[2024-01-24 13:57:43,000] [INFO] DFAST_QC pipeline started. [2024-01-24 13:57:43,001] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 13:57:43,001] [INFO] DQC Reference Directory: /var/lib/cwl/stg916e70df-b482-4acc-a555-2716a4f1b4cd/dqc_reference [2024-01-24 13:57:44,373] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 13:57:44,374] [INFO] Task started: Prodigal [2024-01-24 13:57:44,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg208aef77-db42-404e-a3ce-36fcab514054/GCF_003700725.1_ASM370072v1_genomic.fna.gz | prodigal -d GCF_003700725.1_ASM370072v1_genomic.fna/cds.fna -a GCF_003700725.1_ASM370072v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 13:58:06,778] [INFO] Task succeeded: Prodigal [2024-01-24 13:58:06,778] [INFO] Task started: HMMsearch [2024-01-24 13:58:06,778] [INFO] Running command: hmmsearch --tblout GCF_003700725.1_ASM370072v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg916e70df-b482-4acc-a555-2716a4f1b4cd/dqc_reference/reference_markers.hmm GCF_003700725.1_ASM370072v1_genomic.fna/protein.faa > /dev/null [2024-01-24 13:58:07,210] [INFO] Task succeeded: HMMsearch [2024-01-24 13:58:07,212] [INFO] Found 6/6 markers. [2024-01-24 13:58:07,280] [INFO] Query marker FASTA was written to GCF_003700725.1_ASM370072v1_genomic.fna/markers.fasta [2024-01-24 13:58:07,280] [INFO] Task started: Blastn [2024-01-24 13:58:07,280] [INFO] Running command: blastn -query GCF_003700725.1_ASM370072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916e70df-b482-4acc-a555-2716a4f1b4cd/dqc_reference/reference_markers.fasta -out GCF_003700725.1_ASM370072v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:58:08,243] [INFO] Task succeeded: Blastn [2024-01-24 13:58:08,250] [INFO] Selected 15 target genomes. [2024-01-24 13:58:08,250] [INFO] Target genome list was writen to GCF_003700725.1_ASM370072v1_genomic.fna/target_genomes.txt [2024-01-24 13:58:08,257] [INFO] Task started: fastANI [2024-01-24 13:58:08,257] [INFO] Running command: fastANI --query /var/lib/cwl/stg208aef77-db42-404e-a3ce-36fcab514054/GCF_003700725.1_ASM370072v1_genomic.fna.gz --refList GCF_003700725.1_ASM370072v1_genomic.fna/target_genomes.txt --output GCF_003700725.1_ASM370072v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 13:58:31,918] [INFO] Task succeeded: fastANI [2024-01-24 13:58:31,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg916e70df-b482-4acc-a555-2716a4f1b4cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 13:58:31,920] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg916e70df-b482-4acc-a555-2716a4f1b4cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 13:58:31,936] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold) [2024-01-24 13:58:31,936] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-24 13:58:31,937] [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 marginalis strain=ICMP 3553 GCA_003700725.1 298 298 suspected-type True 100.0 2031 2043 95 conclusive Pseudomonas marginalis strain=ICMP 3553 GCA_001645105.1 298 298 suspected-type True 99.9876 2034 2043 95 conclusive Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 91.29 1660 2043 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 91.0516 1642 2043 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 90.5536 1632 2043 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 90.5083 1663 2043 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 90.4795 1602 2043 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 90.4165 1612 2043 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 90.2837 1593 2043 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 90.256 1591 2043 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 89.4077 1641 2043 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 88.1404 1499 2043 95 below_threshold Pseudomonas salmasensis strain=SWRI126 GCA_014268375.2 2745514 2745514 type True 87.7848 1468 2043 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 86.1193 1386 2043 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.3019 1280 2043 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 13:58:31,938] [INFO] DFAST Taxonomy check result was written to GCF_003700725.1_ASM370072v1_genomic.fna/tc_result.tsv [2024-01-24 13:58:31,939] [INFO] ===== Taxonomy check completed ===== [2024-01-24 13:58:31,939] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 13:58:31,939] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg916e70df-b482-4acc-a555-2716a4f1b4cd/dqc_reference/checkm_data [2024-01-24 13:58:31,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 13:58:32,002] [INFO] Task started: CheckM [2024-01-24 