Augustus compilation error when installed from Conda

[Xueliang24]

Are you using the latest release? I used mamba create -n funannotate funannotate to install and use funannotate 1.8.11.

Describe the bug ERROR: augustus --proteinprofile test failed, likely a compilation error. This is required to run BUSCO, exiting. augustus is installed along with the installation of funannotate

What command did you issue? After I completed the installation，I ran funannotate test -t all --cpus 10

Logfiles Running funannotate clean unit testing: minimap2 mediated assembly duplications Downloading: https://osf.io/8pjbe/download?version=1 Bytes: 252076 CMD: funannotate clean -i test.clean.fa -o test.exhaustive.fa --exhaustive #########################################################

6 input contigs, 6 larger than 500 bp, N50 is 427,039 bp Checking duplication of 6 contigs

scaffold_73 appears duplicated: 100% identity over 100% of the contig. contig length: 15153 scaffold_91 appears duplicated: 100% identity over 100% of the contig. contig length: 8858 scaffold_27 appears duplicated: 100% identity over 100% of the contig. contig length: 427039

6 input contigs; 6 larger than 500 bp; 3 duplicated; 3 written to file ######################################################### SUCCESS: funannotate clean test complete. #########################################################

######################################################### Running funannotate mask unit testing: RepeatModeler --> RepeatMasker Downloading: https://osf.io/hbryz/download?version=1 Bytes: 375687 CMD: funannotate mask -i test.fa -o test.masked.fa --cpus 10 #########################################################

[Aug 01 09:26 AM]: OS: Ubuntu 20.04, 72 cores, ~ 264 GB RAM. Python: 3.8.12 [Aug 01 09:26 AM]: Running funanotate v1.8.11 [Aug 01 09:26 AM]: Soft-masking simple repeats with tantan [Aug 01 09:26 AM]: Repeat soft-masking finished: Masked genome: /home/chenxl/test-mask_4cb9d15e-0441-4475-97d9-9d9b0142c5c1/test.masked.fa num scaffolds: 2 assembly size: 1,216,048 bp masked repeats: 50,965 bp (4.19%)

######################################################### SUCCESS: funannotate mask test complete. #########################################################

######################################################### Running funannotate predict unit testing Downloading: https://osf.io/te2pf/download?version=1 Bytes: 1489808 CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 10 --species Awesome testicus]]]]]]]]]]]]#########################################################

[Aug 01 09:26 AM]: OS: Ubuntu 20.04, 72 cores, ~ 264 GB RAM. Python: 3.8.12 [Aug 01 09:26 AM]: Running funannotate v1.8.11 [Aug 01 09:26 AM]: Skipping CodingQuarry as no --rna_bam passed [Aug 01 09:26 AM]: Parsed training data, run ab-initio gene predictors as follows: Program Training-Method augustus pretrained
genemark selftraining
glimmerhmm busco
snap busco
augustus: ERROR PP::Profile: Error parsing pattern file"/pub/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/config/EOG092C0B3U.prfl", line 8. [Aug 01 09:26 AM]: ERROR: augustus --proteinprofile test failed, likely a compilation error. This is required to run BUSCO, exiting. ######################################################### Traceback (most recent call last): File "/pub/anaconda3/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/pub/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/pub/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 405, in main runPredictTest(args) File "/pub/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 160, in runPredictTest assert 1500 <= countGFFgenes(os.path.join( File "/pub/anaconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 45, in countGFFgenes with open(input, 'r') as f: FileNotFoundError: [Errno 2] No such file or directory: 'test-predict_4cb9d15e-0441-4475-97d9-9d9b0142c5c1/annotate/predict_results/Awesome_testicus.gff3'

OS/Install Information

Checking dependencies for 1.8.11

You are running Python v 3.8.12. Now checking python packages... biopython: 1.77 goatools: 1.2.3 matplotlib: 3.4.3 natsort: 8.1.0 numpy: 1.23.1 pandas: 1.4.3 psutil: 5.9.1 requests: 2.28.1 scikit-learn: 1.1.1 scipy: 1.9.0 seaborn: 0.11.2 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: 1.17 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: 2.000029 threads: 2.15 threads::shared: 1.56 All 27 Perl modules installed

Checking Environmental Variables... $FUNANNOTATE_DB=/pub/anaconda3/envs/funannotate/funannotate_db $PASAHOME=/pub/anaconda3/envs/funannotate/opt/pasa-2.5.2 $TRINITY_HOME=/pub/anaconda3/envs/funannotate/opt/trinity-2.8.5 $EVM_HOME=/pub/anaconda3/envs/funannotate/opt/evidencemodeler-1.1.1 $AUGUSTUS_CONFIG_PATH=/pub/anaconda3/envs/maker/config/ $GENEMARK_PATH=/pub/anaconda3/envs/funannotate/bin/gmes_petap All 6 environmental variables are set

Checking external dependencies... PASA: 2.5.2 CodingQuarry: 2.0 Trinity: 2.8.5 augustus: 3.4.0 bamtools: bamtools 2.5.1 bedtools: bedtools v2.30.0 blat: BLAT v35 diamond: 2.0.15 emapper.py: 2.1.9 ete3: 3.1.2 exonerate: exonerate 2.4.0 fasta: no way to determine glimmerhmm: 3.0.4 gmap: 2021-08-25 gmes_petap.pl: 4.69_lic hisat2: 2.2.1 hmmscan: HMMER 3.3.2 (Nov 2020) hmmsearch: HMMER 3.3.2 (Nov 2020) java: 1.8.0_332 kallisto: 0.46.1 mafft: v7.505 (2022/Apr/10) makeblastdb: makeblastdb 2.2.31+ minimap2: 2.24-r1122 pigz: pigz 2.6 proteinortho: 6.1.0 pslCDnaFilter: no way to determine salmon: salmon 0.14.1 samtools: samtools 1.12 signalp: 5.0b snap: 2006-07-28 stringtie: 2.2.1 tRNAscan-SE: 2.0.9 (July 2021) tantan: tantan 39 tbl2asn: no way to determine, likely 25.X tblastn: tblastn 2.2.31+ trimal: trimAl v1.4.rev15 build[2013-12-17] trimmomatic: 0.39 All 37 external dependencies are installed

[Xueliang24]

When I raised the issue, I have tried to replace the augustus. But the error also happened.

It means the error also happened when the augustus is 3.3.3 when augustus is installed along with the installation of funannotate

[nextgenusfs]

I don't know why the conda version of augustus are broken. Work around is to remove augustus installed via conda and install augustus from elsewhere, ie apt-get or manually compile.

[Xueliang24]

I have used the lastest version of singularity. It could be worked successfully.

[YDD99]

where i can get the lastest version of singularity？