[2024-01-24 12:13:28,958] [INFO] DFAST_QC pipeline started. [2024-01-24 12:13:28,960] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:13:28,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg74101738-3d7b-4317-b5d2-0415397b110d/dqc_reference [2024-01-24 12:13:30,348] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:13:30,349] [INFO] Task started: Prodigal [2024-01-24 12:13:30,349] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0ca0d8c-947a-4a2f-8f30-6a71c6e46c40/GCF_001702265.1_ASM170226v1_genomic.fna.gz | prodigal -d GCF_001702265.1_ASM170226v1_genomic.fna/cds.fna -a GCF_001702265.1_ASM170226v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:13:55,807] [INFO] Task succeeded: Prodigal [2024-01-24 12:13:55,808] [INFO] Task started: HMMsearch [2024-01-24 12:13:55,808] [INFO] Running command: hmmsearch --tblout GCF_001702265.1_ASM170226v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74101738-3d7b-4317-b5d2-0415397b110d/dqc_reference/reference_markers.hmm GCF_001702265.1_ASM170226v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:13:56,221] [INFO] Task succeeded: HMMsearch [2024-01-24 12:13:56,222] [INFO] Found 6/6 markers. [2024-01-24 12:13:56,306] [INFO] Query marker FASTA was written to GCF_001702265.1_ASM170226v1_genomic.fna/markers.fasta [2024-01-24 12:13:56,307] [INFO] Task started: Blastn [2024-01-24 12:13:56,307] [INFO] Running command: blastn -query GCF_001702265.1_ASM170226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74101738-3d7b-4317-b5d2-0415397b110d/dqc_reference/reference_markers.fasta -out GCF_001702265.1_ASM170226v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:13:57,391] [INFO] Task succeeded: Blastn [2024-01-24 12:13:57,396] [INFO] Selected 23 target genomes. [2024-01-24 12:13:57,396] [INFO] Target genome list was writen to GCF_001702265.1_ASM170226v1_genomic.fna/target_genomes.txt [2024-01-24 12:13:57,419] [INFO] Task started: fastANI [2024-01-24 12:13:57,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ca0d8c-947a-4a2f-8f30-6a71c6e46c40/GCF_001702265.1_ASM170226v1_genomic.fna.gz --refList GCF_001702265.1_ASM170226v1_genomic.fna/target_genomes.txt --output GCF_001702265.1_ASM170226v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:14:32,744] [INFO] Task succeeded: fastANI [2024-01-24 12:14:32,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74101738-3d7b-4317-b5d2-0415397b110d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:14:32,745] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74101738-3d7b-4317-b5d2-0415397b110d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:14:32,762] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold) [2024-01-24 12:14:32,762] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 12:14:32,762] [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=DSM 13124 GCA_007858155.1 298 298 suspected-type True 89.5425 1736 2306 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 89.4492 1808 2306 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_900103345.1 47878 47878 suspected-type True 89.2178 1790 2306 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_001870415.1 47878 47878 suspected-type True 89.2124 1789 2306 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 89.162 1770 2306 95 below_threshold Pseudomonas azotoformans strain=DSM 18862 GCA_001983205.1 47878 47878 suspected-type True 89.156 1807 2306 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 89.1466 1791 2306 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 89.127 1762 2306 95 below_threshold Pseudomonas cremoris strain=WS 5106 GCA_014230465.1 2724178 2724178 type True 88.5235 1764 2306 95 below_threshold Pseudomonas nabeulensis strain=E10B GCA_004682045.1 2293833 2293833 type True 88.3362 1657 2306 95 below_threshold Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 88.2234 1537 2306 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 88.1735 1686 2306 95 below_threshold Pseudomonas fluorescens strain=ATCC 13525 GCA_900215245.1 294 294 suspected-type True 88.1624 1685 2306 95 below_threshold Pseudomonas fluorescens strain=ATCC 13525 GCA_002943685.1 294 294 suspected-type True 88.1478 1641 2306 95 below_threshold Pseudomonas fluorescens strain=NBRC 14160 GCA_002091595.1 294 294 suspected-type True 88.1392 1663 2306 95 below_threshold Pseudomonas fluorescens strain=NCTC10038 GCA_900475215.1 294 294 suspected-type True 88.1314 1689 2306 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_001269845.1 294 294 suspected-type True 88.1174 1684 2306 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 88.1159 1634 2306 95 below_threshold Pseudomonas gessardii GCA_900625085.1 78544 78544 type True 86.594 1404 2306 95 below_threshold Pseudomonas gessardii strain=DSM 17152 GCA_009671285.1 78544 78544 type True 86.5509 1412 2306 95 below_threshold Pseudomonas gessardii strain=DSM 17152 GCA_001983165.1 78544 78544 type True 86.5411 1412 2306 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 86.2178 1512 2306 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.3539 1365 2306 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:14:32,764] [INFO] DFAST Taxonomy check result was written to GCF_001702265.1_ASM170226v1_genomic.fna/tc_result.tsv [2024-01-24 12:14:32,764] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:14:32,765] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:14:32,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74101738-3d7b-4317-b5d2-0415397b110d/dqc_reference/checkm_data [2024-01-24 12:14:32,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:14:32,833] [INFO] Task started: CheckM [2024-01-24 12:14:32,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001702265.1_ASM170226v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001702265.1_ASM170226v1_genomic.fna/checkm_input GCF_001702265.1_ASM170226v1_genomic.fna/checkm_result [2024-01-24 12:15:41,724] [INFO] Task succeeded: CheckM [2024-01-24 12:15:41,725] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:15:41,749] [INFO] ===== Completeness check finished ===== [2024-01-24 12:15:41,750] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:15:41,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001702265.1_ASM170226v1_genomic.fna/markers.fasta) [2024-01-24 12:15:41,751] [INFO] Task started: Blastn [2024-01-24 12:15:41,751] [INFO] Running command: blastn -query GCF_001702265.1_ASM170226v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74101738-3d7b-4317-b5d2-0415397b110d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001702265.1_ASM170226v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:15:43,411] [INFO] Task succeeded: Blastn [2024-01-24 12:15:43,415] [INFO] Selected 22 target genomes. [2024-01-24 12:15:43,416] [INFO] Target genome list was writen to GCF_001702265.1_ASM170226v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:15:43,440] [INFO] Task started: fastANI [2024-01-24 12:15:43,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0ca0d8c-947a-4a2f-8f30-6a71c6e46c40/GCF_001702265.1_ASM170226v1_genomic.fna.gz --refList GCF_001702265.1_ASM170226v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001702265.1_ASM170226v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:16:19,190] [INFO] Task succeeded: fastANI [2024-01-24 12:16:19,213] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:16:19,213] [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_003612935.1 s__Pseudomonas_E sp003013355 98.5589 2127 2306 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.87 98.56 0.95 0.92 7 conclusive GCF_003097075.1 s__Pseudomonas_E sp003097075 89.863 1745 2306 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_900580675.1 s__Pseudomonas_E sp900580675 89.8038 1625 2306 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_002843605.1 s__Pseudomonas_E sp002843605 89.7662 1789 2306 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_001269925.1 s__Pseudomonas_E sp001269925 89.6652 1706 2306 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_900591205.1 s__Pseudomonas_E sp900591205 89.6459 1761 2306 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_900105325.1 s__Pseudomonas_E marginalis 89.5443 1757 2306 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.53 96.47 0.90 0.85 19 - GCF_007858185.1 s__Pseudomonas_E grimontii 89.4315 1700 2306 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 2 - GCF_002007785.1 s__Pseudomonas_E azotoformans_B 89.4269 1814 2306 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 89.2166 1790 2306 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_002563895.1 s__Pseudomonas_E lurida 89.1368 1760 2306 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_001870465.1 s__Pseudomonas_E extremorientalis 89.0312 1735 2306 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_900102035.1 s__Pseudomonas_E extremaustralis 88.9786 1564 2306 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.74 98.99 0.98 0.92 5 - GCF_001050345.1 s__Pseudomonas_E fildesensis 88.9687 1624 2306 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_014851685.1 s__Pseudomonas_E sp014851685 88.6421 1616 2306 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_003852315.1 s__Pseudomonas_E sp003014915 88.5205 1743 2306 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_001647715.1 s__Pseudomonas_E antarctica_A 88.3056 1704 2306 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_900624995.1 s__Pseudomonas_E antarctica 88.2313 1536 2306 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 88.1558 1559 2306 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_900215245.1 s__Pseudomonas_E fluorescens 88.1474 1687 2306 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_001439815.1 s__Pseudomonas_E orientalis 87.7133 1543 2306 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 97.01 96.05 0.91 0.89 6 - GCF_001983165.1 s__Pseudomonas_E gessardii 86.5324 1413 2306 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.96 98.08 0.94 0.88 9 - -------------------------------------------------------------------------------- [2024-01-24 12:16:19,215] [INFO] GTDB search result was written to GCF_001702265.1_ASM170226v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:16:19,215] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:16:19,222] [INFO] DFAST_QC result json was written to GCF_001702265.1_ASM170226v1_genomic.fna/dqc_result.json [2024-01-24 12:16:19,222] [INFO] DFAST_QC completed! [2024-01-24 12:16:19,222] [INFO] Total running time: 0h2m50s