funannotate check produces TypeError

Hi,

I am sorry I am coming to you but I seem to have exhausted all my options.

I have installed funannotate in an LSF but I can't seem to get it to work. When I run funannotate check I get the following:

Checking dependencies for funannotate v1.4.2-b1d62e5

To print all dependencies and versions: funannotate check --show-versions

You are running Python v 2.7.5. Now checking python packages... All 11 python packages installed

You are running Perl v 5.016003. Now checking perl modules... All 27 Perl modules installed

Checking external dependencies... [main] unrecognized command '--version' Traceback (most recent call last): File "/homes/joachim/Tools/funannotate/funannotate/util/check_modules.py", line 250, in ExtDeps[prog] = check_version2(prog) File "/homes/joachim/Tools/funannotate/funannotate/util/check_modules.py", line 93, in check_version2 if 'exonerate' in vers: TypeError: argument of type 'bool' is not iterable.

What do you think I can do about getting it to work?

A little hint: I have also been struggling with the standalone version of gmes_petap.pl. The program keeps giving the following error:

warning on: /homes/joachim/Downloads/GeneMark/gm_et_linux_64/gmes_petap/gmhmme3 -m /nfs/nobackup/ensemblgenomes/joachim/annotation_cgppipeline/run/ES_ini/es_ini.mod -f tr -o /nfs/nobackup/ensemblgenomes/joachim/annotation_cgppipeline/run/ES_A_1/hmmout/dna.fa_12340.out /nfs/nobackup/ensemblgenomes/joachim/annotation_cgppipeline/data/training/dna.fa_12340 error, file not found /homes/joachim/Downloads/GeneMark/gm_et_linux_64/gmes_petap/parse_set.pl: set.out error on call: /homes/joachim/Downloads/GeneMark/gm_et_linux_64/gmes_petap/parse_set.pl --section ES_A --cfg /nfs/nobackup/ensemblgenomes/joachim/annotation_cgppipeline/run.cfg --v

I look forward to your response.

Many thanks,

Joachim

Is exonerate installed?, i.e. what is result of exonerate --version? Maybe old version of exonerate that doesn't have the --version flag?

But maybe something else entirely as seems like that part of the script dies right away when looking at the external dependencies. Basically its using the subprocess python module to launch those external dependencies and try to look for version numbers -- it is of course a pain because these programs have different syntax, i.e. --version doesn't work on everything and thus there are several different methods employed from subprocess result parsing to get the desired results. Your version of Python is also quite old (released in 2013) -- wondering if the script is using something not present in your Python release.

Hi Jon,

Thank you very much for getting back to me.

I do have exonerate and when I run exonerate --version, I get the following output:

"exonerate from exonerate version 2.4.0

Using glib version 2.46.2

Built on Jul 26 2018"

I have also changed my default python so that when I type python --version, I now get:

Python 3.5.2

However when I run the funannotate check again, I still get the same error.

What else do you think I should try?

Many thanks,

Joachim

From: Jon Palmer notifications@github.com Sent: 01 August 2018 16:51 To: nextgenusfs/funannotate Cc: Joachim Nwezeobi; Author Subject: Re: [nextgenusfs/funannotate] funannotate check produces TypeError (#205)

Is exonerate installed?, i.e. what is result of exonerate --version? Maybe old version of exonerate that doesn't have the --version flag?

But maybe something else entirely as seems like that part of the script dies right away when looking at the external dependencies. Basically its using the subprocess python module to launch those external dependencies and try to look for version numbers -- it is of course a pain because these programs have different syntax, i.e. --version doesn't work on everything and thus there are several different methods employed from subprocess result parsing to get the desired results. Your version of Python is also quite old (released in 2013) -- wondering if the script is using something not present in your Python release.

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nextgenusfs/funannotate/issues/205#issuecomment-409622411, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Af3f3bCvVH7Tl-vFH8EUedJfsSgy7Cgyks5uMc6PgaJpZM4Vm3cI.

University of Greenwich, a charity and company limited by guarantee, registered in England (reg. no. 986729). Registered office: Old Royal Naval College, Park Row, Greenwich, London SE10 9LS.

