[2024-01-24 12:53:41,586] [INFO] DFAST_QC pipeline started. [2024-01-24 12:53:41,587] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 12:53:41,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c8f3a32-6513-4d19-9329-242b8084430d/dqc_reference [2024-01-24 12:53:42,868] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 12:53:42,869] [INFO] Task started: Prodigal [2024-01-24 12:53:42,869] [INFO] Running command: gunzip -c /var/lib/cwl/stg05a0b857-c020-40c1-839f-148aea3c6240/GCF_001050345.1_ASM105034v1_genomic.fna.gz | prodigal -d GCF_001050345.1_ASM105034v1_genomic.fna/cds.fna -a GCF_001050345.1_ASM105034v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 12:54:05,370] [INFO] Task succeeded: Prodigal [2024-01-24 12:54:05,371] [INFO] Task started: HMMsearch [2024-01-24 12:54:05,371] [INFO] Running command: hmmsearch --tblout GCF_001050345.1_ASM105034v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c8f3a32-6513-4d19-9329-242b8084430d/dqc_reference/reference_markers.hmm GCF_001050345.1_ASM105034v1_genomic.fna/protein.faa > /dev/null [2024-01-24 12:54:05,723] [INFO] Task succeeded: HMMsearch [2024-01-24 12:54:05,725] [INFO] Found 6/6 markers. [2024-01-24 12:54:05,781] [INFO] Query marker FASTA was written to GCF_001050345.1_ASM105034v1_genomic.fna/markers.fasta [2024-01-24 12:54:05,782] [INFO] Task started: Blastn [2024-01-24 12:54:05,782] [INFO] Running command: blastn -query GCF_001050345.1_ASM105034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c8f3a32-6513-4d19-9329-242b8084430d/dqc_reference/reference_markers.fasta -out GCF_001050345.1_ASM105034v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:54:06,816] [INFO] Task succeeded: Blastn [2024-01-24 12:54:06,821] [INFO] Selected 20 target genomes. [2024-01-24 12:54:06,822] [INFO] Target genome list was writen to GCF_001050345.1_ASM105034v1_genomic.fna/target_genomes.txt [2024-01-24 12:54:06,837] [INFO] Task started: fastANI [2024-01-24 12:54:06,837] [INFO] Running command: fastANI --query /var/lib/cwl/stg05a0b857-c020-40c1-839f-148aea3c6240/GCF_001050345.1_ASM105034v1_genomic.fna.gz --refList GCF_001050345.1_ASM105034v1_genomic.fna/target_genomes.txt --output GCF_001050345.1_ASM105034v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 12:54:38,501] [INFO] Task succeeded: fastANI [2024-01-24 12:54:38,503] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c8f3a32-6513-4d19-9329-242b8084430d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 12:54:38,503] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c8f3a32-6513-4d19-9329-242b8084430d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 12:54:38,595] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold) [2024-01-24 12:54:38,595] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 12:54:38,596] [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 89.1394 1672 2083 95 below_threshold Pseudomonas marginalis strain=ICMP 3553 GCA_003700725.1 298 298 suspected-type True 88.9101 1549 2083 95 below_threshold Pseudomonas marginalis strain=ICMP 3553 GCA_001645105.1 298 298 suspected-type True 88.897 1646 2083 95 below_threshold Pseudomonas pergaminensis strain=1008 GCA_024112395.1 2853159 2853159 type True 88.8044 1623 2083 95 below_threshold Pseudomonas lurida strain=LMG 21995 GCA_002563895.1 244566 244566 type True 88.6053 1603 2083 95 below_threshold Pseudomonas fluorescens strain=NBRC 14160 GCA_002091595.1 294 294 suspected-type True 88.4335 1578 2083 95 below_threshold Pseudomonas salomonii strain=ICMP 14252 GCA_900107155.1 191391 191391 type True 88.4241 1570 2083 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_007858165.1 294 294 suspected-type True 88.3945 1618 2083 95 below_threshold Pseudomonas antarctica strain=CMS 35 GCA_010634845.1 219572 219572 type True 88.3925 1556 2083 95 below_threshold Pseudomonas antarctica GCA_900624995.1 219572 219572 type True 88.3823 1481 2083 95 below_threshold Pseudomonas fluorescens strain=DSM 50090 GCA_001269845.1 294 294 suspected-type True 88.3809 1624 2083 95 below_threshold Pseudomonas fluorescens strain=ATCC 13525 GCA_002943685.1 294 294 suspected-type True 88.3708 1586 2083 95 below_threshold Pseudomonas fluorescens strain=NCTC10038 GCA_900475215.1 294 294 suspected-type True 88.3605 1628 2083 95 below_threshold Pseudomonas asgharzadehiana strain=SWRI132 GCA_019139815.1 2842349 2842349 type True 88.3231 1576 2083 95 below_threshold Pseudomonas cedrina subsp. cedrina GCA_900625035.1 76762 651740 type True 88.1715 1574 2083 95 below_threshold Pseudomonas cedrina subsp. cedrina strain=DSM 17516 GCA_001983175.1 76762 651740 type True 88.1414 1566 2083 95 below_threshold Pseudomonas kitaguniensis strain=MAFF 212408 GCA_009296165.1 2607908 2607908 type True 87.5553 1363 2083 95 below_threshold Pseudomonas yamanorum strain=LMG 27247 GCA_900105735.1 515393 515393 suspected-type True 87.4054 1568 2083 95 below_threshold Pseudomonas spelaei strain=CCM 7893 GCA_009724245.1 1055469 1055469 type True 86.3867 1470 2083 95 below_threshold Pseudomonas karstica strain=CCM 7891 GCA_009707515.1 1055468 1055468 type True 85.6059 1314 2083 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 12:54:38,597] [INFO] DFAST Taxonomy check result