INFO: genbank_get_genomes_by_taxon.py: Tue Mar 21 11:28:14 2017 INFO: command-line: /Users/lpritc/Desktop/venv-pyani/bin/genbank_get_genomes_by_taxon.py -o Caulobacter_downloads -v -t 75 -l Caulobacter_downloads.log --email myownmail@hello INFO: Namespace(batchsize=10000, email='myownmail@hello', force=False, format='gbk,fasta', logfile='Caulobacter_downloads.log', noclobber=False, outdirname='Caulobacter_downloads', retries=20, taxon='75', timeout=10, verbose=True) INFO: Set NCBI contact email to myownmail@hello INFO: Creating directory Caulobacter_downloads INFO: Output directory: Caulobacter_downloads INFO: Passed taxon IDs: 75 INFO: Entrez ESearch with query: txid75[Organism:exp] INFO: Entrez ESearch returns 30 assembly IDs INFO: Identified 30 unique assemblies INFO: Taxon 75: 30 assemblies INFO: Identifying assembly information from NCBI for 881911 INFO: Organism: Caulobacter sp. UNC279MFTsu5.1 (a-proteobacteria) INFO: Taxid: 1502775 INFO: Accession: GCA_900114015.1 INFO: Name: IMG-taxon 2590828858 annotated assembly INFO: Label: GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly_genomic C. sp. UNC279MFTsu5.1 UNC279MFTsu5.1 INFO: Class: GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly_genomic Caulobacter sp. UNC279MFTsu5.1 INFO: Retrieving assembly sequence for GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/114/015/GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly/GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/900/114/015/GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly/GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly_genomic.fna.gz (1590698 bytes) INFO: 1048576 [65.92%] INFO: 1590698 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly_genomic.fna.gz to Caulobacter_downloads/GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCA_900114015.1_IMG-taxon_2590828858_annotated_assembly_genomic.fna INFO: Identifying assembly information from NCBI for 668598 INFO: Organism: Caulobacter crescentus OR37 (a-proteobacteria) INFO: Taxid: 155892 INFO: Accession: GCF_000372645.1 INFO: Name: Caulobacter.strain_OR37_v1.0 INFO: Label: GCF_000372645.1_Caulobacter.strain_OR37_v1.0_genomic C. vibrioides OR37 INFO: Class: GCF_000372645.1_Caulobacter.strain_OR37_v1.0_genomic Caulobacter vibrioides INFO: Retrieving assembly sequence for GCF_000372645.1_Caulobacter.strain_OR37_v1.0 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/372/645/GCF_000372645.1_Caulobacter.strain_OR37_v1.0/GCF_000372645.1_Caulobacter.strain_OR37_v1.0_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/372/645/GCF_000372645.1_Caulobacter.strain_OR37_v1.0/GCF_000372645.1_Caulobacter.strain_OR37_v1.0_genomic.fna.gz (1266679 bytes) INFO: 1048576 [82.78%] INFO: 1266679 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000372645.1_Caulobacter.strain_OR37_v1.0_genomic.fna.gz to Caulobacter_downloads/GCF_000372645.1_Caulobacter.strain_OR37_v1.0_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000372645.1_Caulobacter.strain_OR37_v1.0_genomic.fna INFO: Identifying assembly information from NCBI for 664938 INFO: Organism: Caulobacter sp. JGI 0001010-J14 (a-proteobacteria) INFO: Taxid: 1157689 INFO: Accession: GCF_000382625.1 INFO: Name: ASM38262v1 INFO: Label: GCF_000382625.1_ASM38262v1_genomic C. sp. JGI 0001010-J14 JGI 0001010-J14 INFO: Class: GCF_000382625.1_ASM38262v1_genomic Caulobacter sp. JGI 0001010-J14 INFO: Retrieving assembly sequence for GCF_000382625.1_ASM38262v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/382/625/GCF_000382625.1_ASM38262v1/GCF_000382625.1_ASM38262v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/382/625/GCF_000382625.1_ASM38262v1/GCF_000382625.1_ASM38262v1_genomic.fna.gz (514606 bytes) INFO: 514606 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000382625.1_ASM38262v1_genomic.fna.gz to Caulobacter_downloads/GCF_000382625.1_ASM38262v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000382625.1_ASM38262v1_genomic.fna INFO: Identifying assembly information from NCBI for 639671 INFO: Organism: Caulobacter sp. CCH5-E12 (a-proteobacteria) INFO: Taxid: 1768770 INFO: Accession: GCF_001556585.1 INFO: Name: ASM155658v1 INFO: Label: GCF_001556585.1_ASM155658v1_genomic C. sp. CCH5-E12 CCH5-E12 INFO: Class: GCF_001556585.1_ASM155658v1_genomic Caulobacter sp. CCH5-E12 INFO: Retrieving assembly sequence for