[2024-01-24 11:34:55,003] [INFO] DFAST_QC pipeline started. [2024-01-24 11:34:55,006] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:34:55,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg74e75db5-7245-476d-ae4b-192b733da0b3/dqc_reference [2024-01-24 11:34:56,508] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:34:56,509] [INFO] Task started: Prodigal [2024-01-24 11:34:56,509] [INFO] Running command: gunzip -c /var/lib/cwl/stg3039bc0d-33b9-4f00-bbf8-05e8188da1e2/GCF_019145355.1_ASM1914535v1_genomic.fna.gz | prodigal -d GCF_019145355.1_ASM1914535v1_genomic.fna/cds.fna -a GCF_019145355.1_ASM1914535v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:35:22,412] [INFO] Task succeeded: Prodigal [2024-01-24 11:35:22,413] [INFO] Task started: HMMsearch [2024-01-24 11:35:22,413] [INFO] Running command: hmmsearch --tblout GCF_019145355.1_ASM1914535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74e75db5-7245-476d-ae4b-192b733da0b3/dqc_reference/reference_markers.hmm GCF_019145355.1_ASM1914535v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:35:22,759] [INFO] Task succeeded: HMMsearch [2024-01-24 11:35:22,761] [INFO] Found 6/6 markers. [2024-01-24 11:35:22,816] [INFO] Query marker FASTA was written to GCF_019145355.1_ASM1914535v1_genomic.fna/markers.fasta [2024-01-24 11:35:22,816] [INFO] Task started: Blastn [2024-01-24 11:35:22,816] [INFO] Running command: blastn -query GCF_019145355.1_ASM1914535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e75db5-7245-476d-ae4b-192b733da0b3/dqc_reference/reference_markers.fasta -out GCF_019145355.1_ASM1914535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:35:23,806] [INFO] Task succeeded: Blastn [2024-01-24 11:35:23,810] [INFO] Selected 20 target genomes. [2024-01-24 11:35:23,811] [INFO] Target genome list was writen to GCF_019145355.1_ASM1914535v1_genomic.fna/target_genomes.txt [2024-01-24 11:35:23,818] [INFO] Task started: fastANI [2024-01-24 11:35:23,818] [INFO] Running command: fastANI --query /var/lib/cwl/stg3039bc0d-33b9-4f00-bbf8-05e8188da1e2/GCF_019145355.1_ASM1914535v1_genomic.fna.gz --refList GCF_019145355.1_ASM1914535v1_genomic.fna/target_genomes.txt --output GCF_019145355.1_ASM1914535v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:35:56,309] [INFO] Task succeeded: fastANI [2024-01-24 11:35:56,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74e75db5-7245-476d-ae4b-192b733da0b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:35:56,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74e75db5-7245-476d-ae4b-192b733da0b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:35:56,329] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold) [2024-01-24 11:35:56,329] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 11:35:56,329] [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 cedrina subsp. cedrina GCA_900625035.1 76762 651740 type True 94.3937 1727 2034 95 below_threshold Pseudomonas cedrina subsp. cedrina strain=DSM 17516 GCA_001983175.1 76762 651740 type True 94.3885 1736 2034 95 below_threshold Pseudomonas marginalis strain=ICMP 3553 GCA_003700725.1 298 298 suspected-type True 89.3383 1542 2034 95 below_threshold Pseudomonas marginalis strain=ICMP 3553 GCA_001645105.1 298 298 suspected-type True 89.3073 1617 2034 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 89.2872 1640 2034 95 below_threshold Pseudomonas azotoformans strain=NBRC 12693 GCA_002091515.1 47878 47878 suspected-type True 89.2203 1612 2034 95 below_threshold Pseudomonas azotoformans strain=LMG 21611 GCA_900103345.1 47878 47878 suspected-type True 89.2169 1655 2034 95 below_threshold Pseudomonas azotoformans GCA_900624915.1 47878 47878 suspected-type True 89.2107 1622 2034 95 below_threshold Pseudomonas extremorientalis strain=LMG 19695 GCA_001870465.1 169669 169669 type True 89.1464 1617 2034 95 below_threshold Pseudomonas extremorientalis GCA_900625005.1 169669 169669 type True 89.1362 1627 2034 95 below_threshold Pseudomonas extremorientalis strain=CCUG 51517 GCA_008801565.1 169669 169669 type True 89.1222 1618 2034 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_001730615.1 321846 321846 type True 89.0811 1575 2034 95 below_threshold Pseudomonas canadensis strain=2-92 GCA_000503215.1 915099 915099 type True 89.0809 1608 2034 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 89.0591 1597 2034 95 below_threshold Pseudomonas simiae strain=CCUG 50988 GCA_900111895.1 321846 321846 type True 89.0029 1593 2034 95 below_threshold Pseudomonas marginalis strain=DSM 13124 GCA_007858155.1 298 298 suspected-type True 88.5737 1597 2034 95 below_threshold Pseudomonas extremaustralis strain=DSM 17835 GCA_007858235.1 359110 359110 type True 88.0458 1403 2034 95 below_threshold Pseudomonas synxantha strain=LMG 2190 GCA_900105675.1 47883 47883 type True 87.3982 1500 2034 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 85.6707 1399 2034 