[2023-03-17 23:15:40,547] [INFO] DFAST_QC pipeline started. [2023-03-17 23:15:40,547] [INFO] DFAST_QC version: 0.5.7 [2023-03-17 23:15:40,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1b0a507-883e-4e10-af96-1685bf6bf790/dqc_reference [2023-03-17 23:15:41,650] [INFO] ===== Start taxonomy check using ANI ===== [2023-03-17 23:15:41,651] [INFO] Task started: Prodigal [2023-03-17 23:15:41,651] [INFO] Running command: cat /var/lib/cwl/stgcb0e8b54-449a-4a79-8b4a-156653f6a6a4/OceanDNA-b20976.fa | prodigal -d OceanDNA-b20976/cds.fna -a OceanDNA-b20976/protein.faa -g 11 -q > /dev/null [2023-03-17 23:16:21,918] [INFO] Task succeeded: Prodigal [2023-03-17 23:16:21,919] [INFO] Task started: HMMsearch [2023-03-17 23:16:21,919] [INFO] Running command: hmmsearch --tblout OceanDNA-b20976/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1b0a507-883e-4e10-af96-1685bf6bf790/dqc_reference/reference_markers.hmm OceanDNA-b20976/protein.faa > /dev/null [2023-03-17 23:16:22,191] [INFO] Task succeeded: HMMsearch [2023-03-17 23:16:22,192] [INFO] Found 6/6 markers. [2023-03-17 23:16:22,240] [INFO] Query marker FASTA was written to OceanDNA-b20976/markers.fasta [2023-03-17 23:16:22,241] [INFO] Task started: Blastn [2023-03-17 23:16:22,242] [INFO] Running command: blastn -query OceanDNA-b20976/markers.fasta -db /var/lib/cwl/stgf1b0a507-883e-4e10-af96-1685bf6bf790/dqc_reference/reference_markers.fasta -out OceanDNA-b20976/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-03-17 23:16:22,901] [INFO] Task succeeded: Blastn [2023-03-17 23:16:22,903] [INFO] Selected 40 target genomes. [2023-03-17 23:16:22,903] [INFO] Target genome list was writen to OceanDNA-b20976/target_genomes.txt [2023-03-17 23:16:22,919] [INFO] Task started: fastANI [2023-03-17 23:16:22,919] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb0e8b54-449a-4a79-8b4a-156653f6a6a4/OceanDNA-b20976.fa --refList OceanDNA-b20976/target_genomes.txt --output OceanDNA-b20976/fastani_result.tsv --threads 1 [2023-03-17 23:16:54,477] [INFO] Task succeeded: fastANI [2023-03-17 23:16:54,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1b0a507-883e-4e10-af96-1685bf6bf790/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2023-03-17 23:16:54,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1b0a507-883e-4e10-af96-1685bf6bf790/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2023-03-17 23:16:54,498] [INFO] Found 40 fastANI hits (0 hits with ANI > threshold) [2023-03-17 23:16:54,498] [INFO] The taxonomy check result is classified as 'below_threshold'. [2023-03-17 23:16:54,498] [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 Schlegelella thermodepolymerans strain=DSM 15344 GCA_015476235.1 215580 215580 type True 75.1769 143 2218 95 below_threshold Schlegelella thermodepolymerans strain=DSM 15344 GCA_002933415.1 215580 215580 type True 75.1273 147 2218 95 below_threshold Noviherbaspirillum humi strain=U15 GCA_900188095.1 1688639 1688639 type True 75.1069 93 2218 95 below_threshold Vulgatibacter incomptus strain=DSM 27710 GCA_001263175.1 1391653 1391653 type True 75.0989 137 2218 95 below_threshold Luteimonas yindakuii strain=S-1072 GCA_004803715.2 2565782 2565782 type True 75.0693 85 2218 95 below_threshold Luteimonas arsenica strain=26-35 GCA_004352825.1 1586242 1586242 type True 75.0412 114 2218 95 below_threshold Vulcaniibacterium tengchongense strain=YIM 77520 GCA_008033455.1 1273429 1273429 type True 74.9938 155 2218 95 below_threshold Vulcaniibacterium tengchongense strain=DSM 25623 GCA_003814555.1 1273429 1273429 type True 74.991 162 2218 95 below_threshold Geomonas paludis strain=Red736 GCA_014193585.1 2740185 2740185 type True 74.9902 76 2218 95 below_threshold Geomonas azotofigens strain=Red51 GCA_018919395.1 2843196 2843196 type True 74.9887 71 2218 95 below_threshold Haliangium ochraceum strain=DSM 14365 GCA_000024805.1 80816 80816 type True 74.9763 295 2218 95 below_threshold Xanthobacter tagetidis strain=DSM 11105 GCA_014206845.1 60216 60216 type True 74.9669 139 2218 95 below_threshold Myxococcus stipitatus