GCF_001556585.1_ASM155658v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/556/585/GCF_001556585.1_ASM155658v1/GCF_001556585.1_ASM155658v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/556/585/GCF_001556585.1_ASM155658v1/GCF_001556585.1_ASM155658v1_genomic.fna.gz (1408181 bytes) INFO: 1048576 [74.46%] INFO: 1408181 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001556585.1_ASM155658v1_genomic.fna.gz to Caulobacter_downloads/GCF_001556585.1_ASM155658v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001556585.1_ASM155658v1_genomic.fna INFO: Identifying assembly information from NCBI for 639631 INFO: Organism: Caulobacter sp. CCH9-E1 (a-proteobacteria) INFO: Taxid: 1768768 INFO: Accession: GCF_001556515.1 INFO: Name: ASM155651v1 INFO: Label: GCF_001556515.1_ASM155651v1_genomic C. sp. CCH9-E1 CCH9-E1 INFO: Class: GCF_001556515.1_ASM155651v1_genomic Caulobacter sp. CCH9-E1 INFO: Retrieving assembly sequence for GCF_001556515.1_ASM155651v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/556/515/GCF_001556515.1_ASM155651v1/GCF_001556515.1_ASM155651v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/556/515/GCF_001556515.1_ASM155651v1/GCF_001556515.1_ASM155651v1_genomic.fna.gz (1330512 bytes) INFO: 1048576 [78.81%] INFO: 1330512 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001556515.1_ASM155651v1_genomic.fna.gz to Caulobacter_downloads/GCF_001556515.1_ASM155651v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001556515.1_ASM155651v1_genomic.fna INFO: Identifying assembly information from NCBI for 639581 INFO: Organism: Caulobacter sp. CCH4-E1 (a-proteobacteria) INFO: Taxid: 1768763 INFO: Accession: GCF_001556425.1 INFO: Name: ASM155642v1 INFO: Label: GCF_001556425.1_ASM155642v1_genomic C. sp. CCH4-E1 CCH4-E1 INFO: Class: GCF_001556425.1_ASM155642v1_genomic Caulobacter sp. CCH4-E1 INFO: Retrieving assembly sequence for GCF_001556425.1_ASM155642v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/556/425/GCF_001556425.1_ASM155642v1/GCF_001556425.1_ASM155642v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/556/425/GCF_001556425.1_ASM155642v1/GCF_001556425.1_ASM155642v1_genomic.fna.gz (1136812 bytes) INFO: 1048576 [92.24%] INFO: 1136812 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001556425.1_ASM155642v1_genomic.fna.gz to Caulobacter_downloads/GCF_001556425.1_ASM155642v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001556425.1_ASM155642v1_genomic.fna INFO: Identifying assembly information from NCBI for 632778 INFO: Organism: Caulobacter sp. JGI 0001013-D04 (a-proteobacteria) INFO: Taxid: 1157680 INFO: Accession: GCF_000376305.1 INFO: Name: ASM37630v1 INFO: Label: GCF_000376305.1_ASM37630v1_genomic C. sp. JGI 0001013-D04 JGI 0001013-D04 INFO: Class: GCF_000376305.1_ASM37630v1_genomic Caulobacter sp. JGI 0001013-D04 INFO: Retrieving assembly sequence for GCF_000376305.1_ASM37630v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/376/305/GCF_000376305.1_ASM37630v1/GCF_000376305.1_ASM37630v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/376/305/GCF_000376305.1_ASM37630v1/GCF_000376305.1_ASM37630v1_genomic.fna.gz (262636 bytes) INFO: 262636 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000376305.1_ASM37630v1_genomic.fna.gz to Caulobacter_downloads/GCF_000376305.1_ASM37630v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000376305.1_ASM37630v1_genomic.fna INFO: Identifying assembly information from NCBI for 632458 INFO: Organism: Caulobacter sp. JGI 0001013-O16 (a-proteobacteria) INFO: Taxid: 1157681 INFO: Accession: GCF_000376365.1 INFO: Name: ASM37636v1 INFO: Label: GCF_000376365.1_ASM37636v1_genomic C. sp. JGI 0001013-O16 JGI 0001013-O16 INFO: Class: GCF_000376365.1_ASM37636v1_genomic Caulobacter sp. JGI 0001013-O16 INFO: Retrieving assembly sequence for GCF_000376365.1_ASM37636v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/376/365/GCF_000376365.1_ASM37636v1/GCF_000376365.1_ASM37636v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/376/365/GCF_000376365.1_ASM37636v1/GCF_000376365.1_ASM37636v1_genomic.fna.gz (539378 bytes) INFO: 539378 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000376365.1_ASM37636v1_genomic.fna.gz to Caulobacter_downloads/GCF_000376365.1_ASM37636v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000376365.1_ASM37636v1_genomic.fna INFO: Identifying assembly information from NCBI for 586051 INFO: Organism: Caulobacter vibrioides (a-proteobacteria) INFO: Taxid: 155892 INFO: Accession: GCF_001449105.1 INFO: Name: ASM144910v1 INFO: Label: GCF_001449105.1_ASM144910v1_genomic C. vibrioides T5M6 INFO: Class: GCF_001449105.1_ASM144910v1_genomic Caulobacter vibrioides INFO: Retrieving assembly sequence for GCF_001449105.1_ASM144910v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/449/105/GCF_001449105.1_ASM144910v1/GCF_001449105.1_ASM144910v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/449/105/GCF_001449105.1_ASM144910v1/GCF_001449105.1_ASM144910v1_genomic.fna.gz (1507106 bytes) INFO: 1048576 [69.58%] INFO: 1507106 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001449105.1_ASM144910v1_genomic.fna.gz to Caulobacter_downloads/GCF_001449105.1_ASM144910v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001449105.1_ASM144910v1_genomic.fna INFO: Identifying assembly information from NCBI for 575291 INFO: Organism: Caulobacter sp. Root656 (a-proteobacteria) INFO: Taxid: 1736579 INFO: Accession: GCF_001427685.1 INFO: Name: Root656 INFO: Label: GCF_001427685.1_Root656_genomic C. sp. Root656 Root656 INFO: Class: GCF_001427685.1_Root656_genomic Caulobacter sp. Root656 INFO: Retrieving assembly sequence for GCF_001427685.1_Root656 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/427/685/GCF_001427685.1_Root656/GCF_001427685.1_Root656_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/427/685/GCF_001427685.1_Root656/GCF_001427685.1_Root656_genomic.fna.gz (1565494 bytes) INFO: 1048576 [66.98%] INFO: 1565494 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001427685.1_Root656_genomic.fna.gz to Caulobacter_downloads/GCF_001427685.1_Root656_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001427685.1_Root656_genomic.fna INFO: Identifying assembly information from NCBI for 575281 INFO: Organism: Caulobacter sp. Root655 (a-proteobacteria) INFO: Taxid: 1736578 INFO: Accession: GCF_001427665.1 INFO: Name: Root655 INFO: Label: GCF_001427665.1_Root655_genomic C. sp. Root655 Root655 INFO: Class: GCF_001427665.1_Root655_genomic Caulobacter sp. Root655 INFO: Retrieving assembly sequence for GCF_001427665.1_Root655 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/427/665/GCF_001427665.1_Root655/GCF_001427665.1_Root655_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/427/665/GCF_001427665.1_Root655/GCF_001427665.1_Root655_genomic.fna.gz (1482464 bytes) INFO: 1048576 [70.73%] INFO: 1482464 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001427665.1_Root655_genomic.fna.gz to Caulobacter_downloads/GCF_001427665.1_Root655_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001427665.1_Root655_genomic.fna INFO: Identifying assembly information from NCBI for 575031 INFO: Organism: Caulobacter sp. Root487D2Y (a-proteobacteria) INFO: Taxid: 1736547 INFO: Accession: GCF_001427165.1 INFO: Name: Root487D2Y INFO: Label: GCF_001427165.1_Root487D2Y_genomic C. sp. Root487D2Y Root487D2Y INFO: Class: GCF_001427165.1_Root487D2Y_genomic Caulobacter sp. Root487D2Y INFO: Retrieving assembly sequence for GCF_001427165.1_Root487D2Y INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/427/165/GCF_001427165.1_Root487D2Y/GCF_001427165.1_Root487D2Y_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/427/165/GCF_001427165.1_Root487D2Y/GCF_001427165.1_Root487D2Y_genomic.fna.gz (1443123 bytes) INFO: 1048576 [72.66%] INFO: 1443123 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001427165.1_Root487D2Y_genomic.fna.gz to Caulobacter_downloads/GCF_001427165.1_Root487D2Y_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001427165.1_Root487D2Y_genomic.fna INFO: Identifying assembly information from NCBI for 574941 INFO: Organism: Caulobacter sp. Root1472 (a-proteobacteria) INFO: Taxid: 1736470 INFO: Accession: GCF_001426985.1 INFO: Name: Root1472 INFO: Label: GCF_001426985.1_Root1472_genomic C. sp. Root1472 Root1472 INFO: Class: GCF_001426985.1_Root1472_genomic Caulobacter sp. Root1472 INFO: Retrieving assembly sequence for GCF_001426985.1_Root1472 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/426/985/GCF_001426985.1_Root1472/GCF_001426985.1_Root1472_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/426/985/GCF_001426985.1_Root1472/GCF_001426985.1_Root1472_genomic.fna.gz (1625526 bytes) INFO: 1048576 [64.51%] INFO: 1625526 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001426985.1_Root1472_genomic.fna.gz to Caulobacter_downloads/GCF_001426985.1_Root1472_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001426985.1_Root1472_genomic.fna INFO: Identifying assembly information from NCBI for 