04-18 16:29 DEBUG    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
04-18 16:29 DEBUG    ***Logger started up at /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/log/logger.log***
04-18 16:29 DEBUG    Command to run dRep was: ['/home/ubuntu/miniconda3/envs/irep/bin/dRep', 'dereplicate_wf', '.', '-g', 'genomes/GCF_000153905.1_ASM15390v1_genomic.fna', 'genomes/GCF_000156675.1_ASM15667v1_genomic.fna', 'genomes/GCF_000157975.1_ASM15797v1_genomic.fna', 'genomes/GCF_000373885.1_ASM37388v1_genomic.fna', 'genomes/GCF_000424085.1_ASM42408v1_genomic.fna', 'genomes/GCF_000439125.1_ASM43912v1_genomic.fna', 'genomes/GCF_000466565.1_ASM46656v1_genomic.fna', 'genomes/GCF_000484655.1_ASM48465v1_genomic.fna', 'genomes/GCF_000702025.1_ASM70202v1_genomic.fna', 'genomes/GCF_000765245.1_ASM76524v1_genomic.fna', 'genomes/GCF_001404455.1_13414_6_22_genomic.fna', 'genomes/GCF_001404535.1_13414_6_21_genomic.fna', 'genomes/GCF_001404735.1_14207_7_34_genomic.fna', 'genomes/GCF_001404755.1_13470_2_82_genomic.fna', 'genomes/GCF_001404775.1_14207_7_80_genomic.fna', 'genomes/GCF_001404935.1_13414_6_41_genomic.fna', 'genomes/GCF_001405215.1_14207_7_44_genomic.fna', 'genomes/GCF_001405455.1_13470_2_80_genomic.fna', 'genomes/GCF_001487165.1_Blautia_massiliensis1_genomic.fna', 'genomes/GCF_900078295.1_PRJEB13136_genomic.fna', 'genomes/GCF_900120195.1_PRJEB18016_genomic.fna', 'genomes/GCF_900120295.1_PRJEB18018_genomic.fna', '-o', '-p', '16', '--checkM_method', 'taxonomy_wf', '--run_tax', '--S_algorithm', 'gANI', '-sa', '0.99', '--cent_index', '/home/ubuntu/scripts/github/centrifuge/indices/b+h+v']

04-18 16:29 DEBUG    dRep version 0.5.5 was run 

04-18 16:29 DEBUG    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

04-18 16:29 DEBUG    Namespace(Chdb=None, MASH_sketch=1000, N50_weight=0.5, P_ani=0.9, S_algorithm='gANI', S_ani=0.99, SkipMash=False, SkipSecondary=False, cent_index='/home/ubuntu/scripts/github/centrifuge/indices/b+h+v', checkM_method='taxonomy_wf', clusterAlg='average', completeness=75, completeness_weight=1, contamination=25, contamination_weight=5, cov_thresh=0.1, coverage_method='larger', dry=False, genomes=['genomes/GCF_000153905.1_ASM15390v1_genomic.fna', 'genomes/GCF_000156675.1_ASM15667v1_genomic.fna', 'genomes/GCF_000157975.1_ASM15797v1_genomic.fna', 'genomes/GCF_000373885.1_ASM37388v1_genomic.fna', 'genomes/GCF_000424085.1_ASM42408v1_genomic.fna', 'genomes/GCF_000439125.1_ASM43912v1_genomic.fna', 'genomes/GCF_000466565.1_ASM46656v1_genomic.fna', 'genomes/GCF_000484655.1_ASM48465v1_genomic.fna', 'genomes/GCF_000702025.1_ASM70202v1_genomic.fna', 'genomes/GCF_000765245.1_ASM76524v1_genomic.fna', 'genomes/GCF_001404455.1_13414_6_22_genomic.fna', 'genomes/GCF_001404535.1_13414_6_21_genomic.fna', 'genomes/GCF_001404735.1_14207_7_34_genomic.fna', 'genomes/GCF_001404755.1_13470_2_82_genomic.fna', 'genomes/GCF_001404775.1_14207_7_80_genomic.fna', 'genomes/GCF_001404935.1_13414_6_41_genomic.fna', 'genomes/GCF_001405215.1_14207_7_44_genomic.fna', 'genomes/GCF_001405455.1_13470_2_80_genomic.fna', 'genomes/GCF_001487165.1_Blautia_massiliensis1_genomic.fna', 'genomes/GCF_900078295.1_PRJEB13136_genomic.fna', 'genomes/GCF_900120195.1_PRJEB18016_genomic.fna', 'genomes/GCF_900120295.1_PRJEB18018_genomic.fna'], length=50000, n_PRESET='normal', operation='dereplicate_wf', overwrite=True, processors=16, run_tax=True, size_weight=0, skipCheckM=False, strain_heterogeneity_weight=1, strain_htr=25, warn_aln=0.25, warn_dist=0.25, warn_sim=0.98, work_directory='.')
04-18 16:29 DEBUG    Starting the dereplicate_wf operation
04-18 16:29 INFO     ***************************************************
    ..:: dRep Step 1. Filter ::..
***************************************************
    