It’s not python3 compatible at the moment. If you think all dependencies are installed you can try to run the sample data and see what happens.

Hi Jon,

I ran the run_unit_tests.sh file on the sample folder. The program ran for a short while and was killed. When I checked the log file, I got the following:

2018-08-01 19:20:07,149: /homes/joachim/Tools/funannotate/funannotate-1.0.0/bin/funannotate-functional.py --gff genome1/predict_results/genome_one.gff3 --fasta genome1/predict_results/genome_one.scaffolds.fa --proteins genome1/predict_results/genome_one.proteins.fa --iprscan test_data.iprscan.xml --eggnog genome1.emapper.annotations -o direct -s Aspergillus fumigatus

2018-08-01 19:20:07,193: OS: linux2, 80 cores, ~ 262 GB RAM. Python: 2.7.5 2018-08-01 19:20:07,362: Running funannotate v1.0.0 2018-08-01 19:20:07,378: Augustus species folder not found at /homes/joachim/perl5/bin:/usr/lib64/qt-3.3/bin:/ebi/lsf/ebi/9.1/linux2.6-glibc2.3-x86_64/etc:/ebi/lsf/ebi/9.1/linux2.6-glibc2.3-x86_64/bin:/usr/kerberos/sbin:/usr/kerberos/bin:/usr/lpp/mmfs/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/homes/joachim/Database/ncbi_blast_2.6.0/ncbi-blast-2.6.0+/bin:/homes/joachim/Tools/SPAdes-3.11.1-Linux/bin:/homes/joachim/bin:/homes/joachim/.local/bin:/homes/joachim/Tools/bbmap:/homes/joachim/Tools/Trimmomatic-0.36/trimmomatic-0.36.jar:/homes/joachim/Downloads/Quake/bin:/home/.local/bin:/homes/joachim/pear/bin/pear:/homes/joachim/Downloads/redundans:/homes/joachim/Downloads/redundans/bin:/homes/joachim/Downloads/FastUniq/source:/homes/joachim/Tools/GapCloser:/nfs/production/panda/ensemblgenomes/development/iarmean/sw/discovardenovo-52488/src:/homes/joachim/Downloads/bwa-0.5.0:/homes/joachim/Downloads/bamtools-2.4.1/bin:/homes/joachim/Downloads/Reapr_1.0.18:/nfs/panda/ensemblgenomes/external/hmmer-3/binaries:/homes/joachim/Downloads/augustus/bin:/homes/joachim/Downloads/augustus/scripts:/homes/joachim/Downloads/augustus/config/species, exiting

It seem it is not able to find the augustus species folder. The folder do exist and I have set the following environments as follows:

export FUNANNOTATE_DB=/nfs/nobackup/ensemblgenomes/joachim/annotation_funannotate/funannotate_database export PASAHOME=/homes/joachim/Tools/funannotate/PASApipeline-v2.3.3 export TRINITYHOME=/nfs/panda/ensemblgenomes/external/trinity export EVM_HOME=/homes/joachim/Tools/funannotate/EVidenceModeler-1.1.1 export AUGUSTUS_CONFIG_PATH=/homes/joachim/augustus/config export GENEMARK_PATH=/homes/joachim/Downloads/GeneMark/gm_et_linux_64/gmes_petap export BAMTOOLS_PATH=/homes/joachim//Downloads/bamtools-2.4.1/bin?

What do you think I am doing wrong?

Many thanks,

Joachim

From: Jon Palmer notifications@github.com Sent: 01 August 2018 18:21 To: nextgenusfs/funannotate Cc: Joachim Nwezeobi; Author Subject: Re: [nextgenusfs/funannotate] funannotate check produces TypeError (#205)

It's not python3 compatible at the moment. If you think all dependencies are installed you can try to run the sample data and see what happens.

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nextgenusfs/funannotate/issues/205#issuecomment-409653292, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Af3f3WcfNtOJpep5VvxpAn2MFbivXh6Bks5uMeOGgaJpZM4Vm3cI.

University of Greenwich, a charity and company limited by guarantee, registered in England (reg. no. 986729). Registered office: Old Royal Naval College, Park Row, Greenwich, London SE10 9LS.

