Use HTTPS instead for plasmids, update path

[thomcuddihy]

Addresses #412 with plasmid FTP connections dropping constantly, while HTTPS to same service are rock-solid. Changed xargs command to remove "xargs: warning: options --max-args and --replace/-I/-i are mutually exclusive, ignoring previous --max-args value" warning. Have kept FTP for .listing and manifest generating.

[sachinharle]

I have same issue while building database:
$ kraken2-build --standard --threads 24 --db UniVec_Core
Downloading nucleotide gb accession to taxon map... done.
Downloading nucleotide wgs accession to taxon map... done.
Downloaded accession to taxon map(s)
Downloading taxonomy tree data... done.
Uncompressing taxonomy data... done.
Untarring taxonomy tree data... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
Processed 547 projects (1009 sequences, 1.57 Gbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
Processed 38595 projects (91046 sequences, 161.35 Gbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Step 1/2: Performing rsync file transfer of requested files
Rsync file transfer complete.
Step 2/2: Assigning taxonomic IDs to sequences
Processed 14970 projects (18636 sequences, 549.91 Mbp)... done.
All files processed, cleaning up extra sequence files... done, library complete.
Masking low-complexity regions of downloaded library... done.
Downloading plasmid files from FTP...xargs: warning: options --max-args and --replace/-I/-i are mutually exclusive, ignoring previous --max-args value
xargs: warning: options --max-args and --replace/-I/-i are mutually exclusive, ignoring previous --max-args value

gzip: plasmid.4.2.genomic.fna.gz: invalid compressed data--format violated