13:58:32,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003700725.1_ASM370072v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003700725.1_ASM370072v1_genomic.fna/checkm_input GCF_003700725.1_ASM370072v1_genomic.fna/checkm_result [2024-01-24 13:59:36,001] [INFO] Task succeeded: CheckM [2024-01-24 13:59:36,002] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 13:59:36,022] [INFO] ===== Completeness check finished ===== [2024-01-24 13:59:36,022] [INFO] ===== Start GTDB Search ===== [2024-01-24 13:59:36,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003700725.1_ASM370072v1_genomic.fna/markers.fasta) [2024-01-24 13:59:36,023] [INFO] Task started: Blastn [2024-01-24 13:59:36,023] [INFO] Running command: blastn -query GCF_003700725.1_ASM370072v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg916e70df-b482-4acc-a555-2716a4f1b4cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003700725.1_ASM370072v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 13:59:37,622] [INFO] Task succeeded: Blastn [2024-01-24 13:59:37,626] [INFO] Selected 20 target genomes. [2024-01-24 13:59:37,626] [INFO] Target genome list was writen to GCF_003700725.1_ASM370072v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 13:59:37,649] [INFO] Task started: fastANI [2024-01-24 13:59:37,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg208aef77-db42-404e-a3ce-36fcab514054/GCF_003700725.1_ASM370072v1_genomic.fna.gz --refList GCF_003700725.1_ASM370072v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003700725.1_ASM370072v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 14:00:08,041] [INFO] Task succeeded: fastANI [2024-01-24 14:00:08,058] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 14:00:08,058] [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_001645105.1 s__Pseudomonas_E marginalis_B 99.9876 2034 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.28 0.91 0.87 10 conclusive GCF_000612585.1 s__Pseudomonas_E sp000612585 91.3964 1566 2043 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_002007785.1 s__Pseudomonas_E azotoformans_B 91.1567 1660 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.95 98.86 0.94 0.92 6 - GCF_002563895.1 s__Pseudomonas_E lurida 91.0314 1644 2043 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_900103345.1 s__Pseudomonas_E azotoformans 90.55 1656 2043 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 90.4266 1611 2043 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_001579805.1 s__Pseudomonas_E azotoformans_A 90.3358 1643 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.75 96.24 0.87 0.84 8 - GCF_900111895.1 s__Pseudomonas_E simiae 90.2937 1592 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.45 99.32 0.95 0.92 20 - GCF_001186335.1 s__Pseudomonas_E trivialis_B 90.2438 1659 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.34 95.31 0.86 0.86 8 - GCF_013385825.1 s__Pseudomonas_E reactans 90.2175 1580 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 96.45 96.30 0.89 0.87 7 - GCF_003097075.1 s__Pseudomonas_E sp003097075 89.5392 1594 2043 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_014207255.1 s__Pseudomonas_E sp014207255 89.4765 1631 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.31 98.90 0.95 0.91 5 - GCF_012844475.1 s__Pseudomonas_E sp012844475 89.2762 1456 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 2 - GCA_016937595.1 s__Pseudomonas_E fulgida 89.0544 1058 2043 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_001050345.1 s__Pseudomonas_E fildesensis 88.8836 1584 2043 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_009834565.1 s__Pseudomonas_E sp009834565 88.7513 1554 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.71 97.35 0.93 0.93 3 - GCF_013386585.1 s__Pseudomonas_E sp013386585 88.7181 1531 2043 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_001439695.1 s__Pseudomonas_E veronii 88.4666 1488 2043 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_900583165.1 s__Pseudomonas_E sp900583165 88.1416 1484 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.99 99.99 1.00 0.99 4 - GCF_001902145.1 s__Pseudomonas_E fluorescens_BV 87.6533 1441 2043 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.76 95.23 0.87 0.84 22 - -------------------------------------------------------------------------------- [2024-01-24 14:00:08,060] [INFO] GTDB search result was written to GCF_003700725.1_ASM370072v1_genomic.fna/result_gtdb.tsv [2024-01-24 14:00:08,061] [INFO] ===== GTDB Search completed ===== [2024-01-24 14:00:08,065] [INFO] DFAST_QC result json was written to GCF_003700725.1_ASM370072v1_genomic.fna/dqc_result.json [2024-01-24 14:00:08,065] [INFO] DFAST_QC completed! [2024-01-24 14:00:08,065] [INFO] Total running time: 0h2m25s