Yes, sorry about that - that bash script is what I run locally and there aren't some of those files on there so the repo doesn't become large in size. If the first 3 examples worked out, then you should be okay for prediction step at least. You can open that bash script and pull out the commands for funannotate annotate and see if that is working as well (will need to modify as per the IPRscan results).

But there is potentially something else wrong, i.e. the version of funannotate says v1.0.0. So is there another install on your cluster? Seems like something isn't quite right?

Hi Jon,

You are right. I have had to uninstall the former version and installed v1.0.0.

When I ran a section of funannotate predict I got the following error:

funannotate predict -i genome3.fasta -s "Genome three" --name GN3_ -o genome3 --protein_evidence proteins.fa --transcript_evidence transcripts.fa --augustus_species botrytis_cinerea --cpus 6

[08:59:23 PM]: OS: linux2, 32 cores, ~ 132 GB RAM. Python: 2.7.5 [08:59:24 PM]: Running funannotate v1.0.0 [08:59:25 PM]: Augustus training set for botrytis_cinerea already exists, using existing parameters. If you want to re-train, provide a unique name for the --augustus_species argument [08:59:28 PM]: AUGUSTUS (3.3) detected, version seems to be compatible with BRAKER1 and BUSCO [08:59:28 PM]: Loading sequences and soft-masking genome [08:59:28 PM]: Soft-masking: building RepeatModeler database [08:59:28 PM]: Soft-masking: generating repeat library using RepeatModeler [09:00:07 PM]: Soft-masking: running RepeatMasker with default library (RepeatModeler found 0 models)

Traceback (most recent call last): File "/homes/joachim/Tools/funannotate/funannotate-1.0.0/bin/funannotate-predict.py", line 363, in lib.RepeatModelMask(Genome, args.cpus, os.path.join(args.out, 'predict_misc'), MaskGenome, debug) File "/homes/joachim/Tools/funannotate/funannotate-1.0.0/lib/library.py", line 1797, in RepeatModelMask runSubprocess2(cmd, outdir2, log, rm_gff3) File "/homes/joachim/Tools/funannotate/funannotate-1.0.0/lib/library.py", line 391, in runSubprocess2 proc = subprocess.Popen(cmd, cwd=dir, stdout=out, stderr=subprocess.PIPE) File "/usr/lib64/python2.7/subprocess.py", line 711, in init errread, errwrite) File "/usr/lib64/python2.7/subprocess.py", line 1327, in _execute_child raise child_exception OSError: [Errno 40] Too many levels of symbolic links?"

I don't know what the OSError means or how to deal with it.

Many thanks,

Joachim

From: Jon Palmer notifications@github.com Sent: 01 August 2018 20:39 To: nextgenusfs/funannotate Cc: Joachim Nwezeobi; Author Subject: Re: [nextgenusfs/funannotate] funannotate check produces TypeError (#205)

But there is potentially something else wrong, i.e. the version of funannotate says v1.0.0. So is there another install on your cluster? Seems like something isn't quite right?

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nextgenusfs/funannotate/issues/205#issuecomment-409696540, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Af3f3YseTG_8XaPVgrGMzIBAKHe_rNemks5uMgPigaJpZM4Vm3cI.

University of Greenwich, a charity and company limited by guarantee, registered in England (reg. no. 986729). Registered office: Old Royal Naval College, Park Row, Greenwich, London SE10 9LS.

I had to install the latest funannotate after realising some of the errors I noticed have been dealt with by newer releases.

I now ran funannotate predict on one of the sample data and it came up with an Attribute error. The log is as follows:

funannotate predict -i genome1.fasta --force -s "Genome one" --name GN1_ -o genome1 --protein_evidence proteins.fa --transcript_evidence transcripts.fa --augustus_species botrytis_cinerea --cpus 16

