Fun2 predict query #16
Description
Dear author i am facing below error at predict step, what could be reason for the same:
However I hvae ran fun2 prediction many times but not observed the same ever.
command> funannotate2 predict -f 11109104200_GS11NU_1.cleaned_consensus.fasta -i 11109104200_GS11NU_1 --cpus 10
[Jul 02 05:59 AM] Python v3.10.14; funannotate2 v25.6.22; gfftk v25.6.10; buscolite v25.4.24
[Jul 02 05:59 AM] Parsed data from --input-dir 11109104200_GS11NU_1
--fasta 11109104200_GS11NU_1.cleaned_consensus.fasta
--species "Komagataella phaffii GS115 chromosome"
--params /mnt/nsa4/projects/bioit/bioit_development/rlb/Test_Funannotate2/Komagataella_phaffii_gff_training/11109104200_GS11NU_1/train_results/Komagataella_phaffii_gs115_chromosome.params.json
--out 11109104200_GS11NU_1
OUTPUT and ERROR:
[Jul 02 05:59 AM] Loaded training params for Komagataella_phaffii_gs115_chromosome: ['augustus', 'glimmerhmm', 'snap', 'genemark']
[Jul 02 05:59 AM] temporary files located in: /tmp/predict_e2f3af90-cc60-4d1b-9cc6-1d3e30514e94
[Jul 02 05:59 AM] Loading genome assembly, running QC checks, searching for mitochondrial contigs, calculating softmasked regions and assembly gaps
[Jul 02 06:00 AM] Separating 1 mitochondrial contig(s) from the nuclear genome, will recombine at the end of predict
{'contig_9': {'NC_015384.1': 0.9994395561284537}}
[Jul 02 06:00 AM] Genome assembly is not softmasked, running pytantan to quickly softmask repeats
[Jul 02 06:00 AM] Genome stats:
{
"n_contigs": 5,
"size": 9472982,
"softmasked": "2.34%",
"gaps": "0.00%",
"n50": 2396210,
"n90": 1716511,
"l50": 2,
"l90": 4,
"avg_length": 1894596
}
[Jul 02 06:00 AM] Parsed 485423 [out of 573661] proteins to align for evidence, derived from:
/mnt/nsa4/projects/bioit/bioit_development/rlb/test/uniprot_sprot.fasta
[Jul 02 06:00 AM] Aligning protein evidence to the genome assembly with miniprot
[Jul 02 06:10 AM] Generated 91047 alignments: 692 were valid gene models
[Jul 02 06:10 AM] Parsing alignments and generating hintsfile for augustus
[Jul 02 06:10 AM] Running ab initio gene predictions using 10 cpus
[Jul 02 06:15 AM] Ab initio predictions finished:
{
"augustus": 2303,
"augustus-hiq": 2483,
"glimmerhmm": 4013,
"snap": 4496,
"genemark": 4941
}
[Jul 02 06:15 AM] Downloading fungi_odb12 model from https://busco-data.ezlab.org/v5/data/lineages/fungi_odb12.2025-04-11.tar.gz
HTTPS download attempt 1 failed: 404 Client Error: Not Found for url: https://busco-data.ezlab.org/v5/data/lineages/fungi_odb12.2025-04-11.tar.gz. Retrying in 5 seconds...
HTTPS download attempt 2 failed: 404 Client Error: Not Found for url: https://busco-data.ezlab.org/v5/data/lineages/fungi_odb12.2025-04-11.tar.gz. Retrying in 5 seconds...
HTTPS download failed after 3 attempts: 404 Client Error: Not Found for url: https://busco-data.ezlab.org/v5/data/lineages/fungi_odb12.2025-04-11.tar.gz
Traceback (most recent call last):
File "/opt/conda/lib/python3.10/site-packages/funannotate2/utilities.py", line 200, in download
r.raise_for_status() # Raise an exception for HTTP errors
File "/opt/conda/lib/python3.10/site-packages/requests/models.py", line 1024, in raise_for_status
raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://busco-data.ezlab.org/v5/data/lineages/fungi_odb12.2025-04-11.tar.gz
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/bin/funannotate2", line 8, in
sys.exit(main())
File "/opt/conda/lib/python3.10/site-packages/funannotate2/main.py", line 26, in main
predict(args)
File "/opt/conda/lib/python3.10/site-packages/funannotate2/predict.py", line 413, in predict
download(busco_url, busco_tgz, wget=False)
File "/opt/conda/lib/python3.10/site-packages/funannotate2/utilities.py", line 226, in download
raise Exception(f"Download failed: {str(e)}")
Exception: Download failed: 404 Client Error: Not Found for url: https://busco-data.ezlab.org/v5/data/lineages/fungi_odb12.2025-04-11.tar.gz
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