[2024-01-25 19:40:50,692] [INFO] DFAST_QC pipeline started. [2024-01-25 19:40:50,693] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:40:50,693] [INFO] DQC Reference Directory: /var/lib/cwl/stgd4c78bf8-20ba-45b2-99e2-1c8db856436c/dqc_reference [2024-01-25 19:40:51,853] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:40:51,853] [INFO] Task started: Prodigal [2024-01-25 19:40:51,853] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbae0f45-0776-40d2-8c45-80bd3326a9c2/GCF_002563895.1_ASM256389v1_genomic.fna.gz | prodigal -d GCF_002563895.1_ASM256389v1_genomic.fna/cds.fna -a GCF_002563895.1_ASM256389v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:41:12,975] [INFO] Task succeeded: Prodigal [2024-01-25 19:41:12,975] [INFO] Task started: HMMsearch [2024-01-25 19:41:12,975] [INFO] Running command: hmmsearch --tblout GCF_002563895.1_ASM256389v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd4c78bf8-20ba-45b2-99e2-1c8db856436c/dqc_reference/reference_markers.hmm GCF_002563895.1_ASM256389v1_genomic.fna/protein.faa > /dev/null [2024-01-25 19:41:13,257] [INFO] Task succeeded: HMMsearch [2024-01-25 19:41:13,258] [INFO] Found 6/6 markers. [2024-01-25 19:41:13,308] [INFO] Query marker FASTA was written to GCF_002563895.1_ASM256389v1_genomic.fna/markers.fasta [2024-01-25 19:41:13,309] [INFO] Task started: Blastn [2024-01-25 19:41:13,309] [INFO] Running command: blastn -query GCF_002563895.1_ASM256389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c78bf8-20ba-45b2-99e2-1c8db856436c/dqc_reference/reference_markers.fasta -out GCF_002563895.1_ASM256389v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:41:14,134] [INFO] Task succeeded: Blastn [2024-01-25 19:41:14,137] [INFO] Selected 20 target genomes. [2024-01-25 19:41:14,137] [INFO] Target genome list was writen to GCF_002563895.1_ASM256389v1_genomic.fna/target_genomes.txt [2024-01-25 19:41:14,144] [INFO] Task started: fastANI [2024-01-25 19:41:14,145] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbae0f45-0776-40d2-8c45-80bd3326a9c2/GCF_002563895.1_ASM256389v1_genomic.fna.gz --refList GCF_002563895.1_ASM256389v1_genomic.fna/target_genomes.txt --output GCF_002563895.1_ASM256389v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:41:42,684] [INFO] Task succeeded: fastANI [2024-01-25 19:41:42,684] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd4c78bf8-20ba-45b2-99e2-1c8db856436c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:41:42,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd4c78bf8-20ba-45b2-99e2-1c8db856436c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:41:42,696] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold) [2024-01-25 19:41:42,696] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:41:42,696] [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 lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 100.0 2102 2103 95 conclusive Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 91.6447 1793 2103 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 90.543 1754 2103 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_001870415.1 47878 47878 suspected-type True 90.5363 1736 2103 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_900103345.1 47878 47878 suspected-type True 90.5277 1764 2103 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 90.5084 1728 2103 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 90.4612 1696 2103 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 90.3652 1717 2103 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 88.8742 1644 2103 95 below_threshold Pseudomonas cremoris strain=WS 5106 GCA_014230465.1 2724178 2724178 type True 88.4784 1612 2103 95 below_threshold Pseudomonas extremaustralis strain=DSM 17835 GCA_900102035.1 359110 359110 type True 88.2491 1506 2103 95 below_threshold Pseudomonas extremaustralis GCA_900625045.1 359110 359110 type True 88.2427 1476 2103 95 below_threshold Pseudomonas extremaustralis strain=DSM 17835 GCA_007858235.1 359110 359110 type True 88.2236 1480 2103 95 below_threshold Pseudomonas edaphica strain=RD25 GCA_005863185.1 2006980 2006980 type True 87.7322 1226 2103 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.8741 1463 2103 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.2509 1321 2103 95 below_threshold Aeromonas rivuli strain=DSM 22539 GCA_000820045.1 648794 648794 type True 76.0386 88 2103 95 below_threshold Ideonella paludis strain=KCTC 32238 GCA_018069865.1 1233411 1233411 type True 75.8924 70 2103 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:41:42,697] [INFO] DFAST Taxonomy check result was written to GCF_002563895.1_ASM256389v1_genomic.fna/tc_result.tsv [2024-01-25 