574901 INFO: Organism: Caulobacter sp. Root1455 (a-proteobacteria) INFO: Taxid: 1736465 INFO: Accession: GCF_001426905.1 INFO: Name: Root1455 INFO: Label: GCF_001426905.1_Root1455_genomic C. sp. Root1455 Root1455 INFO: Class: GCF_001426905.1_Root1455_genomic Caulobacter sp. Root1455 INFO: Retrieving assembly sequence for GCF_001426905.1_Root1455 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/426/905/GCF_001426905.1_Root1455/GCF_001426905.1_Root1455_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/426/905/GCF_001426905.1_Root1455/GCF_001426905.1_Root1455_genomic.fna.gz (1441748 bytes) INFO: 1048576 [72.73%] INFO: 1441748 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001426905.1_Root1455_genomic.fna.gz to Caulobacter_downloads/GCF_001426905.1_Root1455_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001426905.1_Root1455_genomic.fna INFO: Identifying assembly information from NCBI for 574321 INFO: Organism: Caulobacter sp. Root343 (a-proteobacteria) INFO: Taxid: 1736520 INFO: Accession: GCF_001425745.1 INFO: Name: Root343 INFO: Label: GCF_001425745.1_Root343_genomic C. sp. Root343 Root343 INFO: Class: GCF_001425745.1_Root343_genomic Caulobacter sp. Root343 INFO: Retrieving assembly sequence for GCF_001425745.1_Root343 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/425/745/GCF_001425745.1_Root343/GCF_001425745.1_Root343_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/425/745/GCF_001425745.1_Root343/GCF_001425745.1_Root343_genomic.fna.gz (1522402 bytes) INFO: 1048576 [68.88%] INFO: 1522402 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001425745.1_Root343_genomic.fna.gz to Caulobacter_downloads/GCF_001425745.1_Root343_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001425745.1_Root343_genomic.fna INFO: Identifying assembly information from NCBI for 574311 INFO: Organism: Caulobacter sp. Root342 (a-proteobacteria) INFO: Taxid: 1736519 INFO: Accession: GCF_001425725.1 INFO: Name: Root342 INFO: Label: GCF_001425725.1_Root342_genomic C. sp. Root342 Root342 INFO: Class: GCF_001425725.1_Root342_genomic Caulobacter sp. Root342 INFO: Retrieving assembly sequence for GCF_001425725.1_Root342 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/425/725/GCF_001425725.1_Root342/GCF_001425725.1_Root342_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/425/725/GCF_001425725.1_Root342/GCF_001425725.1_Root342_genomic.fna.gz (1494128 bytes) INFO: 1048576 [70.18%] INFO: 1494128 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001425725.1_Root342_genomic.fna.gz to Caulobacter_downloads/GCF_001425725.1_Root342_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001425725.1_Root342_genomic.fna INFO: Identifying assembly information from NCBI for 560191 INFO: Organism: Caulobacter henricii (a-proteobacteria) INFO: Taxid: 69395 INFO: Accession: GCF_001414055.1 INFO: Name: ASM141405v1 INFO: Label: GCF_001414055.1_ASM141405v1_genomic C. henricii CB4 INFO: Class: GCF_001414055.1_ASM141405v1_genomic Caulobacter henricii INFO: Retrieving assembly sequence for GCF_001414055.1_ASM141405v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/414/055/GCF_001414055.1_ASM141405v1/GCF_001414055.1_ASM141405v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/001/414/055/GCF_001414055.1_ASM141405v1/GCF_001414055.1_ASM141405v1_genomic.fna.gz (1139673 bytes) INFO: 1048576 [92.01%] INFO: 1139673 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_001414055.1_ASM141405v1_genomic.fna.gz to Caulobacter_downloads/GCF_001414055.1_ASM141405v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_001414055.1_ASM141405v1_genomic.fna INFO: Identifying assembly information from NCBI for 406268 INFO: Organism: Caulobacter sp. AP07 (a-proteobacteria) INFO: Taxid: 1144304 INFO: Accession: GCF_000281955.1 INFO: Name: Caulobacter.strAP07_v1.0 INFO: Label: GCF_000281955.1_Caulobacter.strAP07_v1.0_genomic C. sp. AP07 AP07 INFO: Class: GCF_000281955.1_Caulobacter.strAP07_v1.0_genomic Caulobacter sp. AP07 INFO: Retrieving assembly sequence for GCF_000281955.1_Caulobacter.strAP07_v1.0 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/281/955/GCF_000281955.1_Caulobacter.strAP07_v1.0/GCF_000281955.1_Caulobacter.strAP07_v1.0_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/281/955/GCF_000281955.1_Caulobacter.strAP07_v1.0/GCF_000281955.1_Caulobacter.strAP07_v1.0_genomic.fna.gz (1601696 bytes) INFO: 1048576 [65.47%] INFO: 1601696 