[08:31 AM]: OS: linux2, 32 cores, ~ 132 GB RAM. Python: 2.7.5 [08:31 AM]: Running funannotate v1.4.2 [08:31 AM]: Augustus training set for botrytis_cinerea already exists. To re-train provide unique --augustus_species argument [08:31 AM]: AUGUSTUS (3.3) detected, version seems to be compatible with BRAKER and BUSCO [08:31 AM]: Loading genome assembly and parsing soft-masked repetitive sequences [08:31 AM]: Genome loaded: 3 scaffolds; 451,050 bp; 0.00% repeats masked [08:31 AM]: Aligning transcript evidence to genome with minimap2 Traceback (most recent call last): File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/bin/funannotate-predict.py", line 510, in minimapCount = lib.bam2ExonsHints(minimapBAM, minimapGFF3, hintsM) File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/lib/library.py", line 1409, in bam2ExonsHints for num,aln in enumerate(pybam.read(os.path.realpath(input))): File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/lib/pybam.py", line 328, in init while len(header_cache) < 8: header_cache += next(self._generator) File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/lib/pybam.py", line 173, in generator except: raise PybamError('\n\nCould not open "' + str(self._file.name) + '" for reading!\n') AttributeError: read instance has no attribute '_file' Exception AttributeError: "read instance has no attribute '_subprocess'" in <bound method read.del of <lib.pybam.read instance at 0x2b039e0>> ignored?

Many thanks

But there is potentially something else wrong, i.e. the version of funannotate says v1.0.0. So is there another install on your cluster? Seems like something isn't quite right?

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nextgenusfs/funannotate/issues/205#issuecomment-409696540, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Af3f3YseTG_8XaPVgrGMzIBAKHe_rNemks5uMgPigaJpZM4Vm3cI.

University of Greenwich, a charity and company limited by guarantee, registered in England (reg. no. 986729). Registered office: Old Royal Naval College, Park Row, Greenwich, London SE10 9LS.

It looks like it can't find transcripts.fa. Not sure if this is related to the realpath call or not? Can you try adding the pull path to these files, i.e. $PWD/transcripts.fa should work. I think I've maybe seen some errors like this before on some clusters -- having to do with how the filesystem is mounted and levels of symlinks, but generally I'm clueless about these types of setups.

I did as you asked but still got the error:

funannotate predict -i genome1.fasta --force -s "Genome one" --name GN1_ -o genome1 --protein_evidence $PWD/proteins.fa --transcript_evidence $PWD/transcripts.fa --augustus_species botrytis_cinerea --cpus 16

[05:14 PM]: OS: linux2, 32 cores, ~ 132 GB RAM. Python: 2.7.5 [05:14 PM]: Running funannotate v1.4.2 [05:14 PM]: Augustus training set for botrytis_cinerea already exists. To re-train provide unique --augustus_species argument [05:14 PM]: AUGUSTUS (3.3) detected, version seems to be compatible with BRAKER and BUSCO [05:14 PM]: Loading genome assembly and parsing soft-masked repetitive sequences [05:14 PM]: Genome loaded: 3 scaffolds; 451,050 bp; 0.00% repeats masked [05:14 PM]: Aligning transcript evidence to genome with minimap2 Traceback (most recent call last): File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/bin/funannotate-predict.py", line 510, in minimapCount = lib.bam2ExonsHints(minimapBAM, minimapGFF3, hintsM) File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/lib/library.py", line 1409, in bam2ExonsHints for num,aln in enumerate(pybam.read(os.path.realpath(input))): File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/lib/pybam.py", line 328, in init while len(header_cache) < 8: header_cache += next(self._generator) File "/homes/joachim/Tools/funannotate/funannotate-1.4.2/lib/pybam.py", line 173, in generator except: raise PybamError('\n\nCould not open "' + str(self._file.name) + '" for reading!\n') AttributeError: read instance has no attribute '_file' Exception AttributeError: "read instance has no attribute '_subprocess'" in <bound method read.del of <lib.pybam.read instance at 0x2dd99e0>> ignored?

From: Jon Palmer notifications@github.com Sent: 02 August 2018 17:08 To: nextgenusfs/funannotate Cc: Joachim Nwezeobi; Author Subject: Re: [nextgenusfs/funannotate] funannotate check produces TypeError (#205)

It looks like it can't find transcripts.fa. Not sure if this is related to the realpath call or not? Can you try adding the pull path to these files, i.e. $PWD/transcripts.fa should work. I think I've maybe seen some errors like this before on some clusters -- having to do with how the filesystem is mounted and levels of symlinks, but generally I'm clueless about these types of setups.

