[2024-01-24 11:58:56,268] [INFO] DFAST_QC pipeline started. [2024-01-24 11:58:56,275] [INFO] DFAST_QC version: 0.5.7 [2024-01-24 11:58:56,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg233630fd-405f-4590-a241-d2b4d2a82280/dqc_reference [2024-01-24 11:58:57,665] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-24 11:58:57,666] [INFO] Task started: Prodigal [2024-01-24 11:58:57,667] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f28d0ce-a6a7-472a-bb62-38a4e1ec0fb4/GCF_023276405.1_ASM2327640v1_genomic.fna.gz | prodigal -d GCF_023276405.1_ASM2327640v1_genomic.fna/cds.fna -a GCF_023276405.1_ASM2327640v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-24 11:59:22,182] [INFO] Task succeeded: Prodigal [2024-01-24 11:59:22,183] [INFO] Task started: HMMsearch [2024-01-24 11:59:22,183] [INFO] Running command: hmmsearch --tblout GCF_023276405.1_ASM2327640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg233630fd-405f-4590-a241-d2b4d2a82280/dqc_reference/reference_markers.hmm GCF_023276405.1_ASM2327640v1_genomic.fna/protein.faa > /dev/null [2024-01-24 11:59:22,660] [INFO] Task succeeded: HMMsearch [2024-01-24 11:59:22,661] [INFO] Found 6/6 markers. [2024-01-24 11:59:22,734] [INFO] Query marker FASTA was written to GCF_023276405.1_ASM2327640v1_genomic.fna/markers.fasta [2024-01-24 11:59:22,735] [INFO] Task started: Blastn [2024-01-24 11:59:22,735] [INFO] Running command: blastn -query GCF_023276405.1_ASM2327640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg233630fd-405f-4590-a241-d2b4d2a82280/dqc_reference/reference_markers.fasta -out GCF_023276405.1_ASM2327640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 11:59:23,388] [INFO] Task succeeded: Blastn [2024-01-24 11:59:23,393] [INFO] Selected 25 target genomes. [2024-01-24 11:59:23,393] [INFO] Target genome list was writen to GCF_023276405.1_ASM2327640v1_genomic.fna/target_genomes.txt [2024-01-24 11:59:23,420] [INFO] Task started: fastANI [2024-01-24 11:59:23,420] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f28d0ce-a6a7-472a-bb62-38a4e1ec0fb4/GCF_023276405.1_ASM2327640v1_genomic.fna.gz --refList GCF_023276405.1_ASM2327640v1_genomic.fna/target_genomes.txt --output GCF_023276405.1_ASM2327640v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-24 11:59:53,731] [INFO] Task succeeded: fastANI [2024-01-24 11:59:53,731] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg233630fd-405f-4590-a241-d2b4d2a82280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-24 11:59:53,731] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg233630fd-405f-4590-a241-d2b4d2a82280/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-24 11:59:53,751] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold) [2024-01-24 11:59:53,751] [INFO] The taxonomy check result is classified as 'below_threshold'. [2024-01-24 11:59:53,752] [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 Paenibacillus flagellatus strain=DXL2 GCA_003217775.1 2211139 2211139 type True 78.3532 461 2931 95 below_threshold Paenibacillus macerans strain=ATCC 8244 GCA_000746875.1 44252 44252 type True 78.2393 268 2931 95 below_threshold Paenibacillus piri strain=MS74 GCA_004354045.1 2547395 2547395 type True 78.0832 511 2931 95 below_threshold Paenibacillus validus strain=NBRC 15382 GCA_004000985.1 44253 44253 type True 78.0734 327 2931 95 below_threshold Paenibacillus thalictri strain=N2SHLJ1 GCA_004307995.1 2527873 2527873 type True 78.0172 653 2931 95 below_threshold Paenibacillus allorhizosphaerae strain=CIP 111802 GCA_910594985.1 2849866 2849866 type True 77.8817 491 2931 95 below_threshold Paenibacillus tianmuensis strain=CGMCC 1.8946 GCA_900100345.1 624147 624147 type True 77.6953 363 2931 95 below_threshold Paenibacillus athensensis strain=MEC069 GCA_004514475.2 1967502 1967502 type True 77.5874 306 2931 95 below_threshold Paenibacillus doosanensis strain=CAU 1055 GCA_025060755.1 1229154 1229154 type True 77.5264 533 2931 95 below_threshold Paenibacillus ginsengihumi