[2023-06-07 20:25:29,944] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:25:29,946] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:25:29,946] [INFO] DQC Reference Directory: /var/lib/cwl/stge2c8aef0-47f7-4f48-9aeb-a7913f88164f/dqc_reference
[2023-06-07 20:25:31,445] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:25:31,446] [INFO] Task started: Prodigal
[2023-06-07 20:25:31,447] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbc00547-2d49-4dc3-a78f-dd51dd103594/GCA_902826065.1_RBC084_genomic.fna.gz | prodigal -d GCA_902826065.1_RBC084_genomic.fna/cds.fna -a GCA_902826065.1_RBC084_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:25:46,083] [INFO] Task succeeded: Prodigal
[2023-06-07 20:25:46,084] [INFO] Task started: HMMsearch
[2023-06-07 20:25:46,084] [INFO] Running command: hmmsearch --tblout GCA_902826065.1_RBC084_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2c8aef0-47f7-4f48-9aeb-a7913f88164f/dqc_reference/reference_markers.hmm GCA_902826065.1_RBC084_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:25:46,443] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:25:46,444] [INFO] Found 6/6 markers.
[2023-06-07 20:25:46,493] [INFO] Query marker FASTA was written to GCA_902826065.1_RBC084_genomic.fna/markers.fasta
[2023-06-07 20:25:46,494] [INFO] Task started: Blastn
[2023-06-07 20:25:46,494] [INFO] Running command: blastn -query GCA_902826065.1_RBC084_genomic.fna/markers.fasta -db /var/lib/cwl/stge2c8aef0-47f7-4f48-9aeb-a7913f88164f/dqc_reference/reference_markers.fasta -out GCA_902826065.1_RBC084_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:25:47,220] [INFO] Task succeeded: Blastn
[2023-06-07 20:25:47,224] [INFO] Selected 34 target genomes.
[2023-06-07 20:25:47,224] [INFO] Target genome list was writen to GCA_902826065.1_RBC084_genomic.fna/target_genomes.txt
[2023-06-07 20:25:47,263] [INFO] Task started: fastANI
[2023-06-07 20:25:47,263] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc00547-2d49-4dc3-a78f-dd51dd103594/GCA_902826065.1_RBC084_genomic.fna.gz --refList GCA_902826065.1_RBC084_genomic.fna/target_genomes.txt --output GCA_902826065.1_RBC084_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:26:12,363] [INFO] Task succeeded: fastANI
[2023-06-07 20:26:12,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2c8aef0-47f7-4f48-9aeb-a7913f88164f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:26:12,365] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2c8aef0-47f7-4f48-9aeb-a7913f88164f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:26:12,392] [INFO] Found 32 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:26:12,392] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:26:12,392] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	76.2601	319	1667	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	75.0659	148	1667	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	75.0554	151	1667	95	below_threshold
Corallococcus silvisoli	strain=c25j21	GCA_009909145.1	2697031	2697031	type	True	75.0478	181	1667	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	75.0008	142	1667	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	74.9928	161	1667	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004343305.1	634155	634155	type	True	74.9731	103	1667	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	74.9575	219	1667	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	74.9557	131	1667	95	below_threshold
Corallococcus soli	strain=ZKHCc1 1396	GCA_014930455.1	2710757	2710757	type	True	74.9533	180	1667	95	below_threshold
Microbacterium telephonicum	strain=S2T63	GCA_003651225.1	1714841	1714841	type	True	74.949	155	1667	95	below_threshold
Pseudofulvimonas gallinarii	strain=DSM 21944	GCA_004798975.1	634155	634155	type	True	74.9433	104	1667	95	below_threshold
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	74.9305	143	1667	95	below_threshold
Xanthobacter tagetidis	strain=ATCC 700314	GCA_003667445.1	60216	60216	type	True	74.896	173	1667	95	below_threshold
Xanthobacter tagetidis	strain=DSM 11105	GCA_014206845.1	60216	60216	type	True	74.8953	174	1667	95	below_threshold
Actinacidiphila alni	strain=CGMCC 4.3510	GCA_900112845.1	380248	380248	type	True	74.8762	245	1667	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	74.8499	187	1667	95	below_threshold
Gordonia hirsuta	strain=DSM 44140	GCA_000420685.1	53427	53427	type	True	74.8278	85	1667	95	below_threshold
Gordonia hirsuta	strain=NBRC 16056	GCA_000333015.1	53427	53427	type	True	74.8278	85	1667	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	74.8178	149	1667	95	below_threshold
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	74.8155	248	1667	95	below_threshold
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	74.8104	285	1667	95	below_threshold
Agrococcus jenensis	strain=DSM 9580	GCA_003752465.1	46353	46353	type	True	74.804	182	1667	95	below_threshold
Mucisphaera calidilacus	strain=Pan265	GCA_007748075.1	2527982	2527982	type	True	74.7929	50	1667	95	below_threshold
Gordonia hankookensis	strain=ON-33	GCA_014673215.1	589403	589403	type	True	74.7891	94	1667	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	74.7646	191	1667	95	below_threshold
Kocuria palustris	strain=TAGA27	GCA_016907795.1	71999	71999	type	True	74.7421	86	1667	95	below_threshold
Methylocella silvestris	strain=BL2	GCA_000021745.1	199596	199596	type	True	74.7298	78	1667	95	below_threshold