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000281955.1_Caulobacter.strAP07_v1.0_genomic.fna.gz to Caulobacter_downloads/GCF_000281955.1_Caulobacter.strAP07_v1.0_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000281955.1_Caulobacter.strAP07_v1.0_genomic.fna INFO: Identifying assembly information from NCBI for 233261 INFO: Organism: Caulobacter sp. OV484 (a-proteobacteria) INFO: Taxid: 1500308 INFO: Accession: GCF_000799245.1 INFO: Name: ASM79924v1 INFO: Label: GCF_000799245.1_ASM79924v1_genomic C. sp. OV484 OV484 INFO: Class: GCF_000799245.1_ASM79924v1_genomic Caulobacter sp. OV484 INFO: Retrieving assembly sequence for GCF_000799245.1_ASM79924v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/799/245/GCF_000799245.1_ASM79924v1/GCF_000799245.1_ASM79924v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/799/245/GCF_000799245.1_ASM79924v1/GCF_000799245.1_ASM79924v1_genomic.fna.gz (1474401 bytes) INFO: 1048576 [71.12%] INFO: 1474401 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000799245.1_ASM79924v1_genomic.fna.gz to Caulobacter_downloads/GCF_000799245.1_ASM79924v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000799245.1_ASM79924v1_genomic.fna INFO: Identifying assembly information from NCBI for 206351 INFO: Organism: Caulobacter henricii (a-proteobacteria) INFO: Taxid: 69395 INFO: Accession: GCF_000745595.1 INFO: Name: ASM74559v1 INFO: Label: GCF_000745595.1_ASM74559v1_genomic C. henricii YR570 INFO: Class: GCF_000745595.1_ASM74559v1_genomic Caulobacter henricii INFO: Retrieving assembly sequence for GCF_000745595.1_ASM74559v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/745/595/GCF_000745595.1_ASM74559v1/GCF_000745595.1_ASM74559v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/745/595/GCF_000745595.1_ASM74559v1/GCF_000745595.1_ASM74559v1_genomic.fna.gz (1677352 bytes) INFO: 1048576 [62.51%] INFO: 1677352 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000745595.1_ASM74559v1_genomic.fna.gz to Caulobacter_downloads/GCF_000745595.1_ASM74559v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000745595.1_ASM74559v1_genomic.fna INFO: Identifying assembly information from NCBI for 206321 INFO: Organism: Caulobacter henricii (a-proteobacteria) INFO: Taxid: 69395 INFO: Accession: GCF_000745545.1 INFO: Name: ASM74554v1 INFO: Label: GCF_000745545.1_ASM74554v1_genomic C. henricii CF287 INFO: Class: GCF_000745545.1_ASM74554v1_genomic Caulobacter henricii INFO: Retrieving assembly sequence for GCF_000745545.1_ASM74554v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/745/545/GCF_000745545.1_ASM74554v1/GCF_000745545.1_ASM74554v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/745/545/GCF_000745545.1_ASM74554v1/GCF_000745545.1_ASM74554v1_genomic.fna.gz (1701531 bytes) INFO: 1048576 [61.63%] INFO: 1701531 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000745545.1_ASM74554v1_genomic.fna.gz to Caulobacter_downloads/GCF_000745545.1_ASM74554v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000745545.1_ASM74554v1_genomic.fna INFO: Identifying assembly information from NCBI for 205781 INFO: Organism: Caulobacter henricii (a-proteobacteria) INFO: Taxid: 69395 INFO: Accession: GCF_000744465.1 INFO: Name: ASM74446v1 INFO: Label: GCF_000744465.1_ASM74446v1_genomic C. henricii OK261 INFO: Class: GCF_000744465.1_ASM74446v1_genomic Caulobacter henricii INFO: Retrieving assembly sequence for GCF_000744465.1_ASM74446v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/744/465/GCF_000744465.1_ASM74446v1/GCF_000744465.1_ASM74446v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/744/465/GCF_000744465.1_ASM74446v1/GCF_000744465.1_ASM74446v1_genomic.fna.gz (1423268 bytes) INFO: 1048576 [73.67%] INFO: 1423268 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000744465.1_ASM74446v1_genomic.fna.gz to Caulobacter_downloads/GCF_000744465.1_ASM74446v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000744465.1_ASM74446v1_genomic.fna INFO: Identifying assembly information from NCBI for 189251 INFO: Organism: Caulobacter sp. UNC358MFTsu5.1 (a-proteobacteria) INFO: Taxid: 1449049 INFO: Accession: GCF_000712075.1 INFO: Name: ASM71207v1 INFO: Label: GCF_000712075.1_ASM71207v1_genomic C. sp. UNC358MFTsu5.1 UNC358MFTsu5.1 INFO: Class: GCF_000712075.1_ASM71207v1_genomic Caulobacter sp. UNC358MFTsu5.1 INFO: Retrieving assembly sequence for