[2024-01-25 19:07:05,810] [INFO] DFAST_QC pipeline started. [2024-01-25 19:07:05,812] [INFO] DFAST_QC version: 0.5.7 [2024-01-25 19:07:05,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg2660355a-c3a8-4d08-b98c-8967484ceda8/dqc_reference [2024-01-25 19:07:06,950] [INFO] ===== Start taxonomy check using ANI ===== [2024-01-25 19:07:06,951] [INFO] Task started: Prodigal [2024-01-25 19:07:06,951] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eb6a189-7185-4a6b-bc8d-2a00a709e279/GCF_013359945.1_ASM1335994v1_genomic.fna.gz | prodigal -d GCF_013359945.1_ASM1335994v1_genomic.fna/cds.fna -a GCF_013359945.1_ASM1335994v1_genomic.fna/protein.faa -g 11 -q > /dev/null [2024-01-25 19:07:21,108] [INFO] Task succeeded: Prodigal [2024-01-25 19:07:21,109] [INFO] Task started: HMMsearch [2024-01-25 19:07:21,109] [INFO] Running command: hmmsearch --tblout GCF_013359945.1_ASM1335994v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2660355a-c3a8-4d08-b98c-8967484ceda8/dqc_reference/reference_markers.hmm GCF_013359945.1_ASM1335994v1_genomic.fna/protein.faa > /dev/null [2024-01-25 19:07:21,535] [INFO] Task succeeded: HMMsearch [2024-01-25 19:07:21,536] [INFO] Found 6/6 markers. [2024-01-25 19:07:21,586] [INFO] Query marker FASTA was written to GCF_013359945.1_ASM1335994v1_genomic.fna/markers.fasta [2024-01-25 19:07:21,586] [INFO] Task started: Blastn [2024-01-25 19:07:21,586] [INFO] Running command: blastn -query GCF_013359945.1_ASM1335994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2660355a-c3a8-4d08-b98c-8967484ceda8/dqc_reference/reference_markers.fasta -out GCF_013359945.1_ASM1335994v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:07:22,160] [INFO] Task succeeded: Blastn [2024-01-25 19:07:22,164] [INFO] Selected 20 target genomes. [2024-01-25 19:07:22,164] [INFO] Target genome list was writen to GCF_013359945.1_ASM1335994v1_genomic.fna/target_genomes.txt [2024-01-25 19:07:22,184] [INFO] Task started: fastANI [2024-01-25 19:07:22,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb6a189-7185-4a6b-bc8d-2a00a709e279/GCF_013359945.1_ASM1335994v1_genomic.fna.gz --refList GCF_013359945.1_ASM1335994v1_genomic.fna/target_genomes.txt --output GCF_013359945.1_ASM1335994v1_genomic.fna/fastani_result.tsv --threads 1 [2024-01-25 19:07:45,913] [INFO] Task succeeded: fastANI [2024-01-25 19:07:45,913] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2660355a-c3a8-4d08-b98c-8967484ceda8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt [2024-01-25 19:07:45,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2660355a-c3a8-4d08-b98c-8967484ceda8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt] [2024-01-25 19:07:45,926] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold) [2024-01-25 19:07:45,926] [INFO] The taxonomy check result is classified as 'conclusive'. [2024-01-25 19:07:45,926] [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 agri strain=JW14 GCA_013359945.1 2744309 2744309 type True 100.0 2068 2077 95 conclusive Paenibacillus ihuae strain=GD6 GCA_001368795.1 1232431 1232431 type True 79.5032 592 2077 95 below_threshold Paenibacillus odorifer strain=DSM 15391 GCA_000758725.1 189426 189426 type True 79.4737 608 2077 95 below_threshold Paenibacillus tianjinensis strain=TB2019 GCA_017086365.1 2810347 2810347 type True 79.4474 593 2077 95 below_threshold Paenibacillus phytohabitans strain=LMG 31459 GCA_013141775.1 2654978 2654978 type True 79.4353 675 2077 95 below_threshold Paenibacillus riograndensis GCA_000981585.1 483937 483937 type True 79.4286 645 2077 95 below_threshold Paenibacillus jilunlii strain=CGMCC 1.10239 GCA_900102965.1 682956 682956 type True 79.4249 632 2077 95 below_threshold Paenibacillus etheri strain=SH7 GCA_001012825.2 1306852 1306852 type True 79.4241 584 2077 95 below_threshold Paenibacillus sonchi strain=X19-5 