Annotate command drops AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start' error

[ufaroooq]

Are you using the latest release? yes. version 1.8.17

Describe the bug When tunning funannotate annotate command with required options, it drops in errors within the python library.py file. AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start'

What command did you issue? funannotate annotate --input ./ --fasta 47514_clean_sort.fna --species 'Fusarium oxysporum' --strain 47514 --isolate 47514 --cpus 16 2>&1 | tee -a 07.annotate.log

Logfiles

[Apr 22 09:30 AM]: OS: Ubuntu 22.04, 32 cores, ~ 264 GB RAM. Python: 3.8.15
[Apr 22 09:30 AM]: Running 1.8.17
[Apr 22 09:30 AM]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt'
[Apr 22 09:30 AM]: Parsing input files
[Apr 22 09:30 AM]: Existing tbl found: ./update_results/Fusarium_oxysporum_47514.tbl
-------------------------------------------------------
Traceback (most recent call last):
  File "/scratch/miniconda_envs/funannotate/bin/funannotate", line 8, in <module>
    sys.exit(main())
  File "/scratch/miniconda_envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 717, in main
    mod.main(arguments)
  File "/scratch/miniconda_envs/funannotate/lib/python3.8/site-packages/funannotate/annotate.py", line 816, in main
    GeneCounts = lib.gb2nucleotides(
  File "/scratch/miniconda_envs/funannotate/lib/python3.8/site-packages/funannotate/library.py", line 3978, in gb2nucleotides
    gb_feature_add2dict(f, record, genes)
  File "/scratch/miniconda_envs/funannotate/lib/python3.8/site-packages/funannotate/library.py", line 4144, in gb_feature_add2dict
    start = f.location.nofuzzy_start + 1
AttributeError: 'SimpleLocation' object has no attribute 'nofuzzy_start'

OS/Install Information

Checking dependencies for 1.8.17
-------------------------------------------------------
You are running Python v 3.8.15. Now checking python packages...
biopython: 1.83
goatools: 1.2.3
matplotlib: 3.4.3
natsort: 8.4.0
numpy: 1.24.4
pandas: 1.5.3
psutil: 5.9.8
requests: 2.31.0
scikit-learn: 1.3.2
scipy: 1.10.1
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: 1.72
DBD::mysql: 4.046
DBI: 1.643
DB_File: 1.858
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=/scratch/miniconda_envs/funannotate/database/
$PASAHOME=/scratch/miniconda_envs/funannotate/opt/pasa-2.5.3
$TRINITY_HOME=/scratch/miniconda_envs/funannotate/opt/trinity-2.8.5
$EVM_HOME=/scratch/miniconda_envs/funannotate/opt/evidencemodeler-1.1.1
$AUGUSTUS_CONFIG_PATH=/scratch/miniconda_envs/funannotate/config/
$GENEMARK_PATH=/home/ufarooq/tools/gmes_linux_64_4/
All 6 environmental variables are set
-------------------------------------------------------
Checking external dependencies...
PASA: 2.5.3
CodingQuarry: 2.0
Trinity: 2.8.5
augustus: 3.5.0
bamtools: bamtools 2.5.1
bedtools: bedtools v2.31.1
blat: BLAT v37x1
diamond: 2.1.9
emapper.py: 2.1.12
ete3: 3.1.3
exonerate: exonerate 2.4.0
fasta: 36.3.8g
glimmerhmm: 3.0.4
gmap: 2024-03-15
hisat2: 2.2.1
hmmscan: HMMER 3.4 (Aug 2023)
hmmsearch: HMMER 3.4 (Aug 2023)
java: 11.0.1
kallisto: 0.46.1
mafft: v7.525 (2024/Mar/13)
makeblastdb: makeblastdb 2.15.0+
minimap2: 2.28-r1209
pigz: 2.8
proteinortho: 6.3.1
pslCDnaFilter: no way to determine
salmon: salmon 0.14.1
samtools: samtools 1.18
signalp: 5.0b
snap: 2006-07-28
stringtie: 2.2.1
tRNAscan-SE: 2.0.12 (Nov 2022)
tantan: tantan 49
tbl2asn: 25.8
tblastn: tblastn 2.15.0+
trimal: trimAl v1.4.rev15 build[2013-12-17]
trimmomatic: 0.39
        ERROR: gmes_petap.pl not installed

[vinsondoyle]

This is caused by a change in Biopython I believe:

"propertynofuzzy_start Start position (integer, approximated if fuzzy, read only) (OBSOLETE).

This is now an alias for int(feature.start), which should be used in preference – unless you are trying to support old versions of Biopython.

propertynofuzzy_end End position (integer, approximated if fuzzy, read only) (OBSOLETE).

This is now an alias for int(feature.end), which should be used in preference – unless you are trying to support old versions of Biopython."

This problem seems to be fixed by a simple find and replace of nofuzzy_start and nofuzzy_end

Ex: sed -i.bak "s/nofuzzy_start/start/g" /home/vinson/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py

sed -i.bak "s/nofuzzy_end/end/g" /home/vinson/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/library.py

[nextgenusfs]

Just downgrade biopython <1.80.

[ydanylko]

Just downgrade biopython <1.80.

Is remote phobius stopping at about 90% of the way also a known issue caused by this incompatibility with biopython < 1.80?