[2024-01-24 15:03:29,497] [INFO] DFAST_QC pipeline started. [2024-01-24 15:03:29,499] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 15:03:29,499] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ce94b16-2a80-48d8-bed7-c396479d01c8/dqc_reference [2024-01-24 15:03:30,707] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 15:03:30,708] [INFO] Task started: Prodigal [2024-01-24 15:03:30,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc125a44-ff8b-44e0-ac69-e1bd35987cc5/GCF_900609065.1_aT11b_genomic.fna.gz | prodigal -d GCF_900609065.1_aT11b_genomic.fna/cds.fna -a GCF_900609065.1_aT11b_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 15:03:42,033] [INFO] Task succeeded: Prodigal [2024-01-24 15:03:42,033] [INFO] Task started: HMMsearch [2024-01-24 15:03:42,033] [INFO] Running command: hmmsearch --tblout GCF_900609065.1_aT11b_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ce94b16-2a80-48d8-bed7-c396479d01c8/dqc_reference/reference_markers.hmm GCF_900609065.1_aT11b_genomic.fna/protein.faa > /dev/null [2024-01-24 15:03:42,361] [INFO] Task succeeded: HMMsearch [2024-01-24 15:03:42,367] [INFO] Found 6/6 markers. [2024-01-24 15:03:42,404] [INFO] Query marker FASTA was written to GCF_900609065.1_aT11b_genomic.fna/markers.fasta [2024-01-24 15:03:42,405] [INFO] Task started: Blastn [2024-01-24 15:03:42,405] [INFO] Running command: blastn -query GCF_900609065.1_aT11b_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ce94b16-2a80-48d8-bed7-c396479d01c8/dqc_reference/reference_markers.fasta -out GCF_900609065.1_aT11b_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:03:43,394] [INFO] Task succeeded: Blastn [2024-01-24 15:03:43,398] [INFO] Selected 17 target genomes. [2024-01-24 15:03:43,399] [INFO] Target genome list was writen to GCF_900609065.1_aT11b_genomic.fna/target_genomes.txt [2024-01-24 15:03:43,407] [INFO] Task started: fastANI [2024-01-24 15:03:43,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc125a44-ff8b-44e0-ac69-e1bd35987cc5/GCF_900609065.1_aT11b_genomic.fna.gz --refList GCF_900609065.1_aT11b_genomic.fna/target_genomes.txt --output GCF_900609065.1_aT11b_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 15:03:57,470] [INFO] Task succeeded: fastANI [2024-01-24 15:03:57,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ce94b16-2a80-48d8-bed7-c396479d01c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 15:03:57,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ce94b16-2a80-48d8-bed7-c396479d01c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 15:03:57,484] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold) [2024-01-24 15:03:57,484] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 15:03:57,484] [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 Arthrobacter ulcerisalmonis GCA_900609065.1 2483813 2483813 type True 100.0 1140 1143 95 conclusive Pseudarthrobacter equi strain=IMMIB L-1606 GCA_900105535.1 728066 728066 type True 81.1578 692 1143 95 below_threshold Pseudarthrobacter chlorophenolicus strain=A6 GCA_000022025.1 85085 85085 type True 81.111 698 1143 95 below_threshold Pseudarthrobacter chlorophenolicus strain=A6 GCA_900104315.1 85085 85085 type True 81.0987 702 1143 95 below_threshold Pseudarthrobacter polychromogenes strain=CGMCC 1.1927 GCA_014644495.1 1676 1676 type True 81.053 643 1143 95 below_threshold Pseudarthrobacter scleromae strain=CGMCC 1.3601 GCA_014644515.1 158897 158897 type True 80.9802 652 1143 95 below_threshold Pseudarthrobacter siccitolerans strain=4J27 GCA_001046895.1 861266 861266 type True 80.9552 670 1143 95 below_threshold Pseudarthrobacter psychrotolerans strain=YJ56 GCA_009911795.1 2697569 2697569 type True 80.9256 651 1143 95 below_threshold Pseudarthrobacter phenanthrenivorans strain=Sphe3 GCA_000189535.1 361575 361575 type True 80.9142 647 1143 95 below_threshold Pseudarthrobacter sulfonivorans strain=ALL GCA_014712225.1 121292 121292 type True 80.8751 620 1143 95 below_threshold Arthrobacter globiformis strain=NBRC 12137 GCA_000238915.2 1665 1665 type True 80.219 574 1143 95 below_threshold Arthrobacter pascens strain=DSM 20545 GCA_017052465.1 1677 1677 type True 80.0593 556 1143 95 below_threshold Arthrobacter cupressi strain=DSM 24664 GCA_013409905.1 1045773 1045773 type True 79.8908 517 1143 95 below_threshold Paenarthrobacter nicotinovorans strain=ATCC 49919 GCA_021919345.1 29320 29320 suspected-type True 79.5068 482 1143 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_017898065.1 2817475 2817475 type True 78.2561 300 1143 95 below_threshold Arthrobacter jiangjiafuii strain=zg-ZUI227 GCA_018622995.1 2817475 2817475 type True 78.2532 306 1143 95 below_threshold Arthrobacter sunyaminii strain=zg-ZUI122 GCA_018866305.1 2816859 2816859 type True 78.1765 276 1143 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 15:03:57,487] [INFO] DFAST Taxonomy check result was written to GCF_900609065.1_aT11b_genomic.fna/tc_result.tsv [2024-01-24 15:03:57,487] [INFO] ===== Taxonomy check completed ===== [2024-01-24 15:03:57,487] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 15:03:57,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ce94b16-2a80-48d8-bed7-c396479d01c8/dqc_reference/checkm_data [2024-01-24 15:03:57,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 15:03:57,528] [INFO] Task started: CheckM [2024-01-24 