GCA_000316285.1 373687 373687 type True 79.3911 531 2077 95 below_threshold Paenibacillus riograndensis strain=SBR5 GCA_000224945.2 483937 483937 type True 79.349 493 2077 95 below_threshold Paenibacillus jilunlii strain=DSM 23019 GCA_001546055.1 682956 682956 type True 79.3346 626 2077 95 below_threshold Paenibacillus sonchi strain=LMG 24727 GCA_016772475.1 373687 373687 type True 79.3334 624 2077 95 below_threshold Paenibacillus borealis strain=DSM 13188 GCA_000758665.1 160799 160799 type True 79.3149 655 2077 95 below_threshold Paenibacillus silagei strain=DSM 101953 GCA_017874735.1 1670801 1670801 type True 79.1351 579 2077 95 below_threshold Paenibacillus piscarius strain=P121 GCA_022234545.1 1089681 1089681 type True 79.101 547 2077 95 below_threshold Paenibacillus tritici strain=LMG 29502 GCA_013204885.1 1873425 1873425 type True 79.0075 606 2077 95 below_threshold Paenibacillus tengchongensis strain=SYSU G01003 GCA_008973665.1 2608684 2608684 type True 78.5145 489 2077 95 below_threshold Paenibacillus sinensis strain=HN-1 GCA_019904155.1 2834413 2834413 type True 77.7943 344 2077 95 below_threshold Paenibacillus yonginensis strain=DCY84 GCA_001685395.1 1462996 1462996 type True 77.0137 143 2077 95 below_threshold Paenibacillus pinistramenti strain=ASL46 GCA_005869875.1 1768003 1768003 type True 76.9184 140 2077 95 below_threshold -------------------------------------------------------------------------------- [2024-01-25 19:07:45,928] [INFO] DFAST Taxonomy check result was written to GCF_013359945.1_ASM1335994v1_genomic.fna/tc_result.tsv [2024-01-25 19:07:45,929] [INFO] ===== Taxonomy check completed ===== [2024-01-25 19:07:45,929] [INFO] ===== Start completeness check using CheckM ===== [2024-01-25 19:07:45,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2660355a-c3a8-4d08-b98c-8967484ceda8/dqc_reference/checkm_data [2024-01-25 19:07:45,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM [2024-01-25 19:07:45,990] [INFO] Task started: CheckM [2024-01-25 19:07:45,991] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013359945.1_ASM1335994v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013359945.1_ASM1335994v1_genomic.fna/checkm_input GCF_013359945.1_ASM1335994v1_genomic.fna/checkm_result [2024-01-25 19:08:28,409] [INFO] Task succeeded: CheckM [2024-01-25 19:08:28,411] [INFO] Completeness check finished. -------------------------------------------------------------------------------- Completeness: 100.00% Contamintation: 0.38% Strain heterogeneity: 0.00% -------------------------------------------------------------------------------- [2024-01-25 19:08:28,433] [INFO] ===== Completeness check finished ===== [2024-01-25 19:08:28,433] [INFO] ===== Start GTDB Search ===== [2024-01-25 19:08:28,434] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013359945.1_ASM1335994v1_genomic.fna/markers.fasta) [2024-01-25 19:08:28,434] [INFO] Task started: Blastn [2024-01-25 19:08:28,435] [INFO] Running command: blastn -query GCF_013359945.1_ASM1335994v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2660355a-c3a8-4d08-b98c-8967484ceda8/dqc_reference/reference_markers_gtdb.fasta -out GCF_013359945.1_ASM1335994v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5 [2024-01-25 19:08:29,268] [INFO] Task succeeded: Blastn [2024-01-25 19:08:29,271] [INFO] Selected 24 target genomes. [2024-01-25 19:08:29,271] [INFO] Target genome list was writen to GCF_013359945.1_ASM1335994v1_genomic.fna/target_genomes_gtdb.txt [2024-01-25 19:08:29,294] [INFO] Task started: fastANI [2024-01-25 19:08:29,295] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eb6a189-7185-4a6b-bc8d-2a00a709e279/GCF_013359945.1_ASM1335994v1_genomic.fna.gz --refList GCF_013359945.1_ASM1335994v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013359945.1_ASM1335994v1_genomic.fna/fastani_result_gtdb.tsv --threads 1 [2024-01-25 19:09:02,330] [INFO] Task succeeded: fastANI [2024-01-25 19:09:02,344] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius) [2024-01-25 19:09:02,345] [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_013359945.1 s__Paenibacillus sp013359945 100.0 2068 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 conclusive GCF_001682855.1 s__Paenibacillus sp001682855 93.892 1817 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_014644435.1 s__Paenibacillus albidus 79.8492 658 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 96.34 96.34 0.80 0.80 2 - GCF_000758525.1 s__Paenibacillus sp000758525 79.5438 662 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 97.46 97.46 0.89 0.89 2 - GCF_000374185.1 s__Paenibacillus sp000374185 79.5361 613 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_001368795.1 s__Paenibacillus ihuae 79.5227 588 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 100.00 100.00 1.00 1.00 2 - GCF_017086365.1 s__Paenibacillus sp017086365 79.4501 594 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_000981585.1 s__Paenibacillus riograndensis 79.4343 644 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 96.4356 97.36 97.36 0.91 0.91 2 - GCF_900102965.1 s__Paenibacillus jilunlii 79.4162 633 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 99.98 99.98 1.00 0.99 3 - GCF_002264395.1 s__Paenibacillus sp002264395 79.3907 565 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 98.86 98.86 0.89 0.89 2 - GCF_016772475.1 s__Paenibacillus sonchi 79.3497 624 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 96.4356 99.97 99.97 1.00 1.00 2 - GCF_001909055.1 s__Paenibacillus helianthi 79.3251 622 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 97.61 95.31 0.90 0.83 4 - GCF_000758665.1 s__Paenibacillus borealis 79.318 653 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_000758705.1 s__Paenibacillus graminis 79.3086 628 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 100.00 100.00 1.00 1.00 2 - GCF_000758605.1 s__Paenibacillus sp000758605 79.2151 637 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_001955925.1 s__Paenibacillus sp001955925 79.1995 564 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 98.91 98.91 0.92 0.92 2 - GCF_017874735.1 s__Paenibacillus silagei 79.1411 577 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 96.84 96.20 0.88 0.87 3 - GCA_002438345.1 s__Paenibacillus sp002438345 79.0923 519 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_017874765.1 s__Paenibacillus rhizoplanae 79.0463 576 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_013204885.1 s__Paenibacillus tritici 79.0075 606 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 98.22 98.22 0.93 0.93 2 - GCF_008973665.1 s__Paenibacillus tengchongensis 78.5103 489 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 N/A N/A N/A N/A 1 - GCF_001685395.1 s__Paenibacillus_A yonginensis 77.0137 143 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_A 95.0 N/A N/A N/A N/A 1 - GCF_002272015.1 s__Paenibacillus campinasensis 76.3299 156 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus 95.0 99.23 99.19 0.91 0.90 3 - GCF_019091135.1 s__Cohnella sp019091135 75.879 69 2077 d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Cohnella 95.0 N/A N/A N/A N/A 1 - -------------------------------------------------------------------------------- [2024-01-25 19:09:02,347] [INFO] GTDB search result was written to GCF_013359945.1_ASM1335994v1_genomic.fna/result_gtdb.tsv [2024-01-25 19:09:02,347] [INFO] ===== GTDB Search completed ===== [2024-01-25 19:09:02,351] [INFO] DFAST_QC result json was written to GCF_013359945.1_ASM1335994v1_genomic.fna/dqc_result.json [2024-01-25 19:09:02,351] [INFO] DFAST_QC completed! [2024-01-25 19:09:02,351] [INFO] Total running time: 0h1m57s