[2024-01-25 19:53:20,410] [INFO] DFAST_QC pipeline started. [2024-01-25 19:53:20,411] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:53:20,411] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa51add0-0bb2-49dd-96bb-cde5d5832016/dqc_reference [2024-01-25 19:53:21,501] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:53:21,501] [INFO] Task started: Prodigal [2024-01-25 19:53:21,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg2543768f-34ca-46db-8fca-fb7898358edf/GCF_003031675.1_ASM303167v1_genomic.fna.gz | prodigal -d GCF_003031675.1_ASM303167v1_genomic.fna/cds.fna -a GCF_003031675.1_ASM303167v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:53:44,342] [INFO] Task succeeded: Prodigal [2024-01-25 19:53:44,342] [INFO] Task started: HMMsearch [2024-01-25 19:53:44,343] [INFO] Running command: hmmsearch --tblout GCF_003031675.1_ASM303167v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa51add0-0bb2-49dd-96bb-cde5d5832016/dqc_reference/reference_markers.hmm GCF_003031675.1_ASM303167v1_genomic.fna/protein.faa > /dev/null [2024-01-25 19:53:44,648] [INFO] Task succeeded: HMMsearch [2024-01-25 19:53:44,649] [INFO] Found 6/6 markers. [2024-01-25 19:53:44,696] [INFO] Query marker FASTA was written to GCF_003031675.1_ASM303167v1_genomic.fna/markers.fasta [2024-01-25 19:53:44,696] [INFO] Task started: Blastn [2024-01-25 19:53:44,696] [INFO] Running command: blastn -query GCF_003031675.1_ASM303167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa51add0-0bb2-49dd-96bb-cde5d5832016/dqc_reference/reference_markers.fasta -out GCF_003031675.1_ASM303167v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:53:45,600] [INFO] Task succeeded: Blastn [2024-01-25 19:53:45,603] [INFO] Selected 20 target genomes. [2024-01-25 19:53:45,603] [INFO] Target genome list was writen to GCF_003031675.1_ASM303167v1_genomic.fna/target_genomes.txt [2024-01-25 19:53:45,625] [INFO] Task started: fastANI [2024-01-25 19:53:45,625] [INFO] Running command: fastANI --query /var/lib/cwl/stg2543768f-34ca-46db-8fca-fb7898358edf/GCF_003031675.1_ASM303167v1_genomic.fna.gz --refList GCF_003031675.1_ASM303167v1_genomic.fna/target_genomes.txt --output GCF_003031675.1_ASM303167v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:54:16,231] [INFO] Task succeeded: fastANI [2024-01-25 19:54:16,232] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa51add0-0bb2-49dd-96bb-cde5d5832016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:54:16,233] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa51add0-0bb2-49dd-96bb-cde5d5832016/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:54:16,244] [INFO] Found 20 fastANI hits (2 hits with ANI > threshold) [2024-01-25 19:54:16,245] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:54:16,245] [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 Pseudomonas palleroniana strain=LMG 23076 GCA_003031675.1 191390 191390 type True 100.0 1994 1998 95 conclusive Pseudomonas palleroniana strain=CCUG 51524 GCA_008801495.1 191390 191390 type True 99.9907 1982 1998 95 conclusive Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 87.8908 1592 1998 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 87.8682 1548 1998 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 87.8678 1602 1998 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 87.8153 1572 1998 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 87.8129 1575 1998 95 below_threshold Pseudomonas fluorescens strain=NBRC 14160 GCA_002091595.1 294 294 suspected-type True 87.7801 1590 1998 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 87.7719 1587 1998 95 below_threshold Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 87.7702 1582 1998 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 87.6817 1621 1998 95 below_threshold Pseudomonas fluorescens strain=NCTC10038 GCA_900475215.1 294 294 suspected-type True 87.6439 1613 1998 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 87.5725 1572 1998 95 below_threshold Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 87.558 1479 1998 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 87.5238 1570 1998 95 below_threshold Pseudomonas paracarnis strain=V5/DAB/2/5 GCA_904063055.1 2750625 2750625 type True 87.2353 1500 1998 95 below_threshold Pseudomonas salmasensis strain=SWRI126 GCA_014268375.2 2745514 2745514 type True 87.2223 1544 1998 95 below_threshold Pseudomonas lactis strain=DSM 29167 GCA_001439845.1 1615674 1615674 type True 87.2212 1536 1998 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.587 1434 1998 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.8378 1250 1998 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:54:16,246] [INFO] DFAST Taxonomy check result was written to GCF_003031675.1_ASM303167v1_genomic.fna/tc_result.tsv [2024-01-25 19:54:16,246] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:54:16,247] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:54:16,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa51add0-0bb2-49dd-96bb-cde5d5832016/dqc_reference/checkm_data [2024-01-25 19:54:16,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:54:16,304] [INFO] Task started: CheckM [2024-01-25 19:54:16,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003031675.1_ASM303167v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003031675.1_ASM303167v1_genomic.fna/checkm_input GCF_003031675.1_ASM303167v1_genomic.fna/checkm_result [2024-01-25 19:55:21,810] [INFO] Task succeeded: CheckM [2024-01-25 19:55:21,811] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:55:21,829] [INFO] ===== Completeness check finished ===== [2024-01-25 19:55:21,830] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:55:21,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003031675.1_ASM303167v1_genomic.fna/markers.fasta) [2024-01-25 19:55:21,830] [INFO] Task started: Blastn [2024-01-25 19:55:21,830] [INFO] Running command: blastn -query GCF_003031675.1_ASM303167v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa51add0-0bb2-49dd-96bb-cde5d5832016/dqc_reference/reference_markers_gtdb.fasta -out GCF_003031675.1_ASM303167v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:55:23,529] [INFO] Task succeeded: Blastn [2024-01-25 19:55:23,532] [INFO] Selected 20 target genomes. [2024-01-25 19:55:23,532] [INFO] Target genome list was writen to GCF_003031675.1_ASM303167v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:55:23,547] [INFO] Task started: fastANI [2024-01-25 19:55:23,547] [INFO] Running command: fastANI --query /var/lib/cwl/stg2543768f-34ca-46db-8fca-fb7898358edf/GCF_003031675.1_ASM303167v1_genomic.fna.gz --refList GCF_003031675.1_ASM303167v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003031675.1_ASM303167v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:55:56,274] [INFO] Task succeeded: fastANI [2024-01-25 19:55:56,286] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:55:56,286] [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_003031675.1 s__Pseudomonas_E palleroniana 100.0 1994 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.85 97.94 0.95 0.90 8 conclusive GCF_004519405.1 s__Pseudomonas_E sp004519405 91.7972 1777 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.60 98.40 0.98 0.92 5 - GCF_000612585.1 s__Pseudomonas_E sp000612585 88.0947 1496 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_013386585.1 s__Pseudomonas_E sp013386585 88.021 1529 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_003097075.1 s__Pseudomonas_E sp003097075 87.9935 1511 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.77 98.77 0.94 0.94 2 - GCF_013385985.1 s__Pseudomonas_E sp013385985 87.9743 1567 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCF_001647715.1 s__Pseudomonas_E antarctica_A 87.8951 1622 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.45 97.45 0.91 0.91 2 - GCF_900103345.1 s__Pseudomonas_E azotoformans 87.8364 1590 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.97 95.87 0.94 0.87 9 - GCF_001870465.1 s__Pseudomonas_E extremorientalis 87.8118 1575 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.37 98.13 0.91 0.89 29 - GCF_002813445.1 s__Pseudomonas_E tolaasii 87.6919 1566 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.61 99.17 0.97 0.93 14 - GCF_900215245.1 s__Pseudomonas_E fluorescens 87.66 1611 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.68 99.25 0.98 0.92 14 - GCF_001439695.1 s__Pseudomonas_E veronii 87.5802 1492 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.79 98.13 0.89 0.82 43 - GCF_002563895.1 s__Pseudomonas_E lurida 87.567 1573 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.19 99.03 0.94 0.91 25 - GCF_900624995.1 s__Pseudomonas_E antarctica 87.5428 1482 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.98 99.98 1.00 1.00 3 - GCF_009659625.1 s__Pseudomonas_E haemolytica 87.5258 1492 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.47 98.83 0.97 0.95 8 - GCF_015163715.1 s__Pseudomonas_E cyclaminis 87.2698 1387 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.88 95.83 0.83 0.80 14 - GCF_904063055.1 s__Pseudomonas_E paracarnis 87.2407 1499 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.75 95.59 0.90 0.84 86 - GCF_001439845.1 s__Pseudomonas_E lactis 87.2159 1537 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.24 95.50 0.88 0.81 30 - GCF_001902145.1 s__Pseudomonas_E fluorescens_BV 87.1742 1497 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.76 95.23 0.87 0.84 22 - GCF_002934065.1 s__Pseudomonas_E orientalis_A 86.9698 1508 1998 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.15 95.96 0.86 0.83 21 - -------------------------------------------------------------------------------- [2024-01-25 19:55:56,288] [INFO] GTDB search result was written to GCF_003031675.1_ASM303167v1_genomic.fna/result_gtdb.tsv [2024-01-25 19:55:56,288] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:55:56,295] [INFO] DFAST_QC result json was written to GCF_003031675.1_ASM303167v1_genomic.fna/dqc_result.json [2024-01-25 19:55:56,295] [INFO] DFAST_QC completed! [2024-01-25 19:55:56,295] [INFO] Total running time: 0h2m36s