[2024-01-24 11:51:11,136] [INFO] DFAST_QC pipeline started. [2024-01-24 11:51:11,138] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:51:11,138] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1777f0b-8eb5-4d82-9fc5-abf92668e0f0/dqc_reference [2024-01-24 11:51:12,416] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:51:12,417] [INFO] Task started: Prodigal [2024-01-24 11:51:12,418] [INFO] Running command: gunzip -c /var/lib/cwl/stg9877c807-2d1c-4988-85b2-bbe3ebf713a9/GCF_018224015.1_ASM1822401v1_genomic.fna.gz | prodigal -d GCF_018224015.1_ASM1822401v1_genomic.fna/cds.fna -a GCF_018224015.1_ASM1822401v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:51:25,437] [INFO] Task succeeded: Prodigal [2024-01-24 11:51:25,437] [INFO] Task started: HMMsearch [2024-01-24 11:51:25,438] [INFO] Running command: hmmsearch --tblout GCF_018224015.1_ASM1822401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1777f0b-8eb5-4d82-9fc5-abf92668e0f0/dqc_reference/reference_markers.hmm GCF_018224015.1_ASM1822401v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:51:25,716] [INFO] Task succeeded: HMMsearch [2024-01-24 11:51:25,717] [INFO] Found 6/6 markers. [2024-01-24 11:51:25,771] [INFO] Query marker FASTA was written to GCF_018224015.1_ASM1822401v1_genomic.fna/markers.fasta [2024-01-24 11:51:25,772] [INFO] Task started: Blastn [2024-01-24 11:51:25,772] [INFO] Running command: blastn -query GCF_018224015.1_ASM1822401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1777f0b-8eb5-4d82-9fc5-abf92668e0f0/dqc_reference/reference_markers.fasta -out GCF_018224015.1_ASM1822401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:51:26,924] [INFO] Task succeeded: Blastn [2024-01-24 11:51:26,928] [INFO] Selected 21 target genomes. [2024-01-24 11:51:26,928] [INFO] Target genome list was writen to GCF_018224015.1_ASM1822401v1_genomic.fna/target_genomes.txt [2024-01-24 11:51:26,936] [INFO] Task started: fastANI [2024-01-24 11:51:26,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg9877c807-2d1c-4988-85b2-bbe3ebf713a9/GCF_018224015.1_ASM1822401v1_genomic.fna.gz --refList GCF_018224015.1_ASM1822401v1_genomic.fna/target_genomes.txt --output GCF_018224015.1_ASM1822401v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:51:45,097] [INFO] Task succeeded: fastANI [2024-01-24 11:51:45,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1777f0b-8eb5-4d82-9fc5-abf92668e0f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:51:45,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1777f0b-8eb5-4d82-9fc5-abf92668e0f0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:51:45,116] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold) [2024-01-24 11:51:45,116] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 11:51:45,116] [INFO] DFAST Taxonomy check final result -------------------------------------------------------------------------------- organism_name strain accession taxid species_taxid relation_to_type validated ani matched_fragments total_fragments ani_threshold status Pseudarthrobacter psychrotolerans strain=YJ56 GCA_009911795.1 2697569 2697569 type True 81.8887 761 1421 95 below_threshold Arthrobacter globiformis strain=NBRC 12137 GCA_000238915.2 1665 1665 type True 81.8886 728 1421 95 below_threshold Arthrobacter pascens strain=DSM 20545 GCA_017052465.1 1677 1677 type True 81.8796 708 1421 95 below_threshold Arthrobacter ipis strain=IA7 GCA_014694315.1 2716202 2716202 type True 81.7148 727 1421 95 below_threshold Pseudarthrobacter sulfonivorans strain=ALL GCA_014712225.1 121292 121292 type True 81.6577 705 1421 95 below_threshold Pseudarthrobacter polychromogenes strain=CGMCC 1.1927 GCA_014644495.1 1676 1676 type True 81.3331 642 1421 95 below_threshold Pseudarthrobacter scleromae strain=CGMCC 1.3601 GCA_014644515.1 158897 158897 type True 81.2935 632 1421 95 below_threshold Pseudarthrobacter equi strain=IMMIB L-1606 GCA_900105535.1 728066 728066 type True 81.2898 638 1421 95 below_threshold Arthrobacter celericrescens strain=NEAU-SA2 GCA_003614925.1 2320851 2320851 type True 81.2468 644 1421 95 below_threshold Pseudarthrobacter enclensis strain=NIO-1008 GCA_900094675.1 993070 993070 type True 81.2021 656 1421 95 below_threshold Pseudarthrobacter enclensis strain=NIO-1008 GCA_001457025.1 993070 993070 type True 81.2007 655 1421 95 below_threshold Pseudarthrobacter siccitolerans strain=4J27 GCA_001046895.1 861266 861266 type True 81.1841 668 1421 95 below_threshold Arthrobacter cupressi strain=DSM 24664 GCA_013409905.1 1045773 1045773 type True 81.1065 629 1421 95 below_threshold Arthrobacter cupressi strain=CGMCC 1.10783 GCA_900099975.1 1045773 1045773 type True 81.0411 625 1421 95 below_threshold Pseudarthrobacter chlorophenolicus strain=A6 GCA_900104315.1 85085 85085 type True 80.9943 684 1421 95 below_threshold Pseudarthrobacter chlorophenolicus strain=A6 GCA_000022025.1 85085 85085 type True 80.9086 685 1421 95 below_threshold Arthrobacter ulcerisalmonis GCA_900609065.1 2483813 2483813 type True 80.1592 527 1421 95 below_threshold Paenarthrobacter nicotinovorans strain=ATCC 49919 GCA_021919345.1 29320 29320 suspected-type True 79.94 542 1421 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_017898065.1 2817475 2817475 type True 79.2996 368 1421 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_018622995.1 