Funannotate test error

[rissidaniel]

Are you using the latest release? 1.8.9

Describe the bug When running funannotate test -t all --cpus 90, I endup having the error below, despite of the "funannotate check --show-versions" show everything installed and with all path defined.

[May 16 01:02 PM]: Pulling out high quality Augustus predictions [May 16 01:02 PM]: Found 314 high quality predictions from Augustus (>90% exon evidence) [May 16 01:02 PM]: Running SNAP gene prediction, using training data: annotate/predict_misc/busco.final.gff3 [May 16 01:02 PM]: 2 predictions from SNAP [May 16 01:02 PM]: Running GlimmerHMM gene prediction, using training data: annotate/predict_misc/busco.final.gff3 [May 16 01:04 PM]: 1,773 predictions from GlimmerHMM [May 16 01:04 PM]: Summary of gene models passed to EVM (weights): [May 16 01:04 PM]: EVM: partitioning input to ~ 35 genes per partition using min 1500 bp interval Traceback (most recent call last): File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-runEVM.py", line 479, in cmdinfo = create_partitions(args.fasta, args.genes, partitions, File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-runEVM.py", line 131, in create_partitions SeqRecords = SeqIO.index_db(f_idx, fasta, 'fasta') File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/Bio/SeqIO/init.py", line 1018, in index_db return _SQLiteManySeqFilesDict( File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/Bio/File.py", line 331, in init self._build_index() File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/Bio/File.py", line 462, in _build_index con.execute("CREATE TABLE meta_data (key TEXT, value TEXT);") sqlite3.OperationalError: database is locked ^[[4mSource Weight Count^[[0m Augustus 1 991 Augustus HiQ 2 314 GeneMark 1 1559 GlimmerHMM 1 1773 snap 1 2 Total - 4639 [May 16 01:04 PM]: Evidence modeler has failed, exiting Traceback (most recent call last): File "/mnt/mountdoom/mnt/work/bioinfo/home/dar21/miniconda3/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/predict.py", line 1790, in main os.remove(EVM_out) FileNotFoundError: [Errno 2] No such file or directory: '/mnt/mountdoom/mnt/work/bioinfo/home/dar21/genomes/ncbi_genomes/funannotate_test/Margaritispora_aquatica/test-busco_62c37d98-95b0-42a2-bc15-82cbdfd2c369/annotate/predict_misc/evm.round1.gff3' CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --augustus_species saccharomyces --cpus 90 --species Awesome testicus ######################################################### ######################################################### SUCCESS: funannotate predict test complete. #########################################################

######################################################### Running funannotate predict BUSCO-mediated training unit testing CMD: funannotate predict -i test.softmasked.fa --protein_evidence protein.evidence.fasta -o annotate --cpus 90 --species Awesome busco ######################################################### ######################################################### Traceback (most recent call last): File "/mnt/mountdoom/mnt/work/bioinfo/home/dar21/miniconda3/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 705, in main mod.main(arguments) File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 407, in main runBuscoTest(args) File "/home/dar21/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 200, in runBuscoTest assert 1500 <= countGFFgenes(os.path.join( File "/home/dar21/miniconda3/envs/funannotat slurm-51658947.txt e/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-busco_62c37d98-95b0-42a2-bc15-82cbdfd2c369/annotate/predict_results/Awesome_busco.gff3' funannotate finished

What command did you issue? funannotate test -t all --cpus 90

Logfiles Done it

OS/Install Information Included in the logfile

[rissidaniel]

slurm-51658947.txt

[nextgenusfs]

Sorry for late response, so in your logfile I see that SNAP seems to be failing, I think on debian systems the conda version of snap is broken. You can remove it and install with apt-get which should fix SNAP and it will hopefully predict genes. I'm not sure, but I think perhaps EVM choked on some incomplete gene model that the broken SNAP executable generated.

[May 16 01:02 PM]: 2 predictions from SNAP

In a functioning version of SNAP you should see something like 1500 gene models predicted.