Thiocapsa roseopersicina	strain=DSM 217	GCA_900106925.1	1058	1058	type	True	74.7291	67	1667	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.7262	266	1667	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	74.7163	214	1667	95	below_threshold
Mycolicibacterium neoaurum	strain=DSM 44074	GCA_005670605.1	1795	1795	type	True	74.7024	97	1667	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:26:12,394] [INFO] DFAST Taxonomy check result was written to GCA_902826065.1_RBC084_genomic.fna/tc_result.tsv
[2023-06-07 20:26:12,395] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:26:12,395] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:26:12,395] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2c8aef0-47f7-4f48-9aeb-a7913f88164f/dqc_reference/checkm_data
[2023-06-07 20:26:12,396] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:26:12,453] [INFO] Task started: CheckM
[2023-06-07 20:26:12,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902826065.1_RBC084_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902826065.1_RBC084_genomic.fna/checkm_input GCA_902826065.1_RBC084_genomic.fna/checkm_result
[2023-06-07 20:26:59,761] [INFO] Task succeeded: CheckM
[2023-06-07 20:26:59,763] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:26:59,789] [INFO] ===== Completeness check finished =====
[2023-06-07 20:26:59,789] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:26:59,789] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902826065.1_RBC084_genomic.fna/markers.fasta)
[2023-06-07 20:26:59,790] [INFO] Task started: Blastn
[2023-06-07 20:26:59,790] [INFO] Running command: blastn -query GCA_902826065.1_RBC084_genomic.fna/markers.fasta -db /var/lib/cwl/stge2c8aef0-47f7-4f48-9aeb-a7913f88164f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902826065.1_RBC084_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:27:00,886] [INFO] Task succeeded: Blastn
[2023-06-07 20:27:00,892] [INFO] Selected 19 target genomes.
[2023-06-07 20:27:00,892] [INFO] Target genome list was writen to GCA_902826065.1_RBC084_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:27:01,000] [INFO] Task started: fastANI
[2023-06-07 20:27:01,000] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbc00547-2d49-4dc3-a78f-dd51dd103594/GCA_902826065.1_RBC084_genomic.fna.gz --refList GCA_902826065.1_RBC084_genomic.fna/target_genomes_gtdb.txt --output GCA_902826065.1_RBC084_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:27:18,886] [INFO] Task succeeded: fastANI
[2023-06-07 20:27:18,907] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:27:18,907] [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
GCA_902826065.1	s__CADEFD01 sp902826065	100.0	1648	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902826515.1	s__CADEFD01 sp902826515	81.5207	975	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789705.1	s__CADEFD01 sp016789705	81.3519	958	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018000455.1	s__CADEFD01 sp018000455	80.414	873	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__CADEFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694735.1	s__12-FULL-67-14b sp009694735	77.5481	293	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737365.1	s__12-FULL-67-14b sp002737365	77.5348	312	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	97.27	96.58	0.83	0.80	6	-
GCA_001768615.1	s__12-FULL-67-14b sp001768615	77.4571	472	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016871275.1	s__12-FULL-67-14b sp016871275	77.3841	386	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__12-FULL-67-14b	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268955.1	s__WHSN01 sp018268955	76.6444	267	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902825985.1	s__WHSN01 sp902825985	76.5662	389	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813075.1	s__JACCSI01 sp013813075	76.1568	128	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__JACCSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826465.1	s__WHSN01 sp902826465	76.1311	210	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__WHSN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003222535.1	s__Gp6-AA45 sp003222535	76.1174	333	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA45	95.0	99.30	99.28	0.90	0.90	3	-
GCA_016210845.1	s__Gp6-AA40 sp016210845	76.0744	237	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__UBA2999;g__Gp6-AA40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377605.1	s__WHTT01 sp009377605	75.3349	137	1667	d__Bacteria;p__Acidobacteriota;c__Vicinamibacteria;o__Vicinamibacterales;f__Vicinamibacteraceae;g__WHTT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408145.1	s__Nocardioides marinus	74.8522	188	1667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCF_003949795.1	s__Streptomyces sp003949795	74.8194	223	1667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001008345.1	s__Streptomyces showdoensis	74.7694	232	1667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003268675.1	s__Streptomyces bacillaris	74.7124	189	1667	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.84	95.80	0.88	0.83	37	-
--------------------------------------------------------------------------------
[2023-06-07 20:27:18,909] [INFO] GTDB search result was written to GCA_902826065.1_RBC084_genomic.fna/result_gtdb.tsv
[2023-06-07 20:27:18,910] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:27:18,914] [INFO] DFAST_QC result json was written to GCA_902826065.1_RBC084_genomic.fna/dqc_result.json
[2023-06-07 20:27:18,915] [INFO] DFAST_QC completed!
[2023-06-07 20:27:18,915] [INFO] Total running time: 0h1m49s