[2024-01-24 15:19:04,472] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,474] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg09cf3a11-36b6-47ef-a5e3-7df39311eaa5/dqc_reference
[2024-01-24 15:19:05,700] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,701] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,701] [INFO] Running command: gunzip -c /var/lib/cwl/stgf7c0a1d0-79f6-4618-97b6-a7d02217c29b/GCF_005747095.1_ASM574709v1_genomic.fna.gz | prodigal -d GCF_005747095.1_ASM574709v1_genomic.fna/cds.fna -a GCF_005747095.1_ASM574709v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:16,037] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:16,038] [INFO] Task started: HMMsearch
[2024-01-24 15:19:16,038] [INFO] Running command: hmmsearch --tblout GCF_005747095.1_ASM574709v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09cf3a11-36b6-47ef-a5e3-7df39311eaa5/dqc_reference/reference_markers.hmm GCF_005747095.1_ASM574709v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:16,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:16,336] [INFO] Found 6/6 markers.
[2024-01-24 15:19:16,381] [INFO] Query marker FASTA was written to GCF_005747095.1_ASM574709v1_genomic.fna/markers.fasta
[2024-01-24 15:19:16,382] [INFO] Task started: Blastn
[2024-01-24 15:19:16,382] [INFO] Running command: blastn -query GCF_005747095.1_ASM574709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09cf3a11-36b6-47ef-a5e3-7df39311eaa5/dqc_reference/reference_markers.fasta -out GCF_005747095.1_ASM574709v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:16,997] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:17,000] [INFO] Selected 28 target genomes.
[2024-01-24 15:19:17,001] [INFO] Target genome list was writen to GCF_005747095.1_ASM574709v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:17,090] [INFO] Task started: fastANI
[2024-01-24 15:19:17,091] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7c0a1d0-79f6-4618-97b6-a7d02217c29b/GCF_005747095.1_ASM574709v1_genomic.fna.gz --refList GCF_005747095.1_ASM574709v1_genomic.fna/target_genomes.txt --output GCF_005747095.1_ASM574709v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:34,968] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:34,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09cf3a11-36b6-47ef-a5e3-7df39311eaa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:34,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09cf3a11-36b6-47ef-a5e3-7df39311eaa5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:34,977] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:34,977] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:34,977] [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
Pseudalkalibacillus caeni	strain=HB172195	GCA_005747095.1	2574798	2574798	type	True	100.0	1542	1544	95	conclusive
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	76.756	52	1544	95	below_threshold
Metabacillus idriensis	strain=DSM 19097	GCA_009674765.1	324768	324768	type	True	76.5207	55	1544	95	below_threshold
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	76.5146	56	1544	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.429	51	1544	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	76.0444	56	1544	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	75.9609	51	1544	95	below_threshold
Sutcliffiella cohnii	strain=NBRC 15565	GCA_001591425.1	33932	33932	type	True	75.7364	54	1544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:34,979] [INFO] DFAST Taxonomy check result was written to GCF_005747095.1_ASM574709v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:34,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:34,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:34,979] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09cf3a11-36b6-47ef-a5e3-7df39311eaa5/dqc_reference/checkm_data
[2024-01-24 15:19:34,981] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:35,028] [INFO] Task started: CheckM
[2024-01-24 15:19:35,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005747095.1_ASM574709v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005747095.1_ASM574709v1_genomic.fna/checkm_input GCF_005747095.1_ASM574709v1_genomic.fna/checkm_result
[2024-01-24 15:20:09,679] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:09,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:09,701] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:09,702] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:09,702] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005747095.1_ASM574709v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:09,702] [INFO] Task started: Blastn
[2024-01-24 15:20:09,703] [INFO] Running command: blastn -query GCF_005747095.1_ASM574709v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09cf3a11-36b6-47ef-a5e3-7df39311eaa5/dqc_reference/reference_markers_gtdb.fasta -out GCF_005747095.1_ASM574709v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:10,489] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:10,618] [INFO] Selected 26 target genomes.
[2024-01-24 15:20:10,618] [INFO] Target genome list was writen to GCF_005747095.1_ASM574709v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:10,657] [INFO] Task started: fastANI
[2024-01-24 15:20:10,658] [INFO] Running command: fastANI --query /var/lib/cwl/stgf7c0a1d0-79f6-4618-97b6-a7d02217c29b/GCF_005747095.1_ASM574709v1_genomic.fna.gz --refList GCF_005747095.1_ASM574709v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005747095.1_ASM574709v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:30,338] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:30,350] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:30,350] [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_005747095.1	s__Bacillus_BR caeni	100.0	1542	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Bacillus_BR	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017303315.1	s__Anaerobacillus_A sp017303315	76.8499	102	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144865.1	s__Anaerobacillus_A hwajinpoensis_A	76.8269	111	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	76.7142	50	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995155.1	s__Cytobacillus dafuensis	76.6138	52	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_003400205.1	s__Fredinandcohnia sp003400205	76.5941	52	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014635025.1	s__Fictibacillus barbaricus	76.5121	57	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018613315.1	s__Mesobacillus sp018613315	76.4173	50	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Mesobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636345.1	s__Cytobacillus gottheilii	76.2214	57	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	96.50	95.11	0.87	0.87	3	-
GCF_001884135.1	s__Bacillus_A nitratireducens	76.2013	50	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	98.14	95.62	0.90	0.85	78	-
GCF_002250055.1	s__Sutcliffiella cohnii	76.0978	57	1544	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella	95.0	100.00	100.00	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:30,352] [INFO] GTDB search result was written to GCF_005747095.1_ASM574709v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:30,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:30,356] [INFO] DFAST_QC result json was written to GCF_005747095.1_ASM574709v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:30,356] [INFO] DFAST_QC completed!
[2024-01-24 15:20:30,356] [INFO] Total running time: 0h1m26s