[2024-01-24 14:14:29,491] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:29,493] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:29,493] [INFO] DQC Reference Directory: /var/lib/cwl/stga16ffdd5-bb94-4bbd-9c19-ccad3e0fc73e/dqc_reference
[2024-01-24 14:14:32,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:32,427] [INFO] Task started: Prodigal
[2024-01-24 14:14:32,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg18fb4679-18e8-422a-80f2-6d968825a60d/GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/cds.fna -a GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:44,605] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:44,606] [INFO] Task started: HMMsearch
[2024-01-24 14:14:44,606] [INFO] Running command: hmmsearch --tblout GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga16ffdd5-bb94-4bbd-9c19-ccad3e0fc73e/dqc_reference/reference_markers.hmm GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:44,944] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:44,945] [INFO] Found 6/6 markers.
[2024-01-24 14:14:44,998] [INFO] Query marker FASTA was written to GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:14:44,999] [INFO] Task started: Blastn
[2024-01-24 14:14:44,999] [INFO] Running command: blastn -query GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga16ffdd5-bb94-4bbd-9c19-ccad3e0fc73e/dqc_reference/reference_markers.fasta -out GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:47,316] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:47,325] [INFO] Selected 27 target genomes.
[2024-01-24 14:14:47,326] [INFO] Target genome list was writen to GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:14:47,350] [INFO] Task started: fastANI
[2024-01-24 14:14:47,350] [INFO] Running command: fastANI --query /var/lib/cwl/stg18fb4679-18e8-422a-80f2-6d968825a60d/GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna.gz --refList GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:06,380] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:06,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga16ffdd5-bb94-4bbd-9c19-ccad3e0fc73e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:06,382] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga16ffdd5-bb94-4bbd-9c19-ccad3e0fc73e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:06,409] [INFO] Found 23 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:15:06,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:06,411] [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
Aliiroseovarius crassostreae	strain=DSM 16950	GCA_900116725.1	154981	154981	type	True	100.0	1165	1174	95	conclusive
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	99.9962	1171	1174	95	conclusive
Aliiroseovarius marinus	strain=A6024	GCA_004360145.1	2500159	2500159	type	True	79.7239	444	1174	95	below_threshold
Aliiroseovarius zhejiangensis	strain=KCTC 42443	GCA_014656375.1	1632025	1632025	type	True	79.4875	457	1174	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	79.4015	405	1174	95	below_threshold
Aliiroseovarius halocynthiae	strain=MA1-10	GCA_007004645.1	985055	985055	type	True	78.9398	401	1174	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.107	302	1174	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	78.091	268	1174	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	78.0413	265	1174	95	below_threshold
Phaeobacter piscinae	strain=P14	GCA_002407245.1	1580596	1580596	type	True	77.9744	290	1174	95	below_threshold
Tritonibacter mobilis	strain=DSM 23403	GCA_900106635.1	379347	379347	type	True	77.9045	241	1174	95	below_threshold
Tritonibacter mobilis	strain=NBRC101030	GCA_001681715.1	379347	379347	type	True	77.8203	245	1174	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.377	255	1174	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	77.3185	205	1174	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	77.2548	194	1174	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	77.2537	211	1174	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.24	188	1174	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.2159	266	1174	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	77.1888	212	1174	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	77.1098	169	1174	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	77.0735	190	1174	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	77.0349	189	1174	95	below_threshold
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	77.0319	192	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:06,413] [INFO] DFAST Taxonomy check result was written to GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:15:06,414] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:06,414] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:06,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga16ffdd5-bb94-4bbd-9c19-ccad3e0fc73e/dqc_reference/checkm_data
[2024-01-24 14:15:06,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:06,462] [INFO] Task started: CheckM
[2024-01-24 14:15:06,462] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/checkm_input GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:15:46,816] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:46,818] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:46,839] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:46,839] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:46,840] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:15:46,840] [INFO] Task started: Blastn
[2024-01-24 14:15:46,840] [INFO] Running command: blastn -query GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stga16ffdd5-bb94-4bbd-9c19-ccad3e0fc73e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:50,494] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:50,498] [INFO] Selected 20 target genomes.
[2024-01-24 14:15:50,498] [INFO] Target genome list was writen to GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:50,515] [INFO] Task started: fastANI
[2024-01-24 14:15:50,516] [INFO] Running command: fastANI --query /var/lib/cwl/stg18fb4679-18e8-422a-80f2-6d968825a60d/GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna.gz --refList GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:06,949] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:07,026] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:07,026] [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_001307765.1	s__Aliiroseovarius crassostreae	99.9962	1171	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	96.06	95.64	0.88	0.84	18	conclusive
GCF_004360145.1	s__Aliiroseovarius marinus	79.7239	444	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500215.1	s__Aliiroseovarius sp010500215	79.6737	448	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656375.1	s__Aliiroseovarius zhejiangensis	79.4765	458	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302485.1	s__Aliiroseovarius pelagivivens	79.4015	405	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002340515.1	s__Aliiroseovarius sp002340515	79.034	455	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004645.1	s__Aliiroseovarius halocynthiae	78.9511	400	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018599245.1	s__Aliiroseovarius lamellibrachiae	78.9256	482	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	78.107	302	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000511385.1	s__Phaeobacter gallaeciensis	78.091	268	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	99.42	98.01	0.98	0.96	8	-
GCF_000473325.1	s__Leisingera caerulea	78.0438	327	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407245.1	s__Phaeobacter piscinae	77.9743	290	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter	95.0	97.42	96.04	0.93	0.90	10	-
GCF_001681715.1	s__Epibacterium mobile	77.8073	246	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	97.01	96.41	0.91	0.87	56	-
GCA_002367285.1	s__Aliiroseovarius sp002367285	77.7649	299	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	77.4901	293	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_900172285.1	s__Roseovarius aestuarii	77.3373	202	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034995.1	s__Phaeovulum veldkampii	77.086	189	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	-
GCA_017854585.1	s__JAFMHK01 sp017854585	76.6439	129	1174	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAFMHK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:07,028] [INFO] GTDB search result was written to GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:07,029] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:07,035] [INFO] DFAST_QC result json was written to GCF_900116725.1_IMG-taxon_2619619030_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:16:07,036] [INFO] DFAST_QC completed!
[2024-01-24 14:16:07,036] [INFO] Total running time: 0h1m38s