Cannot import pyabpoa without Internet - medaka doesn’t make a sequence consensus

[evfratov]

Ask away!

Linux (both normal Ubuntu and WSL Ubuntu) wf-artic fails on demo data without network, argument '--update_dala false' does not help - consensus file contains empty sequences. barcodeNN.artic.log.txt contains this error (49 as an example):

[M::main] CMD: minimap2 -a -x map-ont -t 4 SARS-CoV-2/Midnight-ONT/V3/SARS-CoV-2.reference.fasta barcode49_barcode49.fastq
[M::main] Real time: 0.701 sec; CPU: 1.721 sec; Peak RSS: 0.048 GB
Cannot import pyabpoa, some features may not be available.
Failed to interpret '[email protected]:consensus' as a basecaller model.
Traceback (most recent call last):
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/medaka/medaka.py", line 36, in __call__
    model_fp = medaka.models.resolve_model(val)
  File "/opt/custflow/epi2meuser/conda/lib/python3.8/site-packages/medaka/models.py", line 46, in resolve_model
    raise ValueError(
ValueError: Model [email protected]:consensus is not a known model or existant file.

fail for current wf-artic 1.2.2, both 1.2.1 and 1.2.0
fail for current Nextflow 24.10.2, both 23.10.4 and 22.10.7
manual installation python3-puabpoa is useless

And with the network everything is ok except some probability of fail due to improper network stability.

What is wrong? Why a critical network dependency isn't documented?