[2024-01-24 12:40:51,084] [INFO] DFAST_QC pipeline started. [2024-01-24 12:40:51,086] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:40:51,086] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a8f2832-53bd-4ac5-a15a-5719b5d2e090/dqc_reference [2024-01-24 12:40:52,297] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:40:52,298] [INFO] Task started: Prodigal [2024-01-24 12:40:52,298] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a31d4f5-766a-4b42-a014-ab6d1254c1b4/GCF_008801495.1_ASM880149v1_genomic.fna.gz | prodigal -d GCF_008801495.1_ASM880149v1_genomic.fna/cds.fna -a GCF_008801495.1_ASM880149v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:41:14,570] [INFO] Task succeeded: Prodigal [2024-01-24 12:41:14,570] [INFO] Task started: HMMsearch [2024-01-24 12:41:14,570] [INFO] Running command: hmmsearch --tblout GCF_008801495.1_ASM880149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a8f2832-53bd-4ac5-a15a-5719b5d2e090/dqc_reference/reference_markers.hmm GCF_008801495.1_ASM880149v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:41:14,903] [INFO] Task succeeded: HMMsearch [2024-01-24 12:41:14,905] [INFO] Found 6/6 markers. [2024-01-24 12:41:14,959] [INFO] Query marker FASTA was written to GCF_008801495.1_ASM880149v1_genomic.fna/markers.fasta [2024-01-24 12:41:14,959] [INFO] Task started: Blastn [2024-01-24 12:41:14,959] [INFO] Running command: blastn -query GCF_008801495.1_ASM880149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a8f2832-53bd-4ac5-a15a-5719b5d2e090/dqc_reference/reference_markers.fasta -out GCF_008801495.1_ASM880149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:41:15,841] [INFO] Task succeeded: Blastn [2024-01-24 12:41:15,846] [INFO] Selected 25 target genomes. [2024-01-24 12:41:15,847] [INFO] Target genome list was writen to GCF_008801495.1_ASM880149v1_genomic.fna/target_genomes.txt [2024-01-24 12:41:15,857] [INFO] Task started: fastANI [2024-01-24 12:41:15,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a31d4f5-766a-4b42-a014-ab6d1254c1b4/GCF_008801495.1_ASM880149v1_genomic.fna.gz --refList GCF_008801495.1_ASM880149v1_genomic.fna/target_genomes.txt --output GCF_008801495.1_ASM880149v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:41:54,187] [INFO] Task succeeded: fastANI [2024-01-24 12:41:54,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a8f2832-53bd-4ac5-a15a-5719b5d2e090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:41:54,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a8f2832-53bd-4ac5-a15a-5719b5d2e090/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:41:54,212] [INFO] Found 25 fastANI hits (2 hits with ANI > threshold) [2024-01-24 12:41:54,212] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 12:41:54,212] [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=CCUG 51524 GCA_008801495.1 191390 191390 type True 100.0 2012 2012 95 conclusive Pseudomonas palleroniana strain=LMG 23076 GCA_003031675.1 191390 191390 type True 99.9775 1986 2012 95 conclusive Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 87.9628 1589 2012 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 87.9428 1614 2012 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 87.8708 1554 2012 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 87.8181 1589 2012 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 87.8147 1580 2012 95 below_threshold Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 87.8063 1588 2012 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 87.7995 1597 2012 95 below_threshold Pseudomonas fluorescens strain=NBRC 14160 GCA_002091595.1 294 294 suspected-type True 87.7793 1574 2012 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 87.7051 1624 2012 95 below_threshold Pseudomonas fluorescens strain=NCTC10038 GCA_900475215.1 294 294 suspected-type True 87.664 1624 2012 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 87.5724 1580 2012 95 below_threshold Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 87.5204 1489 2012 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 87.4903 1588 2012 95 below_threshold Pseudomonas salmasensis strain=SWRI126 GCA_014268375.2 2745514 2745514 type True 87.2564 1538 2012 95 below_threshold Pseudomonas paracarnis strain=V5/DAB/2/5 GCA_904063055.1 2750625 2750625 type True 87.2182 1517 2012 95 below_threshold Pseudomonas lactis strain=DSM 29167 GCA_001439845.1 1615674 1615674 type True 87.1946 1555 2012 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.5703 1455 2012 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.8134 1279 2012 95 below_threshold Pseudomonas kilonensis strain=DSM 13647 GCA_001269885.1 132476 132476 type True 83.3732 1168 2012 95 below_threshold Pseudomonas brassicacearum strain=JCM 11938 GCA_012034345.1 930166 930166 suspected-type True 83.104 1216 2012 95 below_threshold Pseudomonas thivervalensis strain=DSM 13194 GCA_001269655.1 86265 86265 type True 83.1003 1202 2012 95 below_threshold Pseudomonas brassicacearum subsp. brassicacearum strain=CCUG 51508 GCA_008801605.1 86264 930166 type True 83.0734 1212 2012 95 below_threshold Pseudomonas zanjanensis strain=SWRI12 GCA_014268745.2 2745496 2745496 type True 83.0526 1153 2012 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:41:54,218] [INFO] DFAST Taxonomy check result was written to