atb download --from <file> --output-dir . does not work from mlst manifest

Tested:

atb mlst --species "Escherichia coli" --st 216 --hq-only > E._coli_ST216/E._coli_ST216_accessions.txt
atb download --from E._coli_ST216_accessions.txt --output-dir .

Result:
This message is printed to screen but no downloads start
Downloading 570 file(s) to .

Workaround:

cut -f1 E._coli_ST216_accessions.txt |
while read -r accession
do
  wget "https://allthebacteria-assemblies.s3.eu-west-2.amazonaws.com/${accession}.fa.gz"
done

Further testing
This however works:

atb query --species-like "Pseudomonas%fluorescens" > pf.txt
atb download --from pf.txt --output-dir .

I wondered if maybe it was because the large number of files in the original query so I tested this, but also did not work

mkdir test
head -n 5 E._coli_ST216_accessions.txt > test/test.txt
cd test
atb download --from test.txt --output-dir .

Output:
Downloading 4 file(s) to .
Completed: 0/4 Failed: 4 Bytes: 0 B
error: SAMEA104027617: Get "SAMEA104027617": unsupported protocol scheme ""
error: SAMEA103923478: Get "SAMEA103923478": unsupported protocol scheme ""
error: SAMEA10300091: Get "SAMEA10300091": unsupported protocol scheme ""
error: SAMD00092883: Get "SAMD00092883": unsupported protocol scheme ""
Error: 4 download(s) failed
4 download(s) failed

Perhaps it needed to loop through all 570 files before failing them all in the original call

Start by tracing the atb download --from ... handling and compare the accession lines produced by atb mlst with those from atb query. Reproduce with the five-line manifest and inspect why entries such as SAMEA104027617 become URLs without a protocol; done means the manifest downloads succeed as the query-generated file does.