strain=DSM 14675 GCA_000331735.1 83455 83455 neotype True 74.9619 264 2218 95 below_threshold Anaeromyxobacter dehalogenans strain=2CP-1 GCA_000022145.1 161493 161493 type True 74.9285 273 2218 95 below_threshold Luteimonas huabeiensis strain=HB2 GCA_000559025.1 1244513 1244513 type True 74.9211 167 2218 95 below_threshold Caulobacter radicis strain=695 GCA_003094615.1 2172650 2172650 type True 74.9148 185 2218 95 below_threshold Micropruina glycogenica GCA_900289045.1 75385 75385 type True 74.9116 71 2218 95 below_threshold Nocardioides seonyuensis strain=MMS17-SY207-3 GCA_004683965.1 2518371 2518371 type True 74.8969 130 2218 95 below_threshold Geomonas anaerohicana strain=Red421 GCA_016458305.1 2798583 2798583 type True 74.8789 77 2218 95 below_threshold Nocardioides lacusdianchii strain=JXJ CY 38 GCA_020102855.1 2783664 2783664 type True 74.8679 138 2218 95 below_threshold Streptomonospora salina strain=DSM 44593 GCA_014204715.1 104205 104205 type True 74.8318 178 2218 95 below_threshold Modestobacter versicolor strain=DSM 16678 GCA_014195485.1 429133 429133 type True 74.8316 227 2218 95 below_threshold Nocardioides flavescens strain=YIM 123512 GCA_009823805.1 2691959 2691959 type True 74.814 192 2218 95 below_threshold Caulobacter hibisci strain=KACC 18849 GCA_016135805.1 2035993 2035993 type True 74.808 157 2218 95 below_threshold Nocardioides marinisabuli strain=DSM 18965 GCA_013409965.1 419476 419476 type True 74.8073 195 2218 95 below_threshold Nocardioides marinisabuli strain=DSM 18965 GCA_013466785.1 419476 419476 type True 74.8019 198 2218 95 below_threshold Nocardioides salarius strain=DSM 18239 GCA_015070765.1 374513 374513 type True 74.7829 193 2218 95 below_threshold Nocardioides salarius strain=DSM 18239 GCA_015339545.1 374513 374513 type True 74.7828 193 2218 95 below_threshold Streptomonospora alba strain=YIM 90003 GCA_000826685.1 183763 183763 type True 74.7699 184 2218 95 below_threshold Labilithrix luteola strain=DSM 27648 GCA_001263205.1 1391654 1391654 type True 74.7534 182 2218 95 below_threshold Modestobacter marinus strain=DSM 45201 GCA_023383595.1 477641 477641 type True 74.7295 210 2218 95 below_threshold Modestobacter marinus strain=CGMCC 4.5581 GCA_014645755.1 477641 477641 type True 74.7294 215 2218 95 below_threshold Jannaschia formosa strain=12N15 GCA_003340555.1 2259592 2259592 type True 74.7227 130 2218 95 below_threshold Modestobacter marinus strain=DSM 45201 GCA_011758655.1 477641 477641 type True 74.7192 222 2218 95 below_threshold Rubrivirga marina strain=SAORIC-28 GCA_002283365.1 1196024 1196024 type True 74.7173 158 2218 95 below_threshold Sciscionella marina strain=DSM 45152 GCA_000379465.1 508770 508770 type True 74.7137 177 2218 95 below_threshold Deinococcus pimensis strain=DSM 21231 GCA_000519345.1 309888 309888 type True 74.7136 127 2218 95 below_threshold Streptomyces phaeofaciens strain=JCM 4125 GCA_014648915.1 68254 68254 type True 74.7071 293 2218 95 below_threshold Streptomyces prasinus strain=NRRL B-2712 GCA_001419705.1 67345 67345 type True 74.7003 177 2218 95 below_threshold Hypericibacter adhaerens strain=R5959 GCA_008728835.1 2602016 2602016 type True 74.6004 124 2218 95 below_threshold -------------------------------------------------------------------------------- [2023-03-17 23:16:54,498] [INFO] DFAST Taxonomy check result was written to OceanDNA-b20976/tc_result.tsv [2023-03-17 23:16:54,498] [INFO] ===== Taxonomy check completed ===== [2023-03-17 23:16:54,499] [INFO] ===== Start completeness check using CheckM ===== [2023-03-17 23:16:54,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1b0a507-883e-4e10-af96-1685bf6bf790/dqc_reference/checkm_data [2023-03-17 23:16:54,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2023-03-17 23:16:54,508] [INFO] Task started: CheckM [2023-03-17 23:16:54,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b20976/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b20976/checkm_input OceanDNA-b20976/checkm_result [2023-03-17 23:18:55,111] [INFO] Task succeeded: CheckM [2023-03-17 23:18:55,112] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 74.86% Contamintation: 0.00% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2023-03-17 23:18:55,115] [INFO] ===== Completeness check finished ===== [2023-03-17 23:18:55,115] [INFO] ===== Start GTDB Search ===== [2023-03-17 23:18:55,116] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b20976/markers.fasta) [2023-03-17 23:18:55,117] [INFO] Task started: Blastn [2023-03-17 23:18:55,117] [INFO] Running command: blastn -query OceanDNA-b20976/markers.fasta -db /var/lib/cwl/stgf1b0a507-883e-4e10-af96-1685bf6bf790/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b20976/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2023-03-17 23:18:56,466] [INFO] Task succeeded: Blastn [2023-03-17 23:18:56,467] [INFO] Selected 44 target genomes. [2023-03-17 23:18:56,468] [INFO] Target genome list was writen to OceanDNA-b20976/target_genomes_gtdb.txt [2023-03-17 23:18:56,706] [INFO] Task started: fastANI [2023-03-17 23:18:56,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb0e8b54-449a-4a79-8b4a-156653f6a6a4/OceanDNA-b20976.fa --refList OceanDNA-b20976/target_genomes_gtdb.txt --output OceanDNA-b20976/fastani_result_gtdb.tsv --threads 1 [2023-03-17 23:19:31,444] [INFO] Task succeeded: fastANI [2023-03-17 23:19:31,466] [INFO] Found 42 fastANI hits (0 hits with ANI > circumscription radius) [2023-03-17 23:19:31,467] [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_002724675.1 s__GCA-2724675 sp002724675 76.1763 159 2218 d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA9615;f__UBA9615;g__GCA-2724675 95.0 N/A N/A N/A N/A 1 - GCA_016875435.1 s__SXON01 sp016875435 75.8986 170 2218 d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__SXON01;g__SXON01 95.0 N/A N/A N/A N/A 1 - GCA_002433485.1 s__UBA6601 sp002433485 75.7787 99 2218 d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA9615;f__UBA9615;g__UBA6601 95.0 99.91 99.91 0.95 0.95 2 - GCA_006226595.1 s__M1803 sp006226595 75.6494 267 2218 d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__M1803 95.0 N/A N/A N/A N/A 1 - GCA_016938035.1 s__JAFGVK01 sp016938035 75.6254 207 2218 d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__JAFGVK01 95.0 N/A N/A N/A N/A 1 - GCA_015489145.1 s__S143-5 sp015489145 75.365 242 2218 d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__S143-5 95.0 N/A N/A N/A N/A 1 - GCA_017644045.1 s__UBA1660 sp017644045 75.2152 254 2218 d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660 95.0 N/A N/A N/A N/A 1 - GCA_016935365.1 s__JAFGRB01 sp016935365 75.1334 214 2218 d__Bacteria;p__Myxococcota;c__B64-G9;o__B64-G9;f__B64-G9;g__JAFGRB01 95.0 N/A N/A N/A N/A 1 - GCA_016792625.1 s__JAEUKK01 sp016792625 75.12 317 2218 d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__UBA2385;g__JAEUKK01 95.0 N/A N/A N/A N/A 1 - GCF_001263175.1 s__Vulgatibacter incomptus 75.1057 134 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Vulgatibacteraceae;g__Vulgatibacter 95.0 N/A N/A N/A N/A 1 - GCA_003818285.1 s__RPRB01 sp003818285 75.058 145 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__RPRB01 95.0 N/A N/A N/A N/A 1 - GCA_002995625.1 s__UDEA-SF1 sp002995625 75.031 95 2218 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Ahniellaceae;g__UDEA-SF1 95.0 N/A N/A N/A N/A 1 - GCA_002898955.1 s__HRBIN39 sp002898955 75.0213 75 2218 d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__HRBIN39 95.0 N/A N/A N/A N/A 1 - GCF_000510725.1 s__Pseudoxanthomonas sp000510725 75.0122 158 2218 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas 95.0 99.33 99.13 0.95 0.92 5 - GCF_000513995.1 s__Pseudoxanthomonas sp000513995 75.0109 146 2218 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas 95.0 N/A N/A N/A N/A 1 - GCA_900696455.1 s__UBA2376 sp900696455 75.0086 378 2218 d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376 95.0 98.40 97.29 0.91 0.90 3 - GCA_011774835.1 s__KS3-K002 sp011774835 75.0084 73 2218 d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__KS3-K002;g__KS3-K002 95.0 N/A N/A N/A N/A 1 - GCA_903874275.1 s__CAIOAK01 sp903874275 74.998 163 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01 95.0 99.83 99.81 0.95 0.94 3 - GCA_016214955.1 s__JACRMN01 sp016214955 74.9912 258 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JACRMN01 95.0 N/A N/A N/A N/A 1 - GCF_003814555.1 s__Lysobacter tengchongensis 74.9758 162 2218 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter 95.0 99.99 99.99 0.99 0.99 2 - GCA_016718565.1 s__JADKCZ01 sp016718565 74.9687 277 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__JADKCZ01 95.0 99.81 99.81 0.97 0.97 2 - GCF_000331735.1 s__Myxococcus stipitatus 74.9674 261 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Myxococcus 95.0 N/A N/A N/A N/A 1 - GCA_018242445.1 s__SZAS-103 sp018242445 74.966 70 2218 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SZAS-103 95.0 N/A N/A N/A N/A 1 - GCA_903904005.1 s__CAIOAK01 sp903904005 74.9547 156 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__CAIOAK01 95.0 99.78 99.64 0.94 0.92 4 - GCF_009659535.1 s__Aggregicoccus sp009659535 74.9208 280 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Aggregicoccus 95.0 100.00 100.00 1.00 1.00 2 - GCF_900289045.1 s__Micropruina glycogenica 74.9176 70 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Micropruina 95.0 N/A N/A N/A N/A 1 - GCF_000559025.1 s__Luteimonas huabeiensis 74.9045 167 2218 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas 95.0 N/A N/A N/A N/A 1 - GCA_016874715.1 s__VGTK01 sp016874715 74.8767 176 2218 d__Bacteria;p__Desulfobacterota_B;c__Binatia;o__UBA12015;f__UBA12015;g__VGTK01 95.0 N/A N/A N/A N/A 1 - GCA_003142855.1 s__Fen-1137 sp003142855 74.8486 59 2218 d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104_A;f__Fen-1088;g__Fen-1137 95.0 99.79 99.79 0.94 0.94 2 - GCA_017881345.1 s__RPRB01 sp017881345 74.8377 148 2218 d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__RPRB01 95.0 N/A N/A N/A N/A 1 - GCA_003158735.1 s__Fen-1137 sp003158735 74.8284 68 2218 d__Bacteria;p__Myxococcota;c__Polyangia;o__Palsa-1104_A;f__Fen-1088;g__Fen-1137 95.0 99.40 99.40 0.88 0.86 3 - GCF_013466785.1 s__Nocardioides marinisabuli 74.8045 195 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides 95.0 99.99 99.99 1.00 1.00 2 - GCF_000220835.1 s__Actinomyces sp000220835 74.8 63 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces 95.0 99.31 99.28 0.97 0.96 3 - GCA_002428015.1 s__Massilia sp002428015 74.7933 141 2218 d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Massilia 95.0 N/A N/A N/A N/A 1 - GCF_016907435.1 s__Nocardioides salarius 74.7862 190 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides 95.0 100.00 100.00 1.00 1.00 3 - GCA_000620205.1 s__Modestobacter sp000620205 74.769 214 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter 95.0 N/A N/A N/A N/A 1 - GCF_011758655.1 s__Modestobacter marinus 74.723 220 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter 95.0 99.99 99.99 0.99 0.99 2 - GCF_011764425.1 s__Phytohabitans houttuyneae 74.7123 296 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans 95.0 N/A N/A N/A N/A 1 - GCA_009379925.1 s__WHSU01 sp009379925 74.6968 81 2218 d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA2979;f__UBA2979;g__WHSU01 95.0 N/A N/A N/A N/A 1 - GCF_004570875.1 s__Blastococcus sp004570875 74.6942 160 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus 95.0 N/A N/A N/A N/A 1 - GCA_003021615.1 s__QS-5-72-10 sp003021615 74.6766 76 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Euzebyales;f__Egibacteraceae;g__QS-5-72-10 95.0 97.51 97.51 0.71 0.71 2 - GCF_011766325.1 s__Streptomyces sp011766325 74.6657 172 2218 d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2023-03-17 23:19:31,467] [INFO] GTDB search result was written to OceanDNA-b20976/result_gtdb.tsv [2023-03-17 23:19:31,467] [INFO] ===== GTDB Search completed ===== [2023-03-17 23:19:31,471] [INFO] DFAST_QC result json was written to OceanDNA-b20976/dqc_result.json [2023-03-17 23:19:31,471] [INFO] DFAST_QC completed! [2023-03-17 23:19:31,471] [INFO] Total running time: 0h3m51s