[2023-03-15 14:47:21,391] [INFO] DFAST_QC pipeline started. [2023-03-15 14:47:21,392] [INFO] DFAST_QC version: 0.5.7 [2023-03-15 14:47:21,392] [INFO] DQC Reference Directory: /var/lib/cwl/stgd163e292-5037-458e-89be-f09c55b18e8a/dqc_reference [2023-03-15 14:47:22,484] [INFO] ===== Start taxonomy check using ANI ===== [2023-03-15 14:47:22,485] [INFO] Task started: Prodigal [2023-03-15 14:47:22,485] [INFO] Running command: cat /var/lib/cwl/stgd1536759-0f53-49c9-be40-effc0374af07/OceanDNA-b40.fa | prodigal -d OceanDNA-b40/cds.fna -a OceanDNA-b40/protein.faa -g 11 -q > /dev/null [2023-03-15 14:48:37,149] [INFO] Task succeeded: Prodigal [2023-03-15 14:48:37,150] [INFO] Task started: HMMsearch [2023-03-15 14:48:37,150] [INFO] Running command: hmmsearch --tblout OceanDNA-b40/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd163e292-5037-458e-89be-f09c55b18e8a/dqc_reference/reference_markers.hmm OceanDNA-b40/protein.faa > /dev/null [2023-03-15 14:48:37,539] [INFO] Task succeeded: HMMsearch [2023-03-15 14:48:37,540] [INFO] Found 6/6 markers. [2023-03-15 14:48:37,606] [INFO] Query marker FASTA was written to OceanDNA-b40/markers.fasta [2023-03-15 14:48:37,608] [INFO] Task started: Blastn [2023-03-15 14:48:37,608] [INFO] Running command: blastn -query OceanDNA-b40/markers.fasta -db /var/lib/cwl/stgd163e292-5037-458e-89be-f09c55b18e8a/dqc_reference/reference_markers.fasta -out OceanDNA-b40/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-03-15 14:48:41,379] [INFO] Task succeeded: Blastn [2023-03-15 14:48:41,385] [INFO] Selected 30 target genomes. [2023-03-15 14:48:41,385] [INFO] Target genome list was writen to OceanDNA-b40/target_genomes.txt [2023-03-15 14:48:41,402] [INFO] Task started: fastANI [2023-03-15 14:48:41,402] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1536759-0f53-49c9-be40-effc0374af07/OceanDNA-b40.fa --refList OceanDNA-b40/target_genomes.txt --output OceanDNA-b40/fastani_result.tsv --threads 1 [2023-03-15 14:49:05,091] [INFO] Task succeeded: fastANI [2023-03-15 14:49:05,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd163e292-5037-458e-89be-f09c55b18e8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2023-03-15 14:49:05,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd163e292-5037-458e-89be-f09c55b18e8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2023-03-15 14:49:05,107] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold) [2023-03-15 14:49:05,107] [INFO] The taxonomy check result is classified as 'below_threshold'. [2023-03-15 14:49:05,107] [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 Desulfuromonas soudanensis strain=WTL GCA_001278055.1 1603606 1603606 type True 75.0837 64 3078 95 below_threshold Halomonas sulfidivorans strain=MCCC 1A13718 GCA_017868935.1 2733488 2733488 type True 75.0717 88 3078 95 below_threshold Halomonas antri strain=Y3S6 GCA_019430905.1 2846777 2846777 type True 75.0389 70 3078 95 below_threshold Mesorhizobium wenxiniae strain=WYCCWR 10195 GCA_002284535.1 2014805 2014805 type True 75.036 66 3078 95 below_threshold Blastochloris viridis strain=ATCC 19567 GCA_001402875.1 1079 1079 type True 75.0012 68 3078 95 below_threshold Blastochloris viridis strain=DSM 133 GCA_001548155.2 1079 1079 type True 74.99 70 3078 95 below_threshold Halomonas nitroreducens strain=11S GCA_003966155.1 447425 447425 type True 74.965 109 3078 95 below_threshold Luteimonas abyssi strain=XH031 GCA_001482195.1 1247514 1247514 type True 74.9475 95 3078 95 below_threshold Desulfuromonas acetexigens GCA_900111775.1 38815 38815 type True 74.9175 57 3078 95 below_threshold Desulfuromonas acetexigens strain=2873 GCA_007051125.1 38815 38815 type True 74.9138 58 3078 95 below_threshold Luteitalea pratensis strain=DSM 100886; HEG_-6_39 GCA_001618865.1 1855912 1855912 type True 74.8535 106 3078 95 below_threshold Devosia geojensis strain=BD-c194 GCA_000969415.1 443610 443610 type True 74.8499 80 3078 95 below_threshold Bradyrhizobium daqingense strain=CGMCC 1.10947 