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 84.9214 1306 2034 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:35:56,331] [INFO] DFAST Taxonomy check result was written to GCF_019145355.1_ASM1914535v1_genomic.fna/tc_result.tsv [2024-01-24 11:35:56,332] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:35:56,332] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:35:56,332] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74e75db5-7245-476d-ae4b-192b733da0b3/dqc_reference/checkm_data [2024-01-24 11:35:56,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:35:56,389] [INFO] Task started: CheckM [2024-01-24 11:35:56,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019145355.1_ASM1914535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019145355.1_ASM1914535v1_genomic.fna/checkm_input GCF_019145355.1_ASM1914535v1_genomic.fna/checkm_result [2024-01-24 11:37:10,307] [INFO] Task succeeded: CheckM [2024-01-24 11:37:10,309] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 11:37:10,331] [INFO] ===== Completeness check finished ===== [2024-01-24 11:37:10,331] [INFO] ===== Start GTDB Search ===== [2024-01-24 11:37:10,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019145355.1_ASM1914535v1_genomic.fna/markers.fasta) [2024-01-24 11:37:10,332] [INFO] Task started: Blastn [2024-01-24 11:37:10,332] [INFO] Running command: blastn -query GCF_019145355.1_ASM1914535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74e75db5-7245-476d-ae4b-192b733da0b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_019145355.1_ASM1914535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:37:11,987] [INFO] Task succeeded: Blastn [2024-01-24 11:37:11,993] [INFO] Selected 17 target genomes. [2024-01-24 11:37:11,993] [INFO] Target genome list was writen to GCF_019145355.1_ASM1914535v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 11:37:12,088] [INFO] Task started: fastANI [2024-01-24 11:37:12,088] [INFO] Running command: fastANI --query /var/lib/cwl/stg3039bc0d-33b9-4f00-bbf8-05e8188da1e2/GCF_019145355.1_ASM1914535v1_genomic.fna.gz --refList GCF_019145355.1_ASM1914535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019145355.1_ASM1914535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 11:37:40,472] [INFO] Task succeeded: fastANI [2024-01-24 11:37:40,494] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 11:37:40,494] [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_012844475.1 s__Pseudomonas_E sp012844475 99.911 1871 2034 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 100.00 100.00 1.00 1.00 2 conclusive GCF_001983175.1 s__Pseudomonas_E cedrina 94.3961 1735 2034 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.10 97.30 0.97 0.92 4 - GCA_016937595.1 s__Pseudomonas_E fulgida 92.1799 1143 2034 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_001186335.1 s__Pseudomonas_E trivialis_B 89.7391 1671 2034 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_001645105.1 s__Pseudomonas_E marginalis_B 89.3149 1617 2034 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.28 0.91 0.87 10 - GCF_001579805.1 s__Pseudomonas_E azotoformans_A 89.2262 1627 2034 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_900103345.1 s__Pseudomonas_E azotoformans 89.2255 1655 2034 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 89.1507 1616 2034 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_002563895.1 s__Pseudomonas_E lurida 89.0485 1598 2034 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_900111895.1 s__Pseudomonas_E simiae 89.0096 1591 2034 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_003097075.1 s__Pseudomonas_E sp003097075 88.7565 1576 2034 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_900105325.1 s__Pseudomonas_E marginalis 88.6183 1639 2034 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_002843605.1 s__Pseudomonas_E sp002843605 88.5457 1587 2034 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_900580675.1 s__Pseudomonas_E sp900580675 88.4327 1489 2034 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_001439815.1 s__Pseudomonas_E orientalis 87.8458 1544 2034 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_002934065.1 s__Pseudomonas_E orientalis_A 87.6709 1528 2034 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_002837185.1 s__Pseudomonas_E fluorescens_AM 87.648 1501 2034 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.23 99.16 0.96 0.94 7 - -------------------------------------------------------------------------------- [2024-01-24 11:37:40,495] [INFO] GTDB search result was written to GCF_019145355.1_ASM1914535v1_genomic.fna/result_gtdb.tsv [2024-01-24 11:37:40,496] [INFO] ===== GTDB Search completed ===== [2024-01-24 11:37:40,504] [INFO] DFAST_QC result json was written to GCF_019145355.1_ASM1914535v1_genomic.fna/dqc_result.json [2024-01-24 11:37:40,504] [INFO] DFAST_QC completed! [2024-01-24 11:37:40,504] [INFO] Total running time: 0h2m46s