bonito failes to load model
teodorabu opened this issue · comments
Hello,
I have been using bonito to basecall a few sets of fast5 files by now and everything worked fine. However now I encounter an error when loading trying to load a model or even download models. My basecalling command is the following, after activating the corresponding environment (bonito version 0.7.2)
bonito basecaller dna_r10.4.1_e8.2_400bps_hac@v4.2.0 fast5/ > Bonito_Data/bonito_lambda_hac.bam
The error I get:
reading fast5
outputting unaligned fastq
loading model dna_r10.4.1_e8.2_400bps_hac@v4.2.0
error: failed to load dna_r10.4.1_e8.2_400bps_hac@v4.2.0
available models:
- dna_r10.4.1_e8.2_260bps_fast@v3.5.2
- dna_r10.4.1_e8.2_260bps_fast@v4.0.0
- dna_r10.4.1_e8.2_260bps_fast@v4.1.0
- dna_r10.4.1_e8.2_260bps_hac@v3.5.2
- dna_r10.4.1_e8.2_260bps_hac@v4.0.0
- dna_r10.4.1_e8.2_260bps_hac@v4.1.0
- dna_r10.4.1_e8.2_260bps_sup@v3.5.2
- dna_r10.4.1_e8.2_260bps_sup@v4.0.0
- dna_r10.4.1_e8.2_260bps_sup@v4.1.0
- dna_r10.4.1_e8.2_400bps_fast@v3.5.2
- dna_r10.4.1_e8.2_400bps_fast@v4.0.0
- dna_r10.4.1_e8.2_400bps_fast@v4.1.0
- dna_r10.4.1_e8.2_400bps_fast@v4.2.0
- dna_r10.4.1_e8.2_400bps_hac@v3.5.2
- dna_r10.4.1_e8.2_400bps_hac@v4.0.0
- dna_r10.4.1_e8.2_400bps_hac@v4.1.0
- dna_r10.4.1_e8.2_400bps_hac@v4.2.0
- dna_r10.4.1_e8.2_400bps_sup@v3.5.2
- dna_r10.4.1_e8.2_400bps_sup@v4.0.0
- dna_r10.4.1_e8.2_400bps_sup@v4.1.0
- dna_r10.4.1_e8.2_400bps_sup@v4.2.0
- dna_r9.4.1_e8_fast@v3.4
- dna_r9.4.1_e8_hac@v3.3
- dna_r9.4.1_e8_sup@v3.3
When downloading all the models using bonito download --models, I get:
OSError: [Errno 101] Network is unreachable
requests.exceptions.ConnectionError: HTTPSConnectionPool(host='cdn.oxfordnanoportal.com', port=443): Max retries exceeded with url: /software/analysis/bonito/dna_r10.4.1_e8.2_400bps_fast@v4.2.0.zip (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2b660316a010>: Failed to establish a new connection: [Errno 101] Network is unreachable'))
I was looking to download the models manually using the url in the download.py function, but the link crashes.
Can you please help me solve this problem?
Cheers,
Teodora
Fixed
And what was the actual problem?
I have taken it up to our cluster maintainers in order to find out if some connections have been blocked for users.
I was able to locally download the models manually in the end and feed them into bonito.