GCA_007830205.1 993502 993502 type True 74.8189 116 3078 95 below_threshold Bradyrhizobium daqingense strain=CCBAU 15774 GCA_021044685.1 993502 993502 type True 74.8152 117 3078 95 below_threshold Streptomyces lichenis strain=LCR6-01 GCA_023218175.1 2306967 2306967 type True 74.8081 177 3078 95 below_threshold Alsobacter metallidurans strain=CGMCC 1.12214 GCA_014636935.1 340221 340221 type True 74.8021 79 3078 95 below_threshold Caulobacter flavus strain=CGMCC1 15093 GCA_002858845.1 1679497 1679497 type True 74.7931 154 3078 95 below_threshold Bradyrhizobium niftali strain=CNPSo 3448 GCA_004571025.1 2560055 2560055 type True 74.7866 121 3078 95 below_threshold Caulobacter flavus strain=RHGG3 GCA_003722335.1 1679497 1679497 type True 74.7854 150 3078 95 below_threshold Methylobrevis albus strain=L22 GCA_015904235.1 2793297 2793297 type True 74.735 132 3078 95 below_threshold Streptomyces physcomitrii strain=LD120 GCA_012273655.1 2724184 2724184 type True 74.733 172 3078 95 below_threshold Nocardioides kongjuensis strain=DSM 19082 GCA_013409625.1 349522 349522 type True 74.7287 187 3078 95 below_threshold Usitatibacter palustris strain=Swamp67 GCA_013003985.1 2732487 2732487 type True 74.7251 53 3078 95 below_threshold Rhodopila globiformis strain=DSM 161 GCA_002937115.1 1071 1071 type True 74.7208 107 3078 95 below_threshold Chelatococcus reniformis strain=CGMCC 1.12919 GCA_014640075.1 1494448 1494448 type True 74.6941 117 3078 95 below_threshold Streptomyces huiliensis strain=SCA2-4 GCA_020037025.1 2876027 2876027 type True 74.6839 158 3078 95 below_threshold Dactylosporangium siamense strain=NBRC 106093 GCA_016862795.1 685454 685454 type True 74.6546 300 3078 95 below_threshold -------------------------------------------------------------------------------- [2023-03-15 14:49:05,110] [INFO] DFAST Taxonomy check result was written to OceanDNA-b40/tc_result.tsv [2023-03-15 14:49:05,113] [INFO] ===== Taxonomy check completed ===== [2023-03-15 14:49:05,113] [INFO] ===== Start completeness check using CheckM ===== [2023-03-15 14:49:05,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd163e292-5037-458e-89be-f09c55b18e8a/dqc_reference/checkm_data [2023-03-15 14:49:05,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2023-03-15 14:49:05,192] [INFO] Task started: CheckM [2023-03-15 14:49:05,192] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b40/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b40/checkm_input OceanDNA-b40/checkm_result [2023-03-15 14:52:10,221] [INFO] Task succeeded: CheckM [2023-03-15 14:52:10,221] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 70.83% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2023-03-15 14:52:10,307] [INFO] ===== Completeness check finished ===== [2023-03-15 14:52:10,307] [INFO] ===== Start GTDB Search ===== [2023-03-15 14:52:10,307] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b40/markers.fasta) [2023-03-15 14:52:10,308] [INFO] Task started: Blastn [2023-03-15 14:52:10,308] [INFO] Running command: blastn -query OceanDNA-b40/markers.fasta -db /var/lib/cwl/stgd163e292-5037-458e-89be-f09c55b18e8a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b40/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-03-15 14:52:11,532] [INFO] Task succeeded: Blastn [2023-03-15 14:52:11,542] [INFO] Selected 29 target genomes. [2023-03-15 14:52:11,542] [INFO] Target genome list was writen to OceanDNA-b40/target_genomes_gtdb.txt [2023-03-15 14:52:11,588] [INFO] Task started: fastANI [2023-03-15 14:52:11,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1536759-0f53-49c9-be40-effc0374af07/OceanDNA-b40.fa --refList OceanDNA-b40/target_genomes_gtdb.txt --output OceanDNA-b40/fastani_result_gtdb.tsv --threads 1 [2023-03-15 14:52:32,665] [INFO] Task succeeded: fastANI [2023-03-15 14:52:32,679] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius) [2023-03-15 14:52:32,679] [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 GCA_003697015.1 s__J023 