Autofill command fails because the column "read_count" cannot be converted into integer

[alexhbnr]

When running AMDirT autofill with the option --library_output fails to return a working library table because the attempt to convert the column read_count into the dtype "integer" fails. The issue is that the ENA table returns the column read_count with commas for separating the blocks of numbers for easier readability.

E.g.
AMDirT autofill -n ancientmetagenome-environmental -l ../../dummy.tsv ERS11453805

returns

ValueError: invalid literal for int() with base 10: '55,698,178': Error while type casting for column 'read_count'