GCF_008801495.1_ASM880149v1_genomic.fna/tc_result.tsv [2024-01-24 12:41:54,218] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:41:54,218] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:41:54,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a8f2832-53bd-4ac5-a15a-5719b5d2e090/dqc_reference/checkm_data [2024-01-24 12:41:54,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:41:54,281] [INFO] Task started: CheckM [2024-01-24 12:41:54,281] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008801495.1_ASM880149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008801495.1_ASM880149v1_genomic.fna/checkm_input GCF_008801495.1_ASM880149v1_genomic.fna/checkm_result [2024-01-24 12:42:58,885] [INFO] Task succeeded: CheckM [2024-01-24 12:42:58,887] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 1.85% Strain heterogeneity: 100.00% -------------------------------------------------------------------------------- [2024-01-24 12:42:58,915] [INFO] ===== Completeness check finished ===== [2024-01-24 12:42:58,915] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:42:58,916] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008801495.1_ASM880149v1_genomic.fna/markers.fasta) [2024-01-24 12:42:58,916] [INFO] Task started: Blastn [2024-01-24 12:42:58,916] [INFO] Running command: blastn -query GCF_008801495.1_ASM880149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a8f2832-53bd-4ac5-a15a-5719b5d2e090/dqc_reference/reference_markers_gtdb.fasta -out GCF_008801495.1_ASM880149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:43:00,344] [INFO] Task succeeded: Blastn [2024-01-24 12:43:00,349] [INFO] Selected 25 target genomes. [2024-01-24 12:43:00,349] [INFO] Target genome list was writen to GCF_008801495.1_ASM880149v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:43:00,421] [INFO] Task started: fastANI [2024-01-24 12:43:00,421] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a31d4f5-766a-4b42-a014-ab6d1254c1b4/GCF_008801495.1_ASM880149v1_genomic.fna.gz --refList GCF_008801495.1_ASM880149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008801495.1_ASM880149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:43:37,911] [INFO] Task succeeded: fastANI [2024-01-24 12:43:37,930] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:43:37,930] [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 99.9775 1986 2012 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 91.8144 1777 2012 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_013386585.1 s__Pseudomonas_E sp013386585 88.0948 1539 2012 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_000612585.1 s__Pseudomonas_E sp000612585 88.0288 1522 2012 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 88.0115 1534 2012 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_001647715.1 s__Pseudomonas_E antarctica_A 87.9873 1612 2012 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 87.9244 1604 2012 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_013385985.1 s__Pseudomonas_E sp013385985 87.887 1604 2012 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_001870465.1 s__Pseudomonas_E extremorientalis 87.7952 1593 2012 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_900215245.1 s__Pseudomonas_E fluorescens 87.6955 1626 2012 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 87.6677 1483 2012 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_002813445.1 s__Pseudomonas_E tolaasii 87.6282 1605 2012 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_002563895.1 s__Pseudomonas_E lurida 87.5645 1581 2012 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 87.5062 1491 2012 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 87.4913 1515 2012 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 87.3107 1396 2012 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_001902145.1 s__Pseudomonas_E fluorescens_BV 87.2223 1506 2012 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_904063055.1 s__Pseudomonas_E paracarnis 87.205 1518 2012 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 87.2005 1554 2012 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_002934065.1 s__Pseudomonas_E orientalis_A 87.0172 1505 2012 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.15 95.96 0.86 0.83 21 - GCF_001269885.1 s__Pseudomonas_E kilonensis 83.3782 1165 2012 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.12 95.91 0.90 0.87 15 - GCF_900581005.1 s__Pseudomonas_E sp900581005 83.1694 1183 2012 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_008801605.1 s__Pseudomonas_E brassicacearum 83.0748 1212 2012 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.43 96.48 0.95 0.86 21 - GCF_009601685.2 s__Pseudomonas_E kilonensis_B 82.9897 1202 2012 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.30 99.26 0.94 0.93 4 - GCF_018325905.1 s__Pseudomonas_E sp018325905 82.9856 1201 2012 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-24 12:43:37,932] [INFO] GTDB search result was written to GCF_008801495.1_ASM880149v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:43:37,933] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:43:37,938] [INFO] DFAST_QC result json was written to GCF_008801495.1_ASM880149v1_genomic.fna/dqc_result.json [2024-01-24 12:43:37,938] [INFO] DFAST_QC completed! [2024-01-24 12:43:37,938] [INFO] Total running time: 0h2m47s