[2024-01-25 20:07:20,447] [INFO] DFAST_QC pipeline started. [2024-01-25 20:07:20,454] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 20:07:20,454] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e633255-3caa-4194-a5ce-5dbedf355f05/dqc_reference [2024-01-25 20:07:21,591] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 20:07:21,592] [INFO] Task started: Prodigal [2024-01-25 20:07:21,592] [INFO] Running command: gunzip -c /var/lib/cwl/stg4efb01b0-3725-436e-ad9c-8c01d62cf858/GCF_002813445.1_ASM281344v1_genomic.fna.gz | prodigal -d GCF_002813445.1_ASM281344v1_genomic.fna/cds.fna -a GCF_002813445.1_ASM281344v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 20:07:51,402] [INFO] Task succeeded: Prodigal [2024-01-25 20:07:51,403] [INFO] Task started: HMMsearch [2024-01-25 20:07:51,403] [INFO] Running command: hmmsearch --tblout GCF_002813445.1_ASM281344v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e633255-3caa-4194-a5ce-5dbedf355f05/dqc_reference/reference_markers.hmm GCF_002813445.1_ASM281344v1_genomic.fna/protein.faa > /dev/null [2024-01-25 20:07:51,707] [INFO] Task succeeded: HMMsearch [2024-01-25 20:07:51,708] [INFO] Found 6/6 markers. [2024-01-25 20:07:51,758] [INFO] Query marker FASTA was written to GCF_002813445.1_ASM281344v1_genomic.fna/markers.fasta [2024-01-25 20:07:51,758] [INFO] Task started: Blastn [2024-01-25 20:07:51,759] [INFO] Running command: blastn -query GCF_002813445.1_ASM281344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e633255-3caa-4194-a5ce-5dbedf355f05/dqc_reference/reference_markers.fasta -out GCF_002813445.1_ASM281344v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 20:07:52,604] [INFO] Task succeeded: Blastn [2024-01-25 20:07:52,607] [INFO] Selected 19 target genomes. [2024-01-25 20:07:52,608] [INFO] Target genome list was writen to GCF_002813445.1_ASM281344v1_genomic.fna/target_genomes.txt [2024-01-25 20:07:52,621] [INFO] Task started: fastANI [2024-01-25 20:07:52,622] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efb01b0-3725-436e-ad9c-8c01d62cf858/GCF_002813445.1_ASM281344v1_genomic.fna.gz --refList GCF_002813445.1_ASM281344v1_genomic.fna/target_genomes.txt --output GCF_002813445.1_ASM281344v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 20:08:23,833] [INFO] Task succeeded: fastANI [2024-01-25 20:08:23,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e633255-3caa-4194-a5ce-5dbedf355f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 20:08:23,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e633255-3caa-4194-a5ce-5dbedf355f05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 20:08:23,846] [INFO] Found 19 fastANI hits (3 hits with ANI > threshold) [2024-01-25 20:08:23,846] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 20:08:23,847] [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 tolaasii strain=NCPPB 2192 GCA_002813445.1 29442 29442 type True 100.0 2261 2264 95 conclusive Pseudomonas tolaasii strain=CCUG 23369 GCA_008801395.1 29442 29442 type True 99.9913 2218 2264 95 conclusive Pseudomonas tolaasii GCA_900625075.1 29442 29442 type True 99.9855 2229 2264 95 conclusive Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 88.3167 1630 2264 95 below_threshold Pseudomonas fluorescens strain=NBRC 14160 GCA_002091595.1 294 294 suspected-type True 88.2619 1621 2264 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 88.2599 1670 2264 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 88.2385 1671 2264 95 below_threshold Pseudomonas canadensis strain=2-92 GCA_000503215.1 915099 915099 type True 88.1781 1616 2264 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 88.1708 1631 2264 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 88.1315 1663 2264 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 88.1046 1548 2264 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 88.0739 1564 2264 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 88.0269 1583 2264 95 below_threshold Pseudomonas nabeulensis strain=E10B GCA_004682045.1 2293833 2293833 type True 87.9469 1537 2264 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 87.9014 1639 2264 95 below_threshold Pseudomonas kairouanensis strain=KC12 GCA_004682055.1 2293832 2293832 type True 87.7496 1520 2264 95 below_threshold Pseudomonas asgharzadehiana strain=SWRI132 GCA_019139815.1 2842349 2842349 type True 87.5792 1506 2264 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.8831 1513 2264 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.9673 1342 2264 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 20:08:23,848] [INFO] DFAST Taxonomy check result was written to GCF_002813445.1_ASM281344v1_genomic.fna/tc_result.tsv [2024-01-25 20:08:23,848] [INFO] ===== Taxonomy check completed ===== [2024-01-25 20:08:23,849] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 20:08:23,849] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e633255-3caa-4194-a5ce-5dbedf355f05/dqc_reference/checkm_data [2024-01-25 20:08:23,850] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 20:08:23,912] [INFO] Task started: CheckM [2024-01-25 