sp003697015 77.0245 538 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__J023 95.0 N/A N/A N/A N/A 1 - GCA_003231035.1 s__SZUA-115 sp003231035 76.0464 155 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__SZUA-115 95.0 N/A N/A N/A N/A 1 - GCA_011525905.1 s__JACTMI01 sp011525905 75.8841 250 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01 95.0 N/A N/A N/A N/A 1 - GCA_016699405.1 s__JAAYLR01 sp016699405 75.8373 243 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAAYLR01 95.0 N/A N/A N/A N/A 1 - GCA_002420005.1 s__UBA5704 sp002420005 75.8181 324 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__UBA5704 95.0 N/A N/A N/A N/A 1 - GCA_003388555.1 s__QQVD01 sp003388555 75.8168 387 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__QQVD01 95.0 99.97 99.97 0.99 0.99 2 - GCA_009836625.1 s__WTGL01 sp009836625 75.7253 156 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01 95.0 99.03 98.03 0.95 0.91 5 - GCA_014584695.1 s__JACTMI01 sp014584695 75.6999 246 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01 95.0 N/A N/A N/A N/A 1 - GCA_017998715.1 s__JAGPDF01 sp017998715 75.6992 172 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JAGPDF01 95.0 N/A N/A N/A N/A 1 - GCA_905479655.1 s__CAJQNK01 sp905479655 75.6605 250 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__CAJQNK01 95.0 N/A N/A N/A N/A 1 - GCA_009837085.1 s__WTGL01 sp009837085 75.6537 157 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01 95.0 99.78 99.78 0.96 0.95 3 - GCA_017860005.1 s__JACTMI01 sp017860005 75.6397 221 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01 95.0 N/A N/A N/A N/A 1 - GCA_011523565.1 s__WTGL01 sp011523565 75.426 111 3078 d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01 95.0 N/A N/A N/A N/A 1 - GCF_017868935.1 s__Halomonas sp017868935 75.0856 86 3078 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas 95.0 N/A N/A N/A N/A 1 - GCA_003972985.1 s__Thiolapillus sp003972985 74.9531 51 3078 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__Thiolapillus 95.0 99.52 99.52 0.88 0.88 2 - GCA_016713665.1 s__JADJOR01 sp016713665 74.9321 174 3078 d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01 95.0 N/A N/A N/A N/A 1 - GCA_016719295.1 s__JADKAF01 sp016719295 74.8755 166 3078 d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01 95.0 N/A N/A N/A N/A 1 - GCA_016793245.1 s__JADKAF01 sp016793245 74.8468 165 3078 d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__JADKAF01;g__JADKAF01 95.0 N/A N/A N/A N/A 1 - GCF_002159495.1 s__Thermophilibacter sp002159495 74.7931 55 3078 d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Thermophilibacter 95.0 N/A N/A N/A N/A 1 - GCA_002687715.1 s__GCA-2687715 sp002687715 74.781 95 3078 d__Bacteria;p__Planctomycetota;c__GCA-002687715;o__GCA-002687715;f__GCA-002687715;g__GCA-2687715 95.0 N/A N/A N/A N/A 1 - GCA_013215605.1 s__JABSQW01 sp013215605 74.7724 91 3078 d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01 95.0 N/A N/A N/A N/A 1 - GCA_016793165.1 s__CAIOSQ01 sp016793165 74.7616 150 3078 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__CAIOSQ01 95.0 N/A N/A N/A N/A 1 - GCF_013409625.1 s__Nocardioides kongjuensis 74.7319 183 3078 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides 95.0 N/A N/A N/A N/A 1 - GCA_018336195.1 s__JAGXQV01 sp018336195 74.7071 50 3078 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Sulfuricellaceae;g__JAGXQV01 95.0 N/A N/A N/A N/A 1 - GCA_019244985.1 s__CADDZP01 sp019244985 74.6879 66 3078 d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__CADDZP01 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2023-03-15 14:52:32,684] [INFO] GTDB search result was written to OceanDNA-b40/result_gtdb.tsv [2023-03-15 14:52:32,694] [INFO] ===== GTDB Search completed ===== [2023-03-15 14:52:32,699] [INFO] DFAST_QC result json was written to OceanDNA-b40/dqc_result.json [2023-03-15 14:52:32,699] [INFO] DFAST_QC completed! [2023-03-15 14:52:32,699] [INFO] Total running time: 0h5m11s