GCF_000712075.1_ASM71207v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/712/075/GCF_000712075.1_ASM71207v1/GCF_000712075.1_ASM71207v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/712/075/GCF_000712075.1_ASM71207v1/GCF_000712075.1_ASM71207v1_genomic.fna.gz (1518701 bytes) INFO: 1048576 [69.04%] INFO: 1518701 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000712075.1_ASM71207v1_genomic.fna.gz to Caulobacter_downloads/GCF_000712075.1_ASM71207v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000712075.1_ASM71207v1_genomic.fna INFO: Identifying assembly information from NCBI for 163998 INFO: Organism: Caulobacter segnis ATCC 21756 (a-proteobacteria) INFO: Taxid: 88688 INFO: Accession: GCF_000092285.1 INFO: Name: ASM9228v1 INFO: Label: GCF_000092285.1_ASM9228v1_genomic C. segnis ATCC 21756 INFO: Class: GCF_000092285.1_ASM9228v1_genomic Caulobacter segnis INFO: Retrieving assembly sequence for GCF_000092285.1_ASM9228v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/092/285/GCF_000092285.1_ASM9228v1/GCF_000092285.1_ASM9228v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/092/285/GCF_000092285.1_ASM9228v1/GCF_000092285.1_ASM9228v1_genomic.fna.gz (1326937 bytes) INFO: 1048576 [79.02%] INFO: 1326937 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000092285.1_ASM9228v1_genomic.fna.gz to Caulobacter_downloads/GCF_000092285.1_ASM9228v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000092285.1_ASM9228v1_genomic.fna INFO: Identifying assembly information from NCBI for 76161 INFO: Organism: Caulobacter sp. JGI 0001002-P11 (a-proteobacteria) INFO: Taxid: 1094930 INFO: Accession: GCF_000464035.1 INFO: Name: ASM46403v2 INFO: Label: GCF_000464035.1_ASM46403v2_genomic C. sp. JGI 0001002-P11 JGI 0001002-P11 INFO: Class: GCF_000464035.1_ASM46403v2_genomic Caulobacter sp. JGI 0001002-P11 INFO: Retrieving assembly sequence for GCF_000464035.1_ASM46403v2 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/464/035/GCF_000464035.1_ASM46403v2/GCF_000464035.1_ASM46403v2_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/464/035/GCF_000464035.1_ASM46403v2/GCF_000464035.1_ASM46403v2_genomic.fna.gz (75785 bytes) INFO: 75785 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000464035.1_ASM46403v2_genomic.fna.gz to Caulobacter_downloads/GCF_000464035.1_ASM46403v2_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000464035.1_ASM46403v2_genomic.fna INFO: Identifying assembly information from NCBI for 60501 INFO: Organism: Caulobacter sp. URHA0033 (a-proteobacteria) INFO: Taxid: 1298862 INFO: Accession: GCF_000426025.1 INFO: Name: ASM42602v1 INFO: Label: GCF_000426025.1_ASM42602v1_genomic C. sp. URHA0033 URHA0033 INFO: Class: GCF_000426025.1_ASM42602v1_genomic Caulobacter sp. URHA0033 INFO: Retrieving assembly sequence for GCF_000426025.1_ASM42602v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/426/025/GCF_000426025.1_ASM42602v1/GCF_000426025.1_ASM42602v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/426/025/GCF_000426025.1_ASM42602v1/GCF_000426025.1_ASM42602v1_genomic.fna.gz (1607551 bytes) INFO: 1048576 [65.23%] INFO: 1607551 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000426025.1_ASM42602v1_genomic.fna.gz to Caulobacter_downloads/GCF_000426025.1_ASM42602v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000426025.1_ASM42602v1_genomic.fna INFO: Identifying assembly information from NCBI for 58271 INFO: Organism: Caulobacter sp. JGI 0001002-P11 (a-proteobacteria) INFO: Taxid: 1094930 INFO: Accession: GCA_000464035.1 INFO: Name: ASM46403v1 INFO: Label: GCA_000464035.1_ASM46403v1_genomic C. sp. JGI 0001002-P11 JGI 0001002-P11 INFO: Class: GCA_000464035.1_ASM46403v1_genomic Caulobacter sp. JGI 0001002-P11 INFO: Retrieving assembly sequence for GCA_000464035.1_ASM46403v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/464/035/GCA_000464035.1_ASM46403v1/GCA_000464035.1_ASM46403v1_genomic.fna.gz ERROR: Download failed for URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/464/035/GCA_000464035.1_ASM46403v1/GCA_000464035.1_ASM46403v1_genomic.fna.gz Traceback (most recent call last): File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2424, in retrfile self.ftp.cwd(file) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 629, in cwd return self.voidcmd(cmd) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 276, in voidcmd return self.voidresp() File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 249, in voidresp resp = self.getresp() File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 244, in getresp raise