19:41:42,698] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:41:42,698] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:41:42,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd4c78bf8-20ba-45b2-99e2-1c8db856436c/dqc_reference/checkm_data [2024-01-25 19:41:42,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:41:42,755] [INFO] Task started: CheckM [2024-01-25 19:41:42,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002563895.1_ASM256389v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002563895.1_ASM256389v1_genomic.fna/checkm_input GCF_002563895.1_ASM256389v1_genomic.fna/checkm_result [2024-01-25 19:42:44,730] [INFO] Task succeeded: CheckM [2024-01-25 19:42:44,731] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:42:44,749] [INFO] ===== Completeness check finished ===== [2024-01-25 19:42:44,749] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:42:44,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002563895.1_ASM256389v1_genomic.fna/markers.fasta) [2024-01-25 19:42:44,751] [INFO] Task started: Blastn [2024-01-25 19:42:44,751] [INFO] Running command: blastn -query GCF_002563895.1_ASM256389v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd4c78bf8-20ba-45b2-99e2-1c8db856436c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002563895.1_ASM256389v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:42:46,182] [INFO] Task succeeded: Blastn [2024-01-25 19:42:46,185] [INFO] Selected 19 target genomes. [2024-01-25 19:42:46,185] [INFO] Target genome list was writen to GCF_002563895.1_ASM256389v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:42:46,200] [INFO] Task started: fastANI [2024-01-25 19:42:46,200] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbae0f45-0776-40d2-8c45-80bd3326a9c2/GCF_002563895.1_ASM256389v1_genomic.fna.gz --refList GCF_002563895.1_ASM256389v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002563895.1_ASM256389v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:43:15,927] [INFO] Task succeeded: fastANI [2024-01-25 19:43:15,939] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:43:15,940] [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_002563895.1 s__Pseudomonas_E lurida 100.0 2101 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.19 99.03 0.94 0.91 25 conclusive GCF_000612585.1 s__Pseudomonas_E sp000612585 92.3684 1716 2103 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 91.6472 1795 2103 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_900103345.1 s__Pseudomonas_E azotoformans 90.5293 1765 2103 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_900111895.1 s__Pseudomonas_E simiae 90.3612 1718 2103 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 89.9328 1712 2103 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_003097075.1 s__Pseudomonas_E sp003097075 89.1445 1652 2103 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_002843605.1 s__Pseudomonas_E sp002843605 89.109 1695 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.70 97.45 0.92 0.91 7 - GCF_013386585.1 s__Pseudomonas_E sp013386585 88.8022 1638 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 - GCA_016937595.1 s__Pseudomonas_E fulgida 88.7715 1095 2103 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_013385985.1 s__Pseudomonas_E sp013385985 88.7172 1685 2103 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 88.5928 1618 2103 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_014230465.1 s__Pseudomonas_E cremoris 88.4757 1614 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.87 96.78 0.87 0.83 4 - GCF_009834565.1 s__Pseudomonas_E sp009834565 88.4305 1701 2103 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_002979555.1 s__Pseudomonas_E sp002979555 88.3704 1475 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.44 99.31 0.96 0.95 11 - GCF_002837185.1 s__Pseudomonas_E fluorescens_AM 87.5167 1487 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.23 99.16 0.96 0.94 7 - GCF_001952855.1 s__Pseudomonas_E sp001952855 86.7724 1616 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.78 98.78 0.94 0.94 2 - GCA_016182845.1 s__JACPFT01 sp016182845 75.9851 111 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__DSM-103792;g__JACPFT01 95.0 N/A N/A N/A N/A 1 - GCF_004362855.1 s__Aquabacterium commune 75.8883 119 2103 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium 95.0 95.44 95.44 0.90 0.90 2 - -------------------------------------------------------------------------------- [2024-01-25 19:43:15,941] [INFO] GTDB search result was written to GCF_002563895.1_ASM256389v1_genomic.fna/result_gtdb.tsv [2024-01-25 19:43:15,942] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:43:15,945] [INFO] DFAST_QC result json was written to GCF_002563895.1_ASM256389v1_genomic.fna/dqc_result.json [2024-01-25 19:43:15,945] [INFO] DFAST_QC completed! [2024-01-25 19:43:15,945] [INFO] Total running time: 0h2m25s