pyani download -o tax326423 --email christoph.knapp01@gmail.com -t 326423 -v -l pyANI_downloadStammbewertung_EFSA.log [INFO] [pyani.scripts.pyani_script]: Processed arguments: Namespace(api_keypath=PosixPath('~/.ncbi/api_key'), batchsize=10000, citation=False, classfname='classes.txt', debug=False, disable_tqdm=False, dryrun=False, email='christoph.knapp01@gmail.com', force=False, func=, kraken=False, labelfname='labels.txt', logfile=PosixPath('pyANI_downloadStammbewertung_EFSA.log'), noclobber=False, outdir=PosixPath('tax326423'), retries=20, taxon='326423', timeout=10, verbose=True, version=False) [INFO] [pyani.scripts.pyani_script]: command-line: /opt/miniforge3/envs/pyani_env/bin/pyani download -o tax326423 --email christoph.knapp01@gmail.com -t 326423 -v -l pyANI_downloadStammbewertung_EFSA.log [INFO] [pyani.scripts.pyani_script]: pyani version: 0.3.0-alpha [INFO] [pyani.scripts.pyani_script]: CITATION INFO [INFO] [pyani.scripts.pyani_script]: If you use pyani in your work, please cite the following publication: [INFO] [pyani.scripts.pyani_script]: Pritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G., [INFO] [pyani.scripts.pyani_script]: & Toth, I.K. (2016) 'Genomics and taxonomy in diagnostics for [INFO] [pyani.scripts.pyani_script]: food security: soft-rotting enterobacterial plant pathogens.' [INFO] [pyani.scripts.pyani_script]: Analytical Methods, 8(1), 12–24. http://doi.org/10.1039/C5AY02550H [INFO] [pyani.scripts.pyani_script]: DEPENDENCIES [INFO] [pyani.scripts.pyani_script]: The authors of pyani gratefully acknowledge its dependence on [INFO] [pyani.scripts.pyani_script]: the following bioinformatics software: [INFO] [pyani.scripts.pyani_script]: MUMmer3: S. Kurtz, A. Phillippy, A.L. Delcher, M. Smoot, M. Shumway, [INFO] [pyani.scripts.pyani_script]: C. Antonescu, and S.L. Salzberg (2004), 'Versatile and open software [INFO] [pyani.scripts.pyani_script]: for comparing large genomes' Genome Biology 5:R12 [INFO] [pyani.scripts.pyani_script]: BLAST+: Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., [INFO] [pyani.scripts.pyani_script]: Bealer K., & Madden T.L. (2008) 'BLAST+: architecture and applications.' [INFO] [pyani.scripts.pyani_script]: BMC Bioinformatics 10:421. [INFO] [pyani.scripts.pyani_script]: BLAST: Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., [INFO] [pyani.scripts.pyani_script]: Zhang, Z., Miller, W. & Lipman, D.J. (1997) 'Gapped BLAST and PSI-BLAST: [INFO] [pyani.scripts.pyani_script]: a new generation of protein database search programs.' Nucleic Acids Res. [INFO] [pyani.scripts.pyani_script]: 25:3389-3402 [INFO] [pyani.scripts.pyani_script]: Biopython: Cock PA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, [INFO] [pyani.scripts.pyani_script]: Friedberg I, Hamelryck T, Kauff F, Wilczynski B and de Hoon MJL [INFO] [pyani.scripts.pyani_script]: (2009) Biopython: freely available Python tools for computational [INFO] [pyani.scripts.pyani_script]: molecular biology and bioinformatics. Bioinformatics, 25, 1422-1423 [INFO] [pyani.scripts.pyani_script]: fastANI: Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis K, and [INFO] [pyani.scripts.pyani_script]: Aluru S (2018) 'High throughput ANI analysis of 90K prokaryotic [INFO] [pyani.scripts.pyani_script]: genomes reveals clear species boundaries.' Nature Communications 9, 5114 [INFO] [pyani.scripts.subcommands.subcmd_download]: Downloading genomes from NCBI [INFO] [pyani.scripts]: Creating output directory tax326423 [INFO] [pyani.scripts.subcommands.subcmd_download]: Setting Entrez email address: christoph.knapp01@gmail.com [WARNING] [pyani.scripts.subcommands.subcmd_download]: API path /home/christoph-knapp/.ncbi/api_key not a valid file. Not using API key. [INFO] [pyani.scripts.subcommands.subcmd_download]: Taxon IDs received: ['326423'] query='txid326423[Organism:exp]' result_count=2 asm_ids=['4693281', '36888'] [INFO] [pyani.scripts.subcommands.subcmd_download]: Downloading contigs for Taxon ID ['4693281', '36888'] [INFO] [pyani.scripts.subcommands.subcmd_download]: Retrieving eSummary information for UID 4693281 asm_uid='4693281' data["Taxid"]='326423' data["SpeciesTaxid"]='492670' data["AssemblyAccession"]='GCF_000015785.2' data["AssemblyName"]='ASM1578v2' data["SpeciesName"]='Bacillus velezensis' filestem='GCF_000015785.2_ASM1578v2' [INFO] [pyani.scripts.subcommands.subcmd_download]: Retrieving URLs for GCF_000015785.2_ASM1578v2 url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.2_ASM1578v2/GCF_000015785.2_ASM1578v2_genomic.fna.gz' hashurl='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.2_ASM1578v2/md5checksums.txt' outfname=PosixPath('tax326423/GCF_000015785.2_ASM1578v2_genomic.fna.gz') outfhash=PosixPath('tax326423/GCF_000015785.2_ASM1578v2_hashes.txt') skipped=False