2817475 2817475 type True 79.2648 372 1421 95 below_threshold Arthrobacter mobilis strain=E918 GCA_012395835.1 2724944 2724944 type True 79.1343 463 1421 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:51:45,118] [INFO] DFAST Taxonomy check result was written to GCF_018224015.1_ASM1822401v1_genomic.fna/tc_result.tsv [2024-01-24 11:51:45,118] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:51:45,118] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:51:45,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1777f0b-8eb5-4d82-9fc5-abf92668e0f0/dqc_reference/checkm_data [2024-01-24 11:51:45,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:51:45,167] [INFO] Task started: CheckM [2024-01-24 11:51:45,167] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018224015.1_ASM1822401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018224015.1_ASM1822401v1_genomic.fna/checkm_input GCF_018224015.1_ASM1822401v1_genomic.fna/checkm_result [2024-01-24 11:52:23,149] [INFO] Task succeeded: CheckM [2024-01-24 11:52:23,150] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:52:23,213] [INFO] ===== Completeness check finished ===== [2024-01-24 11:52:23,213] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:52:23,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018224015.1_ASM1822401v1_genomic.fna/markers.fasta) [2024-01-24 11:52:23,214] [INFO] Task started: Blastn [2024-01-24 11:52:23,214] [INFO] Running command: blastn -query GCF_018224015.1_ASM1822401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1777f0b-8eb5-4d82-9fc5-abf92668e0f0/dqc_reference/reference_markers_gtdb.fasta -out GCF_018224015.1_ASM1822401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:52:24,896] [INFO] Task succeeded: Blastn [2024-01-24 11:52:24,900] [INFO] Selected 18 target genomes. [2024-01-24 11:52:24,900] [INFO] Target genome list was writen to GCF_018224015.1_ASM1822401v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:52:24,913] [INFO] Task started: fastANI [2024-01-24 11:52:24,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg9877c807-2d1c-4988-85b2-bbe3ebf713a9/GCF_018224015.1_ASM1822401v1_genomic.fna.gz --refList GCF_018224015.1_ASM1822401v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018224015.1_ASM1822401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:52:41,468] [INFO] Task succeeded: fastANI [2024-01-24 11:52:41,483] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:52:41,483] [INFO] GTDB search result -------------------------------------------------------------------------------- accession gtdb_species ani matched_fragments total_fragments gtdb_taxonomy ani_circumscription_radius mean_intra_species_ani min_intra_species_ani mean_intra_species_af min_intra_species_af num_clustered_genomes status GCF_018224015.1 s__Arthrobacter_I sp018224015 100.0 1412 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 conclusive GCF_004798705.1 s__Arthrobacter_I sp004798705 88.012 922 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_001750145.1 s__Arthrobacter_I sp001750145 84.7093 861 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_009928425.1 s__Arthrobacter_I sp009928425 84.6661 834 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_000427315.1 s__Arthrobacter_I sp000427315 84.5684 687 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_000374925.1 s__Arthrobacter_I sp000374925 84.4028 866 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 97.54 97.54 0.90 0.90 2 - GCF_007679325.1 s__Arthrobacter_I sp007679325 84.321 813 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_003097355.1 s__Arthrobacter_I sp003097355 84.2705 873 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 95.72 95.72 0.82 0.82 2 - GCF_001512305.1 s__Arthrobacter_I sp001512305 84.2695 820 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_013359735.1 s__Arthrobacter_I sp013359735 84.2501 785 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_900102895.1 s__Arthrobacter_I sp900102895 84.1996 851 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_900168135.1 s__Arthrobacter_I sp900168135 84.1324 864 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 95.10 95.10 0.85 0.85 2 - GCF_900102785.1 s__Arthrobacter_I sp900102785 84.0835 879 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_003352915.1 s__Arthrobacter_I sp003352915 83.9118 850 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_003634095.1 s__Arthrobacter_I oryzae 83.8755 832 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_900116495.1 s__Arthrobacter_I sp900116495 83.7522 827 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_000876655.1 s__Arthrobacter_I sp000876655 82.5675 761 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCF_017368795.1 s__PO-11 sp017368795 81.782 688 1421 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__PO-11 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 11:52:41,485] [INFO] GTDB search result was written to GCF_018224015.1_ASM1822401v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:52:41,486] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:52:41,493] [INFO] DFAST_QC result json was written to GCF_018224015.1_ASM1822401v1_genomic.fna/dqc_result.json [2024-01-24 11:52:41,493] [INFO] DFAST_QC completed! [2024-01-24 11:52:41,493] [INFO] Total running time: 0h1m30s