04-18 16:29 DEBUG    Loading work directory in filter
04-18 16:29 DEBUG    Located: /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1
Datatables: []
Cluster files: []
Arguments: []
04-18 16:29 DEBUG    Validating filter arguments
04-18 16:29 INFO     Will filter the genome list
04-18 16:29 DEBUG    Filtering genomes by size
04-18 16:29 INFO     100.00% of genomes passed length filtering
04-18 16:29 DEBUG    Running CheckM
04-18 16:29 INFO     Running prodigal
04-18 16:31 DEBUG    Running CheckM with command: ['/usr/local/bin/checkm', 'taxonomy_wf', 'domain', 'Bacteria', '/home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/prodigal/', '/home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/checkM/checkM_outdir/', '-f', '/home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/checkM/checkM_outdir//results.tsv', '--tab_table', '-t', '16', '-g', '-x', 'faa']
04-18 16:33 DEBUG    Running CheckM with command: ['/usr/local/bin/checkm', 'qa', '/home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/checkM/checkM_outdir/Bacteria.ms', '/home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/checkM/checkM_outdir/', '-f', '/home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/checkM/checkM_outdir/Chdb.tsv', '-t', '16', '--tab_table', '-o', '2']
04-18 16:33 INFO     100.00% of genomes passed checkM filtering
04-18 16:33 INFO     ***************************************************
    ..:: dRep Step 2. Cluster ::..
***************************************************
    
04-18 16:33 DEBUG    Loading work directory
04-18 16:33 DEBUG    Located: /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1
Datatables: ['Chdb', 'Bdb']
Cluster files: []
Arguments: []
04-18 16:33 INFO     Step 1. Parse Arguments
04-18 16:33 DEBUG    kwargs: {'operation': 'dereplicate_wf', 'work_directory': '.', 'processors': 16, 'dry': False, 'overwrite': True, 'length': 50000, 'completeness': 75, 'contamination': 25, 'strain_htr': 25, 'skipCheckM': False, 'MASH_sketch': 1000, 'P_ani': 0.9, 'S_algorithm': 'gANI', 'S_ani': 0.99, 'cov_thresh': 0.1, 'coverage_method': 'larger', 'n_PRESET': 'normal', 'clusterAlg': 'average', 'SkipMash': False, 'SkipSecondary': False, 'completeness_weight': 1, 'contamination_weight': 5, 'N50_weight': 0.5, 'size_weight': 0, 'strain_heterogeneity_weight': 1, 'run_tax': True, 'cent_index': '/home/ubuntu/scripts/github/centrifuge/indices/b+h+v', 'warn_dist': 0.25, 'warn_sim': 0.98, 'warn_aln': 0.25, 'checkM_method': 'taxonomy_wf', 'mash_exe': '/usr/local/bin/mash', 'n_c': 65, 'n_maxgap': 90, 'n_noextend': False, 'n_method': 'mum'}
04-18 16:33 INFO     Step 2. Perform MASH (primary) clustering
04-18 16:33 INFO     2a. Run pair-wise MASH clustering
04-18 16:33 INFO     2b. Cluster pair-wise MASH clustering
04-18 16:33 DEBUG    Clustering MASH database
04-18 16:33 DEBUG    Saving primary_linkage pickle to /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/Clustering_files/
04-18 16:33 INFO     9 primary clusters made
04-18 16:33 INFO     Step 3. Perform secondary clustering
04-18 16:33 INFO     Running 92 gANI comparisons- should take ~ 0.6 min
04-18 16:33 INFO     Past prodigal runs found- will not re-run
04-18 16:33 DEBUG    Running gANI commands: /usr/local/bin/ANIcalculator -genome1fna /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/prodigal/GCF_001404535.1_13414_6_21_genomic.fna.fna -genome2fna /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/prodigal/GCF_000153905.1_ASM15390v1_genomic.fna.fna -outfile /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/gANI_files/GCF_001404535.1_13414_6_21_genomic.fna_vs_GCF_000153905.1_ASM15390v1_genomic.fna.gANI -outdir /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/gANI_files/GCF_001404535.1_13414_6_21_genomic.fna_vs_GCF_000153905.1_ASM15390v1_genomic.fna.gANITEMP
/usr/local/bin/ANIcalculator -genome1fna /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/prodigal/GCF_001405215.1_14207_7_44_genomic.fna.fna -genome2fna /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/prodigal/GCF_000153905.1_ASM15390v1_genomic.fna.fna -outfile /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/gANI_files/GCF_001405215.1_14207_7_44_genomic.fna_vs_GCF_000153905.1_ASM15390v1_genomic.fna.gANI -outdir /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/gANI_files/GCF_001405215.1_14207_7_44_genomic.fna_vs_GCF_000153905.1_ASM15390v1_genomic.fna.gANITEMP
/usr/local/bin/ANIcalculator -genome1fna /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/prodigal/GCF_001405215.1_14207_7_44_genomic.fna.fna -genome2fna /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/prodigal/GCF_001404535.1_13414_6_21_genomic.fna.fna -outfile /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/gANI_files/GCF_001405215.1_14207_7_44_genomic.fna_vs_GCF_001404535.1_13414_6_21_genomic.fna.gANI -outdir /home/ubuntu/db/ncbi_Blautia_20170418/dRep/gANI_gt99/test_mem1/data/gANI_files/GCF_001405215.1_14207_7_44_genomic.fna_vs_GCF_001404535.1_13414_6_21_genomic.fna.gANITEMP