error='Traceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nConnectionRefusedError: [Errno 111] Connection refused\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 507, in retrieve_genome_and_hash\n download_url(url, outfname, timeout, disable_tqdm)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 446, in download_url\n with urllib.request.urlopen(req) as response:\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 222, in urlopen\n return opener.open(url, data, timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 525, in open\n response = self._open(req, data)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 542, in _open\n result = self._call_chain(self.handle_open, protocol, protocol +\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 502, in _call_chain\n result = func(*args)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1589, in ftp_open\n raise exc.with_traceback(sys.exc_info()[2])\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nurllib.error.URLError: \n' [WARNING] [pyani.download]: RefSeq download failed: skipping! [WARNING] [pyani.scripts.subcommands.subcmd_download]: RefSeq failed. Trying GenBank alternative assembly url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.2_ASM1578v2/GCA_000015785.2_ASM1578v2_genomic.fna.gz' hashurl='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.2_ASM1578v2/md5checksums.txt' outfname=PosixPath('tax326423/GCA_000015785.2_ASM1578v2_genomic.fna.gz') outfhash=PosixPath('tax326423/GCA_000015785.2_ASM1578v2_hashes.txt') skipped=False error='Traceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nConnectionRefusedError: [Errno 111] Connection refused\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 507, in retrieve_genome_and_hash\n download_url(url, outfname, timeout, disable_tqdm)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 446, in download_url\n with urllib.request.urlopen(req) as response:\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 222, in urlopen\n return opener.open(url, data, timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 525, in open\n response = self._open(req, data)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 542, in _open\n result = self._call_chain(self.handle_open, protocol, protocol +\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 502, in _call_chain\n result = func(*args)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1589, in ftp_open\n raise exc.with_traceback(sys.exc_info()[2])\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nurllib.error.URLError: \n' [WARNING] [pyani.download]: GenBank download failed: skipping! [WARNING] [pyani.scripts.subcommands.subcmd_download]: GenBank failed. [INFO] [pyani.scripts.subcommands.subcmd_download]: Retrieving eSummary information for UID 36888 asm_uid='36888' data["Taxid"]='326423' data["SpeciesTaxid"]='492670' data["AssemblyAccession"]='GCF_000015785.1' data["AssemblyName"]='ASM1578v1' data["SpeciesName"]='Bacillus velezensis' filestem='GCF_000015785.1_ASM1578v1' [INFO] [pyani.scripts.subcommands.subcmd_download]: Retrieving URLs for GCF_000015785.1_ASM1578v1 url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.1_ASM1578v1/GCF_000015785.1_ASM1578v1_genomic.fna.gz' hashurl='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.1_ASM1578v1/md5checksums.txt' outfname=PosixPath('tax326423/GCF_000015785.1_ASM1578v1_genomic.fna.gz') outfhash=PosixPath('tax326423/GCF_000015785.1_ASM1578v1_hashes.txt') skipped=False error='Traceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nConnectionRefusedError: [Errno 111] Connection refused\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 507, in retrieve_genome_and_hash\n download_url(url, outfname, timeout, disable_tqdm)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 446, in download_url\n with urllib.request.urlopen(req) as response:\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 222, in urlopen\n return opener.open(url, data, timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 525, in open\n response = self._open(req, data)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 542, in _open\n result = self._call_chain(self.handle_open, protocol, protocol +\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 502, in _call_chain\n result = func(*args)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1589, in ftp_open\n raise exc.with_traceback(sys.exc_info()[2])\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nurllib.error.URLError: \n' [WARNING] [pyani.download]: RefSeq download failed: skipping! [WARNING] [pyani.scripts.subcommands.subcmd_download]: RefSeq failed. Trying GenBank alternative assembly