was written to GCF_001050345.1_ASM105034v1_genomic.fna/tc_result.tsv [2024-01-24 12:54:38,598] [INFO] ===== Taxonomy check completed ===== [2024-01-24 12:54:38,598] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 12:54:38,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c8f3a32-6513-4d19-9329-242b8084430d/dqc_reference/checkm_data [2024-01-24 12:54:38,604] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 12:54:38,667] [INFO] Task started: CheckM [2024-01-24 12:54:38,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050345.1_ASM105034v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050345.1_ASM105034v1_genomic.fna/checkm_input GCF_001050345.1_ASM105034v1_genomic.fna/checkm_result [2024-01-24 12:55:46,236] [INFO] Task succeeded: CheckM [2024-01-24 12:55:46,237] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:55:46,262] [INFO] ===== Completeness check finished ===== [2024-01-24 12:55:46,263] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:55:46,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050345.1_ASM105034v1_genomic.fna/markers.fasta) [2024-01-24 12:55:46,264] [INFO] Task started: Blastn [2024-01-24 12:55:46,264] [INFO] Running command: blastn -query GCF_001050345.1_ASM105034v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c8f3a32-6513-4d19-9329-242b8084430d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050345.1_ASM105034v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:55:50,808] [INFO] Task succeeded: Blastn [2024-01-24 12:55:50,811] [INFO] Selected 21 target genomes. [2024-01-24 12:55:50,811] [INFO] Target genome list was writen to GCF_001050345.1_ASM105034v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:55:50,833] [INFO] Task started: fastANI [2024-01-24 12:55:50,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg05a0b857-c020-40c1-839f-148aea3c6240/GCF_001050345.1_ASM105034v1_genomic.fna.gz --refList GCF_001050345.1_ASM105034v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001050345.1_ASM105034v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:56:29,616] [INFO] Task succeeded: fastANI [2024-01-24 12:56:29,672] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-24 12:56:29,673] [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_001050345.1 s__Pseudomonas_E fildesensis 100.0 2080 2083 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 N/A N/A N/A N/A 1 conclusive GCF_001439695.1 s__Pseudomonas_E veronii 89.3335 1595 2083 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_003097075.1 s__Pseudomonas_E sp003097075 89.2799 1619 2083 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_007858185.1 s__Pseudomonas_E grimontii 89.2004 1665 2083 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_009707325.1 s__Pseudomonas_E sp002263605 89.16 1516 2083 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 99.58 99.58 0.94 0.94 2 - GCF_002843605.1 s__Pseudomonas_E sp002843605 89.1194 1639 2083 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 89.1162 1522 2083 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_003612935.1 s__Pseudomonas_E sp003013355 89.0126 1606 2083 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.87 98.56 0.95 0.92 7 - GCF_009834565.1 s__Pseudomonas_E sp009834565 88.8258 1633 2083 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_001647715.1 s__Pseudomonas_E antarctica_A 88.7396 1595 2083 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_001186335.1 s__Pseudomonas_E trivialis_B 88.6377 1665 2083 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_002563895.1 s__Pseudomonas_E lurida 88.6053 1603 2083 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_900107155.1 s__Pseudomonas_E salomonii 88.3855 1574 2083 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.30 96.43 0.92 0.87 14 - GCF_013385965.1 s__Pseudomonas_E edaphica 88.3655 1592 2083 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_019139815.1 s__Pseudomonas_E sp900005815 88.3239 1576 2083 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 88.1322 1567 2083 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 87.8206 1059 2083 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_013386765.1 s__Pseudomonas_E yamanorum_A 87.6764 1572 2083 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.70 98.16 0.94 0.91 5 - GCF_002204795.1 s__Pseudomonas_E sp002204795 87.5413 1570 2083 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_002874965.1 s__Pseudomonas_E sp002874965 87.5204 1578 2083 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.77 98.46 0.92 0.88 48 - GCF_001952855.1 s__Pseudomonas_E sp001952855 87.4035 1584 2083 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E 95.0 98.78 98.78 0.94 0.94 2 - -------------------------------------------------------------------------------- [2024-01-24 12:56:29,674] [INFO] GTDB search result was written to GCF_001050345.1_ASM105034v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:56:29,675] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:56:29,680] [INFO] DFAST_QC result json was written to GCF_001050345.1_ASM105034v1_genomic.fna/dqc_result.json [2024-01-24 12:56:29,680] [INFO] DFAST_QC completed! [2024-01-24 12:56:29,680] [INFO] Total running time: 0h2m48s