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nextgenusfs / funannotate

Eukaryotic Genome Annotation Pipeline
http://funannotate.readthedocs.io
BSD 2-Clause "Simplified" License
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Funannotate predict stuck at Augustus step #976

Closed krostifangers closed 4 months ago

krostifangers commented 8 months ago

Hello I use funnanotate for my fungus gene prediction and annotation. I used funannotate test using the following command : funannotate test -t busco --cpus 16 and get the following result (see below) : Apparently, augustus_parallel.py cannot import Bio::SeqIO although Bio::SeqIO is available in the funannotate package. I should mention that I removed augustus from funannotate and I use the 3.4.0 version of Augustus installed on my computer. Can you help me? All the best Christophe

funannotate test -t busco --cpus 16 ######################################################### Running funannotate predict BUSCO-mediated training 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 --cpus 16 --species Awesome busco #########################################################

[Oct 27 11:35 AM]: OS: Debian GNU/Linux 11, 16 cores, ~ 32 GB RAM. Python: 3.8.15 [Oct 27 11:35 AM]: Running funannotate v1.8.15 [Oct 27 11:35 AM]: Skipping CodingQuarry as no --rna_bam passed [Oct 27 11:35 AM]: Parsed training data, run ab-initio gene predictors as follows: Program Training-Method augustus busco
genemark selftraining
glimmerhmm busco
snap busco
[Oct 27 11:35 AM]: Loading genome assembly and parsing soft-masked repetitive sequences [Oct 27 11:35 AM]: Genome loaded: 6 scaffolds; 3,776,588 bp; 19.75% repeats masked /home/krostif/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/funannotate-p2g.py:14: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html from pkg_resources import parse_version [Oct 27 11:35 AM]: Mapping 1,065 proteins to genome using diamond and exonerate [Oct 27 11:35 AM]: Found 1,505 preliminary alignments with diamond in 0:00:00 --> generated FASTA files for exonerate in 0:00:00 Progress: 1505 complete, 0 failed, 0 remaining
[Oct 27 11:35 AM]: Exonerate finished in 0:00:08: found 1,270 alignments [Oct 27 11:35 AM]: Running GeneMark-ES on assembly [Oct 27 11:36 AM]: 1,557 predictions from GeneMark [Oct 27 11:36 AM]: Running BUSCO to find conserved gene models for training ab-initio predictors [Oct 27 11:39 AM]: 370 valid BUSCO predictions found, validating protein sequences [Oct 27 11:39 AM]: 367 BUSCO predictions validated [Oct 27 11:39 AM]: Training Augustus using BUSCO gene models [Oct 27 11:39 AM]: Augustus initial training results: Feature Specificity Sensitivity nucleotides 99.4% 83.8%
exons 63.2% 52.6%
genes 76.7% 51.4%
[Oct 27 11:39 AM]: Running Augustus gene prediction using awesome_busco parameters Traceback (most recent call last): File "/home/krostif/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/aux_scripts/augustus_parallel.py", line 9, in from Bio import SeqIO ImportError: No module named Bio [Oct 27 11:39 AM]: CMD ERROR: perl /home/krostif/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl annotate/predict_misc/augustus.gff3 [Oct 27 11:39 AM]: Error, cannot open file annotate/predict_misc/augustus.gff3 at /home/krostif/miniconda3/envs/funannotate/opt/evidencemodeler-1.1.1/EvmUtils/misc/augustus_GFF3_to_EVM_GFF3.pl line 23.

######################################################### Traceback (most recent call last): File "/home/krostif/miniconda3/envs/funannotate/bin/funannotate", line 10, in sys.exit(main()) File "/home/krostif/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/funannotate.py", line 716, in main mod.main(arguments) File "/home/krostif/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 407, in main runBuscoTest(args) File "/home/krostif/miniconda3/envs/funannotate/lib/python3.8/site-packages/funannotate/test.py", line 200, in runBuscoTest assert 1500 <= countGFFgenes(os.path.join( File "/home/krostif/miniconda3/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-busco_fc3b1897-7d4a-4ae0-8184-c8051e44bd13/annotate/predict_results/Awesome_busco.gff3'

Logfiles Please provide relavent log files of the error.

OS/Install Information

hyphaltip commented 8 months ago

Did you check the packages installed for sure. The error is because that biopython is not installed in the env that is running the parallel run. Is your Augustus just added to your path or installed in a separate conda env?

hyphaltip commented 4 months ago

Not seeing any followup so will close this, feel free to reopen if still need help.