[2024-01-25 18:06:35,495] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,500] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,500] [INFO] DQC Reference Directory: /var/lib/cwl/stgaad01990-68f9-40c2-bbc9-7ccd1d675066/dqc_reference
[2024-01-25 18:06:36,650] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,651] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,651] [INFO] Running command: gunzip -c /var/lib/cwl/stg770e33e7-32a7-4a07-9c68-de26b8bf78de/GCF_002019705.1_ASM201970v1_genomic.fna.gz | prodigal -d GCF_002019705.1_ASM201970v1_genomic.fna/cds.fna -a GCF_002019705.1_ASM201970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:45,921] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:45,921] [INFO] Task started: HMMsearch
[2024-01-25 18:06:45,921] [INFO] Running command: hmmsearch --tblout GCF_002019705.1_ASM201970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaad01990-68f9-40c2-bbc9-7ccd1d675066/dqc_reference/reference_markers.hmm GCF_002019705.1_ASM201970v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:46,165] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:46,166] [INFO] Found 6/6 markers.
[2024-01-25 18:06:46,206] [INFO] Query marker FASTA was written to GCF_002019705.1_ASM201970v1_genomic.fna/markers.fasta
[2024-01-25 18:06:46,206] [INFO] Task started: Blastn
[2024-01-25 18:06:46,206] [INFO] Running command: blastn -query GCF_002019705.1_ASM201970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad01990-68f9-40c2-bbc9-7ccd1d675066/dqc_reference/reference_markers.fasta -out GCF_002019705.1_ASM201970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:46,737] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:46,740] [INFO] Selected 19 target genomes.
[2024-01-25 18:06:46,740] [INFO] Target genome list was writen to GCF_002019705.1_ASM201970v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:46,771] [INFO] Task started: fastANI
[2024-01-25 18:06:46,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg770e33e7-32a7-4a07-9c68-de26b8bf78de/GCF_002019705.1_ASM201970v1_genomic.fna.gz --refList GCF_002019705.1_ASM201970v1_genomic.fna/target_genomes.txt --output GCF_002019705.1_ASM201970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:59,705] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:59,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaad01990-68f9-40c2-bbc9-7ccd1d675066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:59,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaad01990-68f9-40c2-bbc9-7ccd1d675066/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:59,714] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:06:59,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:59,714] [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
Alkalihalobacillus patagoniensis	strain=DSM 16117	GCA_002019705.1	228576	228576	type	True	100.0	1545	1547	95	conclusive
Bacillus alkalicellulosilyticus	strain=FJAT-44921	GCA_002019795.1	1912214	1912214	type	True	79.1494	69	1547	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	79.0706	56	1547	95	below_threshold
Alkalihalobacillus clausii	strain=DSM 8716	GCA_002250115.1	79880	79880	suspected-type	True	78.9204	180	1547	95	below_threshold
Alkalihalobacillus xiaoxiensis	strain=DSM 21943	GCA_016907895.1	766895	766895	type	True	78.9172	328	1547	95	below_threshold
Halalkalibacterium halodurans	strain=DSM 497	GCA_004376175.1	86665	86665	type	True	78.5023	58	1547	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	76.906	66	1547	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.6945	77	1547	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.6683	78	1547	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:59,716] [INFO] DFAST Taxonomy check result was written to GCF_002019705.1_ASM201970v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:59,717] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:59,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:59,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaad01990-68f9-40c2-bbc9-7ccd1d675066/dqc_reference/checkm_data
[2024-01-25 18:06:59,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:59,764] [INFO] Task started: CheckM
[2024-01-25 18:06:59,764] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002019705.1_ASM201970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002019705.1_ASM201970v1_genomic.fna/checkm_input GCF_002019705.1_ASM201970v1_genomic.fna/checkm_result
[2024-01-25 18:07:30,313] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:30,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:30,331] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:30,331] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:30,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002019705.1_ASM201970v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:30,332] [INFO] Task started: Blastn
[2024-01-25 18:07:30,332] [INFO] Running command: blastn -query GCF_002019705.1_ASM201970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaad01990-68f9-40c2-bbc9-7ccd1d675066/dqc_reference/reference_markers_gtdb.fasta -out GCF_002019705.1_ASM201970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:31,084] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:31,087] [INFO] Selected 19 target genomes.
[2024-01-25 18:07:31,087] [INFO] Target genome list was writen to GCF_002019705.1_ASM201970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:31,109] [INFO] Task started: fastANI
[2024-01-25 18:07:31,109] [INFO] Running command: fastANI --query /var/lib/cwl/stg770e33e7-32a7-4a07-9c68-de26b8bf78de/GCF_002019705.1_ASM201970v1_genomic.fna.gz --refList GCF_002019705.1_ASM201970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002019705.1_ASM201970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:46,362] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:46,369] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:46,370] [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_002019705.1	s__Bacillus_H patagoniensis	100.0	1546	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001310375.1	s__Bacillus_H sp001310375	88.4437	1182	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019765.1	s__Bacillus_H oshimensis	79.2278	244	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	98.95	98.65	0.95	0.93	6	-
GCF_002797395.1	s__45385 sp002797395	79.2244	85	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019795.1	s__Bacillus_AO alkalicellulosilyticus	79.1336	70	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002250115.1	s__Bacillus_H clausii	79.0258	182	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.4953	98.66	98.17	0.95	0.92	12	-
GCF_002335805.1	s__FJAT-45350 sp002335805	78.991	62	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907895.1	s__Bacillus_H xiaoxiensis	78.9216	329	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	97.73	97.69	0.93	0.93	4	-
GCF_007725405.1	s__Bacillus_H miscanthi	78.7447	236	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.10	99.10	0.94	0.93	3	-
GCF_015234585.1	s__Anaerobacillus_A hwajinpoensis_B	78.2011	56	1547	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_000513135.1	s__Bacillus_L akibai	76.6647	77	1547	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:46,371] [INFO] GTDB search result was written to GCF_002019705.1_ASM201970v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:46,371] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:46,374] [INFO] DFAST_QC result json was written to GCF_002019705.1_ASM201970v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:46,374] [INFO] DFAST_QC completed!
[2024-01-25 18:07:46,374] [INFO] Total running time: 0h1m11s