15:03:57,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900609065.1_aT11b_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900609065.1_aT11b_genomic.fna/checkm_input GCF_900609065.1_aT11b_genomic.fna/checkm_result [2024-01-24 15:04:33,289] [INFO] Task succeeded: CheckM [2024-01-24 15:04:33,290] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 15:04:33,312] [INFO] ===== Completeness check finished ===== [2024-01-24 15:04:33,312] [INFO] ===== Start GTDB Search ===== [2024-01-24 15:04:33,312] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900609065.1_aT11b_genomic.fna/markers.fasta) [2024-01-24 15:04:33,313] [INFO] Task started: Blastn [2024-01-24 15:04:33,313] [INFO] Running command: blastn -query GCF_900609065.1_aT11b_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ce94b16-2a80-48d8-bed7-c396479d01c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900609065.1_aT11b_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 15:04:34,767] [INFO] Task succeeded: Blastn [2024-01-24 15:04:34,770] [INFO] Selected 25 target genomes. [2024-01-24 15:04:34,770] [INFO] Target genome list was writen to GCF_900609065.1_aT11b_genomic.fna/target_genomes_gtdb.txt [2024-01-24 15:04:34,792] [INFO] Task started: fastANI [2024-01-24 15:04:34,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc125a44-ff8b-44e0-ac69-e1bd35987cc5/GCF_900609065.1_aT11b_genomic.fna.gz --refList GCF_900609065.1_aT11b_genomic.fna/target_genomes_gtdb.txt --output GCF_900609065.1_aT11b_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 15:04:56,727] [INFO] Task succeeded: fastANI [2024-01-24 15:04:56,746] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 15:04:56,747] [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_900609065.1 s__Pseudarthrobacter ulcerisalmonis 100.0 1140 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 conclusive GCF_001424565.1 s__Pseudarthrobacter sp001424565 82.0644 772 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 98.93 98.93 0.94 0.94 2 - GCF_900168295.1 s__Pseudarthrobacter sp900168295 81.1775 661 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 98.77 97.56 0.93 0.89 3 - GCF_900105535.1 s__Pseudarthrobacter equi 81.1481 693 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_001428075.1 s__Pseudarthrobacter sp001428075 81.1369 655 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_000022025.1 s__Pseudarthrobacter chlorophenolicus 81.1111 697 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 100.00 100.00 1.00 1.00 2 - GCF_001641125.1 s__Pseudarthrobacter sp001641125 81.0068 668 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_006517815.1 s__Pseudarthrobacter sp006517815 80.9913 643 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 98.42 98.42 0.88 0.88 2 - GCF_000374905.1 s__Pseudarthrobacter sp000374905 80.9649 648 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 98.45 96.91 0.92 0.90 5 - GCF_001046895.1 s__Pseudarthrobacter siccitolerans 80.9617 670 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_902506095.1 s__Pseudarthrobacter sp902506095 80.9463 654 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_006151685.1 s__Pseudarthrobacter sp006151685 80.94 643 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 100.00 100.00 1.00 1.00 2 - GCF_000189535.1 s__Pseudarthrobacter phenanthrenivorans 80.8997 647 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 98.29 98.26 0.89 0.89 3 - GCF_003208335.1 s__Pseudarthrobacter sp003208335 80.8922 646 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_014712225.1 s__Pseudarthrobacter sulfonivorans 80.8751 620 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_001484605.1 s__Pseudarthrobacter sulfonivorans_A 80.8259 659 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_002892835.1 s__Pseudarthrobacter sp002892835 80.8163 592 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_004320525.1 s__Pseudarthrobacter sp004320525 80.8141 669 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_006715305.1 s__Pseudarthrobacter sp006715305 80.8109 652 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCF_000374865.1 s__Pseudarthrobacter sp000374865 80.8048 658 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 98.52 98.50 0.89 0.88 3 - GCF_006715285.1 s__Pseudarthrobacter sp006715285 80.7498 669 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - GCA_002427975.1 s__Pseudarthrobacter sp002427975 80.2662 514 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 99.44 99.44 0.84 0.84 2 - GCF_001422645.1 s__Arthrobacter_I sp001422645 80.2376 569 1143 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_004798705.1 s__Arthrobacter_I sp004798705 80.1928 533 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Arthrobacter_I 95.0 N/A N/A N/A N/A 1 - GCA_013362385.1 s__Pseudarthrobacter sp013362385 80.0605 307 1143 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Pseudarthrobacter 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 15:04:56,748] [INFO] GTDB search result was written to GCF_900609065.1_aT11b_genomic.fna/result_gtdb.tsv [2024-01-24 15:04:56,749] [INFO] ===== GTDB Search completed ===== [2024-01-24 15:04:56,753] [INFO] DFAST_QC result json was written to GCF_900609065.1_aT11b_genomic.fna/dqc_result.json [2024-01-24 15:04:56,753] [INFO] DFAST_QC completed! [2024-01-24 15:04:56,753] [INFO] Total running time: 0h1m27s