url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.1_ASM1578v1/GCA_000015785.1_ASM1578v1_genomic.fna.gz' hashurl='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.1_ASM1578v1/md5checksums.txt' outfname=PosixPath('tax326423/GCA_000015785.1_ASM1578v1_genomic.fna.gz') outfhash=PosixPath('tax326423/GCA_000015785.1_ASM1578v1_hashes.txt') skipped=False error='Traceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nConnectionRefusedError: [Errno 111] Connection refused\n\nDuring handling of the above exception, another exception occurred:\n\nTraceback (most recent call last):\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 507, in retrieve_genome_and_hash\n download_url(url, outfname, timeout, disable_tqdm)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/site-packages/pyani/download.py", line 446, in download_url\n with urllib.request.urlopen(req) as response:\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 222, in urlopen\n return opener.open(url, data, timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 525, in open\n response = self._open(req, data)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 542, in _open\n result = self._call_chain(self.handle_open, protocol, protocol +\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 502, in _call_chain\n result = func(*args)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1589, in ftp_open\n raise exc.with_traceback(sys.exc_info()[2])\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1571, in ftp_open\n fw = self.connect_ftp(user, passwd, host, port, dirs, req.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 1592, in connect_ftp\n return ftpwrapper(user, passwd, host, port, dirs, timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2413, in __init__\n self.init()\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/urllib/request.py", line 2422, in init\n self.ftp.connect(self.host, self.port, self.timeout)\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/ftplib.py", line 154, in connect\n self.sock = socket.create_connection((self.host, self.port), self.timeout,\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 820, in create_connection\n raise err\n File "/opt/miniforge3/envs/pyani_env/lib/python3.8/socket.py", line 808, in create_connection\n sock.connect(sa)\nurllib.error.URLError: \n' [WARNING] [pyani.download]: GenBank download failed: skipping! [WARNING] [pyani.scripts.subcommands.subcmd_download]: GenBank failed. classes=[] labels=[] skippedlist=[Skipped(taxon_id='326423', accession='4693281', organism='Bacillus velezensis', strain='BGSC:10A6; DSM:23117', url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.2_ASM1578v2/GCF_000015785.2_ASM1578v2_genomic.fna.gz', dltype='RefSeq'), Skipped(taxon_id='326423', accession='4693281', organism='Bacillus velezensis', strain='BGSC:10A6; DSM:23117', url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.2_ASM1578v2/GCA_000015785.2_ASM1578v2_genomic.fna.gz', dltype='GenBank'), Skipped(taxon_id='326423', accession='36888', organism='Bacillus velezensis', strain='FZB42', url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.1_ASM1578v1/GCF_000015785.1_ASM1578v1_genomic.fna.gz', dltype='RefSeq'), Skipped(taxon_id='326423', accession='36888', organism='Bacillus velezensis', strain='FZB42', url='ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.1_ASM1578v1/GCA_000015785.1_ASM1578v1_genomic.fna.gz', dltype='GenBank')] [INFO] [pyani.scripts.subcommands.subcmd_download]: Writing classes file to tax326423/classes.txt [INFO] [pyani.scripts.subcommands.subcmd_download]: Writing labels file to tax326423/labels.txt [WARNING] [pyani.scripts.subcommands.subcmd_download]: 4 genome downloads were skipped [WARNING] [pyani.scripts.subcommands.subcmd_download]: Bacillus velezensis BGSC:10A6; DSM:23117: taxon id: 326423 accession: 4693281 URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.2_ASM1578v2/GCF_000015785.2_ASM1578v2_genomic.fna.gz source: RefSeq [WARNING] [pyani.scripts.subcommands.subcmd_download]: Bacillus velezensis BGSC:10A6; DSM:23117: taxon id: 326423 accession: 4693281 URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.2_ASM1578v2/GCA_000015785.2_ASM1578v2_genomic.fna.gz source: GenBank [WARNING] [pyani.scripts.subcommands.subcmd_download]: Bacillus velezensis FZB42: taxon id: 326423 accession: 36888 URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/015/785/GCF_000015785.1_ASM1578v1/GCF_000015785.1_ASM1578v1_genomic.fna.gz source: RefSeq [WARNING] [pyani.scripts.subcommands.subcmd_download]: Bacillus velezensis FZB42: taxon id: 326423 accession: 36888 URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/015/785/GCA_000015785.1_ASM1578v1/GCA_000015785.1_ASM1578v1_genomic.fna.gz source: GenBank [INFO] [pyani.scripts.pyani_script]: Completed. Time taken: 1.436