[2024-01-24 13:57:13,475] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,478] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,479] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ec1ab76-6124-4ff8-ad5f-3e02e07cc2b0/dqc_reference
[2024-01-24 13:57:14,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,764] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,764] [INFO] Running command: gunzip -c /var/lib/cwl/stg67d8c5c2-d9a6-4c74-a381-3bf65eb03545/GCF_000012985.1_ASM1298v1_genomic.fna.gz | prodigal -d GCF_000012985.1_ASM1298v1_genomic.fna/cds.fna -a GCF_000012985.1_ASM1298v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:35,770] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:35,771] [INFO] Task started: HMMsearch
[2024-01-24 13:57:35,771] [INFO] Running command: hmmsearch --tblout GCF_000012985.1_ASM1298v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ec1ab76-6124-4ff8-ad5f-3e02e07cc2b0/dqc_reference/reference_markers.hmm GCF_000012985.1_ASM1298v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:36,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:36,129] [INFO] Found 6/6 markers.
[2024-01-24 13:57:36,184] [INFO] Query marker FASTA was written to GCF_000012985.1_ASM1298v1_genomic.fna/markers.fasta
[2024-01-24 13:57:36,185] [INFO] Task started: Blastn
[2024-01-24 13:57:36,185] [INFO] Running command: blastn -query GCF_000012985.1_ASM1298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ec1ab76-6124-4ff8-ad5f-3e02e07cc2b0/dqc_reference/reference_markers.fasta -out GCF_000012985.1_ASM1298v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:36,964] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:36,967] [INFO] Selected 27 target genomes.
[2024-01-24 13:57:36,968] [INFO] Target genome list was writen to GCF_000012985.1_ASM1298v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:36,978] [INFO] Task started: fastANI
[2024-01-24 13:57:36,978] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d8c5c2-d9a6-4c74-a381-3bf65eb03545/GCF_000012985.1_ASM1298v1_genomic.fna.gz --refList GCF_000012985.1_ASM1298v1_genomic.fna/target_genomes.txt --output GCF_000012985.1_ASM1298v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:57,451] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:57,452] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ec1ab76-6124-4ff8-ad5f-3e02e07cc2b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:57,452] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ec1ab76-6124-4ff8-ad5f-3e02e07cc2b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:57,472] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:57,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:57,472] [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
Hahella chejuensis	strain=KCTC 2396	GCA_000012985.1	158327	158327	type	True	100.0	2404	2405	95	conclusive
Marinobacter caseinilyticus	strain=M3-13	GCA_011074955.1	2692195	2692195	type	True	78.4084	59	2405	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	77.4655	93	2405	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	77.2998	72	2405	95	below_threshold
Marinobacter litoralis	strain=Sw-45	GCA_003336705.1	187981	187981	type	True	77.1473	59	2405	95	below_threshold
Hahella ganghwensis	strain=DSM 17046	GCA_000376785.1	286420	286420	type	True	77.0275	164	2405	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	76.8894	70	2405	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	76.8356	69	2405	95	below_threshold
Alcanivorax pacificus	strain=W11-5	GCA_000299335.2	1306787	1306787	type	True	76.789	62	2405	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	76.7252	70	2405	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	76.708	75	2405	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	76.6328	67	2405	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	76.6201	81	2405	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	76.6089	83	2405	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	76.4914	60	2405	95	below_threshold
Marinobacter segnicrescens	strain=CGMCC 1.6489	GCA_900111555.1	430453	430453	type	True	76.4497	70	2405	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	76.1912	81	2405	95	below_threshold
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	76.0566	59	2405	95	below_threshold
Marinobacter lipolyticus	strain=SM19	GCA_000397065.2	209639	209639	type	True	76.0486	78	2405	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	75.7955	54	2405	95	below_threshold
Pseudomonas cannabina	strain=ICMP 15200	GCA_001401375.1	86840	86840	pathovar	True	75.6165	57	2405	95	below_threshold
Pseudomonas defluvii	strain=WCHP16	GCA_001695625.1	1876757	1876757	type	True	75.4792	67	2405	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	75.4763	73	2405	95	below_threshold
Marinobacterium nitratireducens	strain=CGMCC 1.7286	GCA_014645375.1	518897	518897	type	True	75.4406	76	2405	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:57,474] [INFO] DFAST Taxonomy check result was written to GCF_000012985.1_ASM1298v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:57,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:57,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:57,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ec1ab76-6124-4ff8-ad5f-3e02e07cc2b0/dqc_reference/checkm_data
[2024-01-24 13:57:57,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:57,553] [INFO] Task started: CheckM
[2024-01-24 13:57:57,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000012985.1_ASM1298v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000012985.1_ASM1298v1_genomic.fna/checkm_input GCF_000012985.1_ASM1298v1_genomic.fna/checkm_result
[2024-01-24 13:59:04,356] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:04,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,383] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:04,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:04,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000012985.1_ASM1298v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:04,384] [INFO] Task started: Blastn
[2024-01-24 13:59:04,384] [INFO] Running command: blastn -query GCF_000012985.1_ASM1298v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ec1ab76-6124-4ff8-ad5f-3e02e07cc2b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000012985.1_ASM1298v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:05,642] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:05,646] [INFO] Selected 13 target genomes.
[2024-01-24 13:59:05,647] [INFO] Target genome list was writen to GCF_000012985.1_ASM1298v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:05,660] [INFO] Task started: fastANI
[2024-01-24 13:59:05,660] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d8c5c2-d9a6-4c74-a381-3bf65eb03545/GCF_000012985.1_ASM1298v1_genomic.fna.gz --refList GCF_000012985.1_ASM1298v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000012985.1_ASM1298v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:19,302] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:19,318] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:19,318] [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_000012985.1	s__Hahella chejuensis	100.0	2403	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Hahella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004135205.1	s__Hahella sp004135205	90.048	2043	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Hahella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018986435.1	s__Hahella sp018986435	89.5628	2046	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Hahella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007715.1	s__Marinobacter shengliensis	77.7634	95	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	-
GCF_003007675.1	s__Marinobacter fuscus	77.525	73	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002260525.1	s__Hahella sp002260525	77.3997	178	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Hahella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376785.1	s__Hahella ganghwensis	77.0406	163	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Hahella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744715.1	s__Marinobacter profundi	76.6089	83	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_900114155.1	s__Marinobacter persicus	76.4223	82	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_002717955.1	s__Marinobacter_A sp002717955	76.1674	60	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	99.94	99.88	0.97	0.95	4	-
GCF_000397065.2	s__Marinobacter lipolyticus	76.0668	79	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771435.1	s__Microbulbifer harenosus	75.7915	54	2405	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:19,320] [INFO] GTDB search result was written to GCF_000012985.1_ASM1298v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:19,321] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:19,325] [INFO] DFAST_QC result json was written to GCF_000012985.1_ASM1298v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:19,326] [INFO] DFAST_QC completed!
[2024-01-24 13:59:19,326] [INFO] Total running time: 0h2m6s