cannot find annotate outputdir

[isgilman]

Are you using the latest release?
Version: v1.6.0-dfd805f

Describe the bug
I tried running annotate by passing my update_results directory and specifying a new output directory but received the following error:

Traceback (most recent call last):
  File "/gpfs/ysm/project/isg4/conda_envs/super_funannotate/funannotate/bin/funannotate-functional.py", line 508, in <module>
    annotTBL = os.path.join(outputdir, 'annotate_misc', 'genome.tbl')
NameError: name 'outputdir' is not defined

Looking at lines 494-508 of funannotate-functional.py

else:
    #should be a folder, with funannotate files, thus store results there, no need to create output folder
    if not os.path.isdir(args.input):
        lib.log.error("%s directory does not exist" % args.input)
        sys.exit(1)
    if os.path.isdir(os.path.join(args.input, 'update_results')): #funannotate results 1) in update folder or 2) in predict folder
        inputdir = os.path.join(args.input, 'update_results')
        outputdir = args.input
    elif os.path.isdir(os.path.join(args.input, 'predict_results')):
        inputdir = os.path.join(args.input, 'predict_results')
        outputdir = args.input
    else:
        inputdir = os.path.join(args.input) #here user specified the predict_results folder, or it is a custom folder
    
    annotTBL = os.path.join(outputdir, 'annotate_misc', 'genome.tbl')

it looks like the input it stringent about finding a predict_results or an update_results subdirectory within the directory passed as input, and if not, no outputdir is created, which is then referenced when creating annotTBL. Another set of conditions start at line 520-532 that might allow outputdir=args.out, but the script doesn't get that far because of annotTBL.

Running

funannotate annotate -i ../TRAIN/GeneMarkES_updated_weights_repeats2evm/ -o ./GeneMarkES_updated_weights_repeats2evm/ANNOTATE/ --eggnog GeneMarkES_updated_weights_repeats2evm/eggNOG/emapper.annotations --iprscan GeneMarkES_updated_weights_repeats2evm/InterProScan/Portulaca_amilis.proteins.fa.xml --busco_db embryophyta --cpus 16

where I didn't specify the update_results directory explicitly allowed the command to run without any problems.

What command did you issue?

funannotate annotate -i ../TRAIN/GeneMarkES_updated_weights_repeats2evm/update_results/ -o ./GeneMarkES_updated_weights_repeats2evm/ANNOTATE/ --eggnog GeneMarkES_updated_weights_repeats2evm/eggNOG/emapper.annotations --iprscan GeneMarkES_updated_weights_repeats2evm/InterProScan/Portulaca_amilis.proteins.fa.xml --busco_db embryophyta --cpus 16

Logfiles

[07/08/19 12:05:03]: /gpfs/ysm/project/isg4/conda_envs/super_funannotate/funannotate/bin/funannotate-functional.py -i ../TRAIN/GeneMarkES_updated_weights_repeats2evm/update_results/ -o ./GeneMarkES_updated_weights_repeats2evm/ANNOTATE/ --eggnog GeneMarkES_updated_weights_repeats2evm/eggNOG/emapper.annotations --iprscan GeneMarkES_updated_weights_repeats2evm/InterProScan/Portulaca_amilis.proteins.fa.xml --busco_db embryophyta --cpus 16

[07/08/19 12:05:03]: OS: linux2, 20 cores, ~ 131 GB RAM. Python: 2.7.15
[07/08/19 12:05:03]: Running funannotate v1.6.0-dfd805f
[07/08/19 12:05:03]: No NCBI SBT file given, will use default, however if you plan to submit to NCBI, create one and pass it here '--sbt'
[07/08/19 12:05:03]: Output directory ../TRAIN/GeneMarkES_updated_weights_repeats2evm/update_results already exists, will use any existing data.  If this is not what you want, exit, and provide a unique name for output folder
[07/08/19 12:05:03]: Parsing input files
[07/08/19 12:05:03]: Existing tbl found: ../TRAIN/GeneMarkES_updated_weights_repeats2evm/update_results/Portulaca_amilis.tbl

