SNAP error - ValueError: not enough values to unpack (expected 9, got 3)

[agesantos]

Are you using the latest release?
If you are not using the latest release of funannotate, please upgrade, if bug persists then report here.

R: I am using the latest version available on dockerhub (without GeneMark).

Describe the bug
A clear and concise description of what the bug is.

R: I am trying to run funannotate on a fish genome assembly.
I follow the tutorial https://funannotate.readthedocs.io/en/latest/tutorials.html
I had to run some adjustments (see below) but everything went well until the prediction step tried to run SNAP. The error was as follows:

---

[Dec 27 11:16 AM]: OS: Debian GNU/Linux 10, 32 cores, ~ 66 GB RAM. Python: 3.8.12
[Dec 27 11:16 AM]: Running funannotate v1.8.17
[Dec 27 11:16 AM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.
[Dec 27 11:17 AM]: Found training files, will re-use these files:
--stringtie fun/training/funannotate_train.stringtie.gtf
[Dec 27 11:17 AM]: Skipping CodingQuarry as no --rna_bam passed
[Dec 27 11:17 AM]: Parsed training data, run ab-initio gene predictors as follows:
[4mProgram Training-Method[0m
augustus busco
glimmerhmm busco
snap busco
[Dec 27 11:33 AM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Dec 27 11:36 AM]: Genome loaded: 3,232 scaffolds; 1,871,063,696 bp; 14.10% repeats masked
[Dec 27 11:37 AM]: Existing protein alignments found: fun/predict_misc/protein_alignments.gff3
[Dec 27 11:37 AM]: Existing BUSCO results found: fun/predict_misc/busco.final.gff3 containing 3,667 predictions
[Dec 27 11:37 AM]: Existing Augustus annotations found: fun/predict_misc/augustus.gff3
[Dec 27 11:38 AM]: Pulling out high quality Augustus predictions
[Dec 27 11:38 AM]: Found 146 high quality predictions from Augustus (>90% exon evidence)
[Dec 27 11:38 AM]: Running SNAP gene prediction, using training data: fun/predict_misc/busco.final.gff3
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/predict.py", line 2382, in main
lib.runSnap(
File "/venv/lib/python3.8/site-packages/funannotate/library.py", line 8317, in runSnap
zff2gff3(snapRaw, fasta, output)
File "/venv/lib/python3.8/site-packages/funannotate/library.py", line 8076, in zff2gff3
(
ValueError: not enough values to unpack (expected 9, got 3)

What command did you issue?
Copy/paste the command used.

R: Here are the commands I ran flowing the tutorial - https://funannotate.readthedocs.io/en/latest/tutorials.html

clean

funannotate clean -i genome.fasta --minlen 1000 -o genome.cleaned.fa

sort

funannotate sort -i genome.cleaned.fa --minlen 1 -b scaffold -o genome.cleaned.sorted.fa

mask

funannotate mask -i genome.cleaned.sorted.fa --cpus 32 -o genome.cleaned.sorted.masked.fa

train

funannotate train -i genome.cleaned.sorted.masked.fa -o fun
--left Hdi_TR_F_1.fq.gz
--right Hdi_TR_F_2.fq.gz
--stranded RF --jaccard_clip --species "Species name" --cpus 30

setup

NOTE: I had to run setup for BUSCO, using a local folder (outside the docker) with the databases as it had a permission error using the folder inside the docker.

export AUGUSTUS_CONFIG_PATH=/home/andresantos/App/Augustus/config
funannotate setup -d /home/andresantos/App/funannotate-master/databases -b actinopterygii

predict

export AUGUSTUS_CONFIG_PATH=/home/andresantos/App/Augustus/config
export FUNANNOTATE_DB=/home/andresantos/App/funannotate-master/databases
funannotate predict -i genome.cleaned.sorted.masked.fa --max_intronlen 100000 --organism other --repeats2evm --busco_db actinopterygii -o fun --species "Species name" --cpus 30

Logfiles
Please provide relavent log files of the error.

---

[Dec 27 11:16 AM]: OS: Debian GNU/Linux 10, 32 cores, ~ 66 GB RAM. Python: 3.8.12
[Dec 27 11:16 AM]: Running funannotate v1.8.17
[Dec 27 11:16 AM]: GeneMark not found and $GENEMARK_PATH environmental variable missing. Will skip GeneMark ab-initio prediction.
[Dec 27 11:17 AM]: Found training files, will re-use these files:
--stringtie fun/training/funannotate_train.stringtie.gtf
[Dec 27 11:17 AM]: Skipping CodingQuarry as no --rna_bam passed
[Dec 27 11:17 AM]: Parsed training data, run ab-initio gene predictors as follows:
[4mProgram Training-Method[0m
augustus busco
glimmerhmm busco
snap busco
[Dec 27 11:33 AM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Dec 27 11:36 AM]: Genome loaded: 3,232 scaffolds; 1,871,063,696 bp; 14.10% repeats masked
[Dec 27 11:37 AM]: Existing protein alignments found: fun/predict_misc/protein_alignments.gff3
[Dec 27 11:37 AM]: Existing BUSCO results found: fun/predict_misc/busco.final.gff3 containing 3,667 predictions
[Dec 27 11:37 AM]: Existing Augustus annotations found: fun/predict_misc/augustus.gff3
[Dec 27 11:38 AM]: Pulling out high quality Augustus predictions
[Dec 27 11:38 AM]: Found 146 high quality predictions from Augustus (>90% exon evidence)
[Dec 27 11:38 AM]: Running SNAP gene prediction, using training data: fun/predict_misc/busco.final.gff3
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/predict.py", line 2382, in main
lib.runSnap(
File "/venv/lib/python3.8/site-packages/funannotate/library.py", line 8317, in runSnap
zff2gff3(snapRaw, fasta, output)
File "/venv/lib/python3.8/site-packages/funannotate/library.py", line 8076, in zff2gff3
(
ValueError: not enough values to unpack (expected 9, got 3)

OS/Install Information

• output of funannotate 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: 1.4.12
matplotlib: 3.7.3
natsort: 8.4.0
numpy: 1.22.4
pandas: 2.0.3
psutil: 6.0.0
requests: 2.32.3
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
local::lib: 2.000024
threads: 2.15
threads::shared: 1.56
All 27 Perl modules installed

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: v7.526 (2024/Apr/26)
makeblastdb: makeblastdb 2.2.31+
minimap2: 2.28-r1209
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 50
tbl2asn: 25.8
tblastn: tblastn 2.2.31+
trimal: trimAl v1.5.rev0 build[2024-05-27]
trimmomatic: 0.39
ERROR: emapper.py not installed
ERROR: gmes_petap.pl not installed
ERROR: signalp not installed