- You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/nextgenusfs/funannotate/issues/205#issuecomment-409980260, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Af3f3efaeJsaqdnMblE6gIkf7jJqDx-Bks5uMyP6gaJpZM4Vm3cI.

University of Greenwich, a charity and company limited by guarantee, registered in England (reg. no. 986729). Registered office: Old Royal Naval College, Park Row, Greenwich, London SE10 9LS.

I'm unable to replicate this behavior locally. I setup a python 2.7.5 virtual environment with conda and ran the following:

$ funannotate check --show-versions
-------------------------------------------------------
Checking dependencies for funannotate v1.4.2-9eeef3d
-------------------------------------------------------
You are running Python v 2.7.5. Now checking python packages...
biopython: 1.68
goatools: 0.8.4
matplotlib: 2.2.2
natsort: 5.3.3
numpy: 1.13.1
pandas: 0.23.3
psutil: 5.4.6
requests: 2.19.1
scikit-learn: 0.19.0
scipy: 0.19.1
seaborn: 0.9.0
All 11 python packages installed

You are running Perl v 5.026001. Now checking perl modules...
Bio::Perl: 1.007002
Carp: 1.42
Clone: 0.39
DBD::SQLite: 1.56
DBD::mysql: 4.046
DBI: 1.641
DB_File: 1.84
Data::Dumper: 2.167
File::Basename: 2.85
File::Which: 1.22
Getopt::Long: 2.5
Hash::Merge: 0.300
JSON: 2.97001
LWP::UserAgent: 6.33
Logger::Simple: 2.0
POSIX: 1.76
Parallel::ForkManager: 1.19
Pod::Usage: 1.69
Scalar::Util::Numeric: 0.40
Storable: 2.62
Text::Soundex: 3.05
Thread::Queue: 3.12
Tie::File: 1.02
URI::Escape: 3.31
YAML: 1.24
threads: 2.21
threads::shared: 1.58
All 27 Perl modules installed

Checking external dependencies...
RepeatMasker: RepeatMasker 4.0.7
RepeatModeler: RepeatModeler 1.0.11
Trinity: 2.5.1
augustus: 3.2.1
bamtools: bamtools 2.4.1
bedtools: bedtools v2.27.1
blat: BLAT v35
diamond: diamond 0.9.19
emapper.py: emapper-1.0.3
ete3: 3.1.1
exonerate: exonerate 2.4.0
fasta: no way to determine
gmap: 2017-06-20
gmes_petap.pl: 4.30
hisat2: 2.0.5
hmmscan: HMMER 3.1b2 (February 2015)
hmmsearch: HMMER 3.1b2 (February 2015)
java: 1.8.0_92
kallisto: 0.43.1
mafft: v7.313 (2017/Nov/15)
makeblastdb: makeblastdb 2.7.1+
minimap2: 2.11-r797
nucmer: 3.1
pslCDnaFilter: no way to determine
rmblastn: rmblastn 2.2.27+
samtools: samtools 1.8
tRNAscan-SE: 1.23 (April 2002)
tbl2asn: unknown, likely 25.3
tblastn: tblastn 2.7.1+
trimal: trimAl v1.4.rev15 build[2013-12-17]
All 30 external dependencies are installed

Checking Environmental Variables...
$FUNANNOTATE_DB=/usr/local/share/funannotate
$PASAHOME=/Users/jon/software/PASApipeline
$TRINITYHOME=/usr/local/opt/trinity
$EVM_HOME=/Users/jon/software/evidencemodeler
$AUGUSTUS_CONFIG_PATH=/Users/jon/software/augustus/config
$GENEMARK_PATH=/Users/jon/software/gmes_petap
$BAMTOOLS_PATH=/Users/jon/software/bamtools-2.4.0/bin
All 7 environmental variables are set
-------------------------------------------------------

