2.1.10
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2024-11-20
hisat2: 2.2.1
hmmscan: HMMER 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
java: 22.0.1-internal
kallisto: 0.46.1
mafft: v7.525 (2024/Mar/13)
makeblastdb: makeblastdb 2.16.0+
minimap2: 2.28-r1209
pigz: 2.8
proteinortho: 6.3.3
pslCDnaFilter: no way to determine
salmon: salmon 1.10.3
samtools: samtools 1.21
signalp: 4.1
snap: 2006-07-28
stringtie: 2.2.3
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: gmes_petap.pl not installed
It's on a HPC.
Are you using the latest release?
Yes, 1.8.17.
Describe the bug
GeneMark-ES is failing without much information, so I'm wondering if you could give me some clue for going about debugging this. Thanks in advance!
What command did you issue?
Logfiles
funannotate-predict.loggmes.logOS/Install Information
It's on a HPC.