error_perm(resp) ftplib.error_perm: 550 GCA_000464035.1_ASM46403v1_genomic.fna.gz: No such file or directory The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1542, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2426, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/lpritc/Desktop/venv-pyani/lib/python3.6/site-packages/pyani-0.2.1.dev0-py3.6.egg/EGG-INFO/scripts/genbank_get_genomes_by_taxon.py", line 334, in retrieve_asm_contigs File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 223, in urlopen return opener.open(url, data, timeout) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 526, in open response = self._open(req, data) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 544, in _open '_open', req) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain result = func(*args) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1553, in ftp_open raise exc.with_traceback(sys.exc_info()[2]) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1542, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2426, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: WARNING: Could not download GCA_000464035.1_ASM46403v1, trying GCA_000464035.1_ASM46403v1 INFO: Retrieving assembly sequence for GCA_000464035.1_ASM46403v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/464/035/GCA_000464035.1_ASM46403v1/GCA_000464035.1_ASM46403v1_genomic.fna.gz ERROR: Download failed for URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/464/035/GCA_000464035.1_ASM46403v1/GCA_000464035.1_ASM46403v1_genomic.fna.gz Traceback (most recent call last): File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2424, in retrfile self.ftp.cwd(file) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 629, in cwd return self.voidcmd(cmd) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 276, in voidcmd return self.voidresp() File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 249, in voidresp resp = self.getresp() File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 244, in getresp raise error_perm(resp) ftplib.error_perm: 550 GCA_000464035.1_ASM46403v1_genomic.fna.gz: No such file or directory The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1542, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2426, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/lpritc/Desktop/venv-pyani/lib/python3.6/site-packages/pyani-0.2.1.dev0-py3.6.egg/EGG-INFO/scripts/genbank_get_genomes_by_taxon.py", line 334, in retrieve_asm_contigs File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 223, in urlopen return opener.open(url, data, timeout) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 526, in open response = self._open(req, data) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 544, in _open '_open', req) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain result = func(*args) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1553, in ftp_open raise exc.with_traceback(sys.exc_info()[2]) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1542, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2426, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/lpritc/Desktop/venv-pyani/lib/python3.6/site-packages/pyani-0.2.1.dev0-py3.6.egg/EGG-INFO/scripts/genbank_get_genomes_by_taxon.py", line 272, in get_ncbi_asm File "/Users/lpritc/Desktop/venv-pyani/lib/python3.6/site-packages/pyani-0.2.1.dev0-py3.6.egg/EGG-INFO/scripts/genbank_get_genomes_by_taxon.py", line 338, in retrieve_asm_contigs NCBIDownloadException: Error downloading file from NCBI During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2424, in retrfile self.ftp.cwd(file) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 629, in cwd return self.voidcmd(cmd) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 276, in voidcmd return self.voidresp() File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 249, in voidresp resp = self.getresp() File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/ftplib.py", line 244, in getresp raise error_perm(resp) ftplib.error_perm: 550 GCA_000464035.1_ASM46403v1_genomic.fna.gz: No such file or directory The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1542, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2426, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/Users/lpritc/Desktop/venv-pyani/lib/python3.6/site-packages/pyani-0.2.1.dev0-py3.6.egg/EGG-INFO/scripts/genbank_get_genomes_by_taxon.py", line 334, in retrieve_asm_contigs