$ funannotate predict -i genome1.fasta --force -s "Genome one" --name GN1_ -o genome1 --protein_evidence proteins.fa --transcript_evidence transcripts.fa --augustus_species botrytis_cinerea --cpus 6
-------------------------------------------------------
[Aug 03 08:59 AM]: OS: MacOSX 10.13.6, 8 cores, ~ 17 GB RAM. Python: 2.7.5
[Aug 03 08:59 AM]: Running funannotate v1.4.2-9eeef3d
[Aug 03 08:59 AM]: Augustus training set for botrytis_cinerea already exists. To re-train provide unique --augustus_species argument
[Aug 03 08:59 AM]: AUGUSTUS (3.2.1) detected, version seems to be compatible with BRAKER and BUSCO
[Aug 03 08:59 AM]: Loading genome assembly and parsing soft-masked repetitive sequences
[Aug 03 08:59 AM]: Genome loaded: 3 scaffolds; 451,050 bp; 0.00% repeats masked
[Aug 03 08:59 AM]: Aligning transcript evidence to genome with minimap2
[Aug 03 08:59 AM]: Found 198 alignments, wrote GFF3 and Augustus hints to file
[Aug 03 08:59 AM]: Mapping proteins to genome using Diamond blastx/Exonerate
[Aug 03 08:59 AM]: Using 9,043 proteins as queries
[Aug 03 08:59 AM]: Running Diamond pre-filter search
[Aug 03 08:59 AM]: Found 520 preliminary alignments
[Aug 03 08:59 AM]: Exonerate finished: found 98 alignments
[Aug 03 08:59 AM]: Running GeneMark-ES on assembly
[Aug 03 09:00 AM]: Converting GeneMark GTF file to GFF3
[Aug 03 09:00 AM]: Found 113 gene models
[Aug 03 09:00 AM]: Running Augustus gene prediction
[Aug 03 09:01 AM]: Found 178 gene models
[Aug 03 09:01 AM]: Pulling out high quality Augustus predictions
[Aug 03 09:01 AM]: Found 84 high quality predictions from Augustus (>90% exon evidence)
[Aug 03 09:01 AM]: Summary of gene models passed to EVM (weights):
-------------------------------------------------------
Augustus models (1):    99
Genemark models (1):    113
HiQ models (5):     88
Pasa models (1):    0
Total models:       300
-------------------------------------------------------
[Aug 03 09:01 AM]: Setting up EVM partitions
[Aug 03 09:01 AM]: Generating EVM command list
[Aug 03 09:01 AM]: Running EVM commands with 5 CPUs
[Aug 03 09:01 AM]: Combining partitioned EVM outputs
[Aug 03 09:01 AM]: Converting EVM output to GFF3
[Aug 03 09:01 AM]: Collecting all EVM results
[Aug 03 09:01 AM]: 176 total gene models from EVM
[Aug 03 09:01 AM]: Generating protein fasta files from 176 EVM models
[Aug 03 09:01 AM]: now filtering out bad gene models (< 50 aa in length, transposable elements, etc).
[Aug 03 09:02 AM]: Found 52 gene models to remove: 0 too short; 0 span gaps; 52 transposable elements
[Aug 03 09:02 AM]: 124 gene models remaining
[Aug 03 09:02 AM]: Predicting tRNAs
[Aug 03 09:02 AM]: Found 1 tRNA gene models
[Aug 03 09:02 AM]: 1 tRNAscan models are valid (non-overlapping)
[Aug 03 09:02 AM]: Generating GenBank tbl annotation file
[Aug 03 09:02 AM]: Converting to final Genbank format
[Aug 03 09:02 AM]: Collecting final annotation files for 125 total gene models
[Aug 03 09:02 AM]: Funannotate predict is finished, output files are in the genome1/predict_results folder
[Aug 03 09:02 AM]: Your next step might be functional annotation, suggested commands:
-------------------------------------------------------
Run InterProScan (Docker required): 
funannotate iprscan -i genome1 -m docker -c 6

Run antiSMASH: 
funannotate remote -i genome1 -m antismash -e youremail@server.edu

Annotate Genome: 
funannotate annotate -i genome1 --cpus 6 --sbt yourSBTfile.txt
-------------------------------------------------------

Everything runs as it should. So it doesn't appear to be the Python version or the code. I don't know what to try next.

nextgenusfs / funannotate