20:08:23,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002813445.1_ASM281344v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002813445.1_ASM281344v1_genomic.fna/checkm_input GCF_002813445.1_ASM281344v1_genomic.fna/checkm_result [2024-01-25 20:09:53,690] [INFO] Task succeeded: CheckM [2024-01-25 20:09:53,691] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 20:09:53,708] [INFO] ===== Completeness check finished ===== [2024-01-25 20:09:53,708] [INFO] ===== Start GTDB Search ===== [2024-01-25 20:09:53,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002813445.1_ASM281344v1_genomic.fna/markers.fasta) [2024-01-25 20:09:53,709] [INFO] Task started: Blastn [2024-01-25 20:09:53,709] [INFO] Running command: blastn -query GCF_002813445.1_ASM281344v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e633255-3caa-4194-a5ce-5dbedf355f05/dqc_reference/reference_markers_gtdb.fasta -out GCF_002813445.1_ASM281344v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 20:09:55,097] [INFO] Task succeeded: Blastn [2024-01-25 20:09:55,100] [INFO] Selected 25 target genomes. [2024-01-25 20:09:55,100] [INFO] Target genome list was writen to GCF_002813445.1_ASM281344v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 20:09:55,142] [INFO] Task started: fastANI [2024-01-25 20:09:55,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg4efb01b0-3725-436e-ad9c-8c01d62cf858/GCF_002813445.1_ASM281344v1_genomic.fna.gz --refList GCF_002813445.1_ASM281344v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002813445.1_ASM281344v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 20:10:34,644] [INFO] Task succeeded: fastANI [2024-01-25 20:10:34,659] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 20:10:34,659] [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_002813445.1 s__Pseudomonas_E tolaasii 100.0 2262 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.61 99.17 0.97 0.93 14 conclusive GCF_002022275.1 s__Pseudomonas_E fluorescens_AJ 90.1306 1812 2264 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 89.128 1754 2264 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 88.9949 1745 2264 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 88.6201 1586 2264 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_005938045.2 s__Pseudomonas_E sp005938045 88.6191 1725 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.18 95.16 0.86 0.86 3 - GCF_003852315.1 s__Pseudomonas_E sp003014915 88.524 1739 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.48 96.20 0.95 0.91 10 - GCF_013385965.1 s__Pseudomonas_E edaphica 88.4776 1670 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.04 98.93 0.94 0.92 9 - GCF_000612585.1 s__Pseudomonas_E sp000612585 88.4309 1634 2264 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_900103345.1 s__Pseudomonas_E azotoformans 88.3269 1653 2264 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_013385825.1 s__Pseudomonas_E reactans 88.3228 1668 2264 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_001647715.1 s__Pseudomonas_E antarctica_A 88.2677 1706 2264 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_900215245.1 s__Pseudomonas_E fluorescens 88.1746 1652 2264 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_000503215.1 s__Pseudomonas_E canadensis 88.1745 1617 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.83 97.74 0.94 0.91 12 - GCF_001870465.1 s__Pseudomonas_E extremorientalis 88.1519 1618 2264 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_900111895.1 s__Pseudomonas_E simiae 88.0314 1583 2264 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_004682045.1 s__Pseudomonas_E nabeulensis 87.9808 1533 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 95.61 95.59 0.85 0.85 3 - GCF_002563895.1 s__Pseudomonas_E lurida 87.9256 1636 2264 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_009866765.1 s__Pseudomonas_E sp009866765 87.8086 1527 2264 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_004682055.1 s__Pseudomonas_E kairouanensis 87.7469 1520 2264 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_019139815.1 s__Pseudomonas_E sp900005815 87.5846 1501 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.55 99.31 0.95 0.92 7 - GCF_001983175.1 s__Pseudomonas_E cedrina 87.5439 1503 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.10 97.30 0.97 0.92 4 - GCF_004519405.1 s__Pseudomonas_E sp004519405 87.4688 1562 2264 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_000263715.2 s__Pseudomonas_E synxantha_A 87.3467 1558 2264 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.66 97.33 0.90 0.88 8 - GCF_002934065.1 s__Pseudomonas_E orientalis_A 87.3406 1500 2264 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 20:10:34,661] [INFO] GTDB search result was written to GCF_002813445.1_ASM281344v1_genomic.fna/result_gtdb.tsv [2024-01-25 20:10:34,661] [INFO] ===== GTDB Search completed ===== [2024-01-25 20:10:34,665] [INFO] DFAST_QC result json was written to GCF_002813445.1_ASM281344v1_genomic.fna/dqc_result.json [2024-01-25 20:10:34,665] [INFO] DFAST_QC completed! [2024-01-25 20:10:34,665] [INFO] Total running time: 0h3m14s