File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 223, in urlopen return opener.open(url, data, timeout) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 526, in open response = self._open(req, data) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 544, in _open '_open', req) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 504, in _call_chain result = func(*args) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1553, in ftp_open raise exc.with_traceback(sys.exc_info()[2]) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 1542, in ftp_open fp, retrlen = fw.retrfile(file, type) File "/usr/local/Cellar/python3/3.6.0/Frameworks/Python.framework/Versions/3.6/lib/python3.6/urllib/request.py", line 2426, in retrfile raise URLError('ftp error: %r' % reason) from reason urllib.error.URLError: ERROR: Skipping download for 58271 INFO: Identifying assembly information from NCBI for 42988 INFO: Organism: Caulobacter crescentus NA1000 (a-proteobacteria) INFO: Taxid: 155892 INFO: Accession: GCF_000022005.1 INFO: Name: ASM2200v1 INFO: Label: GCF_000022005.1_ASM2200v1_genomic C. vibrioides NA1000 INFO: Class: GCF_000022005.1_ASM2200v1_genomic Caulobacter vibrioides INFO: Retrieving assembly sequence for GCF_000022005.1_ASM2200v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/022/005/GCF_000022005.1_ASM2200v1/GCF_000022005.1_ASM2200v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/022/005/GCF_000022005.1_ASM2200v1/GCF_000022005.1_ASM2200v1_genomic.fna.gz (1155186 bytes) INFO: 1048576 [90.77%] INFO: 1155186 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000022005.1_ASM2200v1_genomic.fna.gz to Caulobacter_downloads/GCF_000022005.1_ASM2200v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000022005.1_ASM2200v1_genomic.fna INFO: Identifying assembly information from NCBI for 40188 INFO: Organism: Caulobacter sp. K31 (a-proteobacteria) INFO: Taxid: 366602 INFO: Accession: GCF_000019145.1 INFO: Name: ASM1914v1 INFO: Label: GCF_000019145.1_ASM1914v1_genomic C. sp. K31 K31 INFO: Class: GCF_000019145.1_ASM1914v1_genomic Caulobacter sp. K31 INFO: Retrieving assembly sequence for GCF_000019145.1_ASM1914v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/019/145/GCF_000019145.1_ASM1914v1/GCF_000019145.1_ASM1914v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/019/145/GCF_000019145.1_ASM1914v1/GCF_000019145.1_ASM1914v1_genomic.fna.gz (1679721 bytes) INFO: 1048576 [62.43%] INFO: 1679721 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000019145.1_ASM1914v1_genomic.fna.gz to Caulobacter_downloads/GCF_000019145.1_ASM1914v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000019145.1_ASM1914v1_genomic.fna INFO: Identifying assembly information from NCBI for 28488 INFO: Organism: Caulobacter crescentus CB15 (a-proteobacteria) INFO: Taxid: 155892 INFO: Accession: GCF_000006905.1 INFO: Name: ASM690v1 INFO: Label: GCF_000006905.1_ASM690v1_genomic C. vibrioides CB15 INFO: Class: GCF_000006905.1_ASM690v1_genomic Caulobacter vibrioides INFO: Retrieving assembly sequence for GCF_000006905.1_ASM690v1 INFO: Using URL: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/905/GCF_000006905.1_ASM690v1/GCF_000006905.1_ASM690v1_genomic.fna.gz INFO: Opened URL and parsed metadata. INFO: Downloading ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/905/GCF_000006905.1_ASM690v1/GCF_000006905.1_ASM690v1_genomic.fna.gz (1147304 bytes) INFO: 1048576 [91.39%] INFO: 1147304 [100.00%] INFO: Extracting archive Caulobacter_downloads/GCF_000006905.1_ASM690v1_genomic.fna.gz to Caulobacter_downloads/GCF_000006905.1_ASM690v1_genomic.fna INFO: Archive extracted to Caulobacter_downloads/GCF_000006905.1_ASM690v1_genomic.fna INFO: Writing classes file to Caulobacter_downloads/classes.txt INFO: Writing labels file to Caulobacter_downloads/labels.txt INFO: Obtained 29 assemblies WARNING: Skipped 1 downloads through error WARNING: Assembly UID 58271 skipped WARNING: UID: 58271 - accession: GCA_000464035.1 WARNING: Accession GCA_000464035 has versions: WARNING: 58271: GCA_000464035.1 - NOT DOWNLOADED WARNING: Accession is GenBank: does RefSeq exist? WARNING: Check under 'history' at http://www.ncbi.nlm.nih.gov/assembly/58271 WARNING: Alternative RefSeq candidate accession: GCF_000464035 WARNING: Were alternative assemblies downloaded? WARNING: 76161: GCF_000464035.1 - DOWNLOADED INFO: Skipped assembly UIDs: ['58271'] INFO: Tue Mar 21 11:29:38 2017 INFO: Done.