OS/Install Information

-------------------------------------------------------
Checking dependencies for funannotate v1.6.0-dfd805f
-------------------------------------------------------
You are running Python v 2.7.15. Now checking python packages...
biopython: 1.73
goatools: 0.8.12
matplotlib: 2.2.3
natsort: 6.0.0
numpy: 1.16.3
pandas: 0.24.2
psutil: 5.6.2
requests: 2.21.0
scikit-learn: 0.20.3
scipy: 1.2.1
seaborn: 0.9.0
All 11 python packages installed


You are running Perl v 5.026002. Now checking perl modules...
Bio::Perl: 1.007002
Carp: 1.38
Clone: 0.41
DBD::SQLite: 1.60
DBD::mysql: 4.046
DBI: 1.642
DB_File: 1.852
Data::Dumper: 2.173
File::Basename: 2.85
File::Which: 1.23
Getopt::Long: 2.5
Hash::Merge: 0.300
JSON: 4.00
LWP::UserAgent: 6.36
Logger::Simple: 2.0
POSIX: 1.76
Parallel::ForkManager: 2.02
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 3.11
Text::Soundex: 3.05
Thread::Queue: 3.13
Tie::File: 1.02
URI::Escape: 3.31
YAML: 1.27
threads: 2.21
threads::shared: 1.59
All 27 Perl modules installed


Checking external dependencies...
CodingQuarry: 2.0
RepeatMasker: RepeatMasker 4.0.8
RepeatModeler: RepeatModeler version DEV
Trinity: 2.5.1
augustus: 3.2.3
bamtools: bamtools 2.4.1
bedtools: bedtools v2.28.0
blat: BLAT v36
diamond: diamond 0.9.24
emapper.py: emapper-0.12.7
ete3: 3.1.1
exonerate: exonerate 2.4.0
fasta: no way to determine
gmap: 2018-07-04
gmes_petap.pl: 4.38
hisat2: 2.1.0
hmmscan: HMMER 3.2.1 (June 2018)
hmmsearch: HMMER 3.2.1 (June 2018)
java: 11.0.1
kallisto: 0.45.1
mafft: v7.407 (2018/Jul/23)
makeblastdb: makeblastdb 2.6.0+
minimap2: 2.16-r922
nucmer: 3.1
pslCDnaFilter: no way to determine
rmblastn: rmblastn 2.6.0+
samtools: samtools 1.9
stringtie: 1.3.6
tRNAscan-SE: 2.0 (December 2017)
tbl2asn: unknown, likely 25.3
tblastn: tblastn 2.6.0+
trimal: trimAl v1.4.rev15 build[2013-12-17]
All 32 external dependencies are installed

Checking Environmental Variables...
$FUNANNOTATE_DB=/gpfs/ysm/scratch60/isg4/Pamilis_funannotate/TRAIN/funannotate_database
$PASAHOME=/gpfs/ysm/project/isg4/conda_envs/super_funannotate/funannotate_deps/PASApipeline
$TRINITYHOME=/gpfs/ysm/project/isg4/conda_envs/super_funannotate/opt/trinity-2.5.1
$EVM_HOME=/gpfs/ysm/project/isg4/conda_envs/super_funannotate/funannotate_deps/evidencemodeler
$AUGUSTUS_CONFIG_PATH=/gpfs/ysm/project/isg4/conda_envs/super_funannotate/config/
$GENEMARK_PATH=/gpfs/ysm/project/isg4/conda_envs/super_funannotate/funannotate_deps/gmes_petap
$BAMTOOLS_PATH=/gpfs/ysm/project/isg4/conda_envs/super_funannotate/bin
All 7 environmental variables are set

[nextgenusfs]

Thanks -- I'll get it fixed.