strain=DSM 21568 GCA_000380965.1 431596 431596 type True 77.5101 480 2931 95 below_threshold Paenibacillus puerhi strain=SJY2 GCA_009846885.1 2692622 2692622 type True 77.4824 303 2931 95 below_threshold Paenibacillus albicereus strain=UniB2 GCA_012676905.1 2726185 2726185 type True 77.3766 244 2931 95 below_threshold Paenibacillus mesophilus strain=SYSU K30004 GCA_005938385.1 2582849 2582849 type True 77.2246 338 2931 95 below_threshold Paenibacillus ginsengarvi strain=KCTC 13059 GCA_003626695.1 400777 400777 type True 77.0828 328 2931 95 below_threshold Paenibacillus cymbidii strain=R196 GCA_004764705.1 1639034 1639034 type True 77.0687 400 2931 95 below_threshold Paenibacillus germinis strain=LMG 31460 GCA_013141785.1 2654979 2654979 type True 76.9462 136 2931 95 below_threshold Paenibacillus contaminans strain=CKOBP-6 GCA_003285015.1 450362 450362 type True 76.9273 322 2931 95 below_threshold Paenibacillus caui strain=81-11 GCA_019904135.1 2873927 2873927 type True 76.8577 110 2931 95 below_threshold Paenibacillus rhizosphaerae strain=CECT 5831 GCA_014192015.1 297318 297318 type True 76.8539 196 2931 95 below_threshold Paenibacillus oceani strain=IB182363 GCA_014705615.1 2772510 2772510 type True 76.8249 284 2931 95 below_threshold Paenibacillus pasadenensis strain=DSM 19293 GCA_000422485.1 217090 217090 type True 76.7648 263 2931 95 below_threshold Paenibacillus pasadenensis strain=NBRC 101214 GCA_004001085.1 217090 217090 type True 76.7599 257 2931 95 below_threshold Paenibacillus timonensis strain=DSM 16943 GCA_022427145.1 225915 225915 type True 76.5641 155 2931 95 below_threshold Paenibacillus gorillae GCA_000513275.1 1243662 1243662 type True 76.3711 109 2931 95 below_threshold Paenibacillus humicus strain=NBRC 102415 GCA_004000905.1 412861 412861 type True 76.35 221 2931 95 below_threshold -------------------------------------------------------------------------------- [2024-01-24 11:59:53,753] [INFO] DFAST Taxonomy check result was written to GCF_023276405.1_ASM2327640v1_genomic.fna/tc_result.tsv [2024-01-24 11:59:53,754] [INFO] ===== Taxonomy check completed ===== [2024-01-24 11:59:53,754] [INFO] ===== Start completeness check using CheckM ===== [2024-01-24 11:59:53,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg233630fd-405f-4590-a241-d2b4d2a82280/dqc_reference/checkm_data [2024-01-24 11:59:53,756] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-24 11:59:53,836] [INFO] Task started: CheckM [2024-01-24 11:59:53,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023276405.1_ASM2327640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023276405.1_ASM2327640v1_genomic.fna/checkm_input GCF_023276405.1_ASM2327640v1_genomic.fna/checkm_result [2024-01-24 12:01:02,226] [INFO] Task succeeded: CheckM [2024-01-24 12:01:02,228] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 4.17% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-24 12:01:02,249] [INFO] ===== Completeness check finished ===== [2024-01-24 12:01:02,249] [INFO] ===== Start GTDB Search ===== [2024-01-24 12:01:02,250] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023276405.1_ASM2327640v1_genomic.fna/markers.fasta) [2024-01-24 12:01:02,250] [INFO] Task started: Blastn [2024-01-24 12:01:02,250] [INFO] Running command: blastn -query GCF_023276405.1_ASM2327640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg233630fd-405f-4590-a241-d2b4d2a82280/dqc_reference/reference_markers_gtdb.fasta -out GCF_023276405.1_ASM2327640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-24 12:01:03,046] [INFO] Task succeeded: Blastn [2024-01-24 12:01:03,049] [INFO] Selected 22 target genomes. [2024-01-24 12:01:03,049] [INFO] Target genome list was writen to GCF_023276405.1_ASM2327640v1_genomic.fna/target_genomes_gtdb.txt [2024-01-24 12:01:03,062] [INFO] Task started: fastANI [2024-01-24 12:01:03,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f28d0ce-a6a7-472a-bb62-38a4e1ec0fb4/GCF_023276405.1_ASM2327640v1_genomic.fna.gz --refList GCF_023276405.1_ASM2327640v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023276405.1_ASM2327640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-24 12:01:29,312] [INFO] Task succeeded: fastANI [2024-01-24 12:01:29,329] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius) [2024-01-24 12:01:29,329] [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_000829455.1 s__VKM-B-2647 sp000829455 78.6058 451 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__VKM-B-2647 95.0 N/A N/A N/A N/A 1 - GCF_003217775.1 s__Paenibacillus_AB flagellatus 78.3508 463 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB 95.0 N/A N/A N/A N/A 1 - GCF_018998565.1 s__Paenibacillus_G sp018998565 78.1974 423 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 N/A N/A N/A N/A 1 - GCF_004354045.1 s__Paenibacillus_S piri 78.0686 512 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_S 95.0 N/A N/A N/A N/A 1 - GCF_004000985.1 s__Paenibacillus_G validus 78.0648 327 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 99.29 99.15 0.90 0.89 6 - GCF_004307995.1 s__Paenibacillus_AF thalictri 78.0139 653 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AF 95.0 N/A N/A N/A N/A 1 - GCF_910594985.1 s__Paenibacillus_G sp910594985 77.8832 490 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 N/A N/A N/A N/A 1 - GCF_910593845.1 s__Paenibacillus_G solanacearum 77.8001 509 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 N/A N/A N/A N/A 1 - GCF_000250655.1 s__Paenibacillus_G mucilaginosus 77.7816 384 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 98.86 98.79 0.96 0.95 3 - GCF_001399685.1 s__Paenibacillus_G sp001399685 77.7368 411 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 N/A N/A N/A N/A 1 - GCF_900100345.1 s__Paenibacillus_G tianmuensis 77.6963 365 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 N/A N/A N/A N/A 1 - GCF_900101595.1 s__Paenibacillus_G sp900101595 77.6143 374 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G 95.0 100.00 100.00 0.99 0.99 2 - GCF_002243345.2 s__Paenibacillus_O sp002243345 77.5068 218 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O 95.0 99.98 99.98 0.98 0.98 4 - GCF_000380965.1 s__Paenibacillus_M ginsengihumi 77.5046 479 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_M 95.0 N/A N/A N/A N/A 1 - GCF_005938385.1 s__Paenibacillus_AB mesophilus 77.2253 339 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB 95.0 N/A N/A N/A N/A 1 - GCF_004764705.1 s__R196 sp004764705 77.0987 396 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__R196 95.0 95.77 95.77 0.86 0.86 2 - GCF_003626695.1 s__Paenibacillus_AB ginsengarvi 77.082 328 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_AB 95.0 N/A N/A N/A N/A 1 - GCF_014705655.1 s__Paenibacillus_C sp014705655 77.0336 306 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_C 95.0 N/A N/A N/A N/A 1 - GCF_003285015.1 s__Paenibacillus_V contaminans 76.9132 322 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_V 95.0 N/A N/A N/A N/A 1 - GCF_907165215.1 s__Thermobacillus xylanilyticus 76.8436 210 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Thermobacillus 95.0 97.85 97.19 0.88 0.86 4 - GCF_000422485.1 s__Paenibacillus_O pasadenensis 76.7647 263 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O 95.0 99.23 98.68 0.94 0.90 4 - GCF_004000905.1 s__Paenibacillus_O humicus 76.3581 220 2931 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_O 95.0 98.90 98.81 0.93 0.93 3 - -------------------------------------------------------------------------------- [2024-01-24 12:01:29,331] [INFO] GTDB search result was written to GCF_023276405.1_ASM2327640v1_genomic.fna/result_gtdb.tsv [2024-01-24 12:01:29,332] [INFO] ===== GTDB Search completed ===== [2024-01-24 12:01:29,336] [INFO] DFAST_QC result json was written to GCF_023276405.1_ASM2327640v1_genomic.fna/dqc_result.json [2024-01-24 12:01:29,336] [INFO] DFAST_QC completed! [2024-01-24 12:01:29,336] [INFO] Total running time: 0h2m33s