[2024-01-24 12:07:04,350] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:07:04,354] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:07:04,355] [INFO] DQC Reference Directory: /var/lib/cwl/stge68991f9-d386-447c-acc6-94d19978968c/dqc_reference
[2024-01-24 12:07:05,646] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:07:05,647] [INFO] Task started: Prodigal
[2024-01-24 12:07:05,647] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fbd3da0-f3dd-4288-ada3-baf48652ba6c/GCF_002514725.1_ASM251472v1_genomic.fna.gz | prodigal -d GCF_002514725.1_ASM251472v1_genomic.fna/cds.fna -a GCF_002514725.1_ASM251472v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:18,512] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:18,513] [INFO] Task started: HMMsearch
[2024-01-24 12:07:18,513] [INFO] Running command: hmmsearch --tblout GCF_002514725.1_ASM251472v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge68991f9-d386-447c-acc6-94d19978968c/dqc_reference/reference_markers.hmm GCF_002514725.1_ASM251472v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:18,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:18,876] [INFO] Found 6/6 markers.
[2024-01-24 12:07:18,920] [INFO] Query marker FASTA was written to GCF_002514725.1_ASM251472v1_genomic.fna/markers.fasta
[2024-01-24 12:07:18,920] [INFO] Task started: Blastn
[2024-01-24 12:07:18,921] [INFO] Running command: blastn -query GCF_002514725.1_ASM251472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68991f9-d386-447c-acc6-94d19978968c/dqc_reference/reference_markers.fasta -out GCF_002514725.1_ASM251472v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:19,765] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:19,770] [INFO] Selected 24 target genomes.
[2024-01-24 12:07:19,770] [INFO] Target genome list was writen to GCF_002514725.1_ASM251472v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:19,780] [INFO] Task started: fastANI
[2024-01-24 12:07:19,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fbd3da0-f3dd-4288-ada3-baf48652ba6c/GCF_002514725.1_ASM251472v1_genomic.fna.gz --refList GCF_002514725.1_ASM251472v1_genomic.fna/target_genomes.txt --output GCF_002514725.1_ASM251472v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:35,171] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge68991f9-d386-447c-acc6-94d19978968c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:35,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge68991f9-d386-447c-acc6-94d19978968c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:35,190] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:35,191] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:35,191] [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
Mangrovitalea sediminis	strain=M11-4	GCA_002514725.1	1982043	1982043	type	True	100.0	1456	1458	95	conclusive
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	77.506	228	1458	95	below_threshold
Marinobacter nanhaiticus	strain=D15-8W	GCA_000364845.1	1305740	1305740	type	True	77.4305	186	1458	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	77.3794	224	1458	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	77.3775	173	1458	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	77.2692	187	1458	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	77.1936	149	1458	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	77.1809	244	1458	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	77.171	150	1458	95	below_threshold
Marinobacter zhejiangensis	strain=CGMCC 1.7061	GCA_900114775.1	488535	488535	type	True	77.1319	145	1458	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	77.1191	143	1458	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	77.1151	159	1458	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	77.1087	144	1458	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	77.0968	190	1458	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	77.0585	149	1458	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	76.9467	147	1458	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	76.4666	57	1458	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	76.4119	58	1458	95	below_threshold
Serpens gallinarum	strain=Sa2CUA2	GCA_014836765.1	2763075	2763075	type	True	76.1545	70	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,193] [INFO] DFAST Taxonomy check result was written to GCF_002514725.1_ASM251472v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:35,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:35,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:35,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge68991f9-d386-447c-acc6-94d19978968c/dqc_reference/checkm_data
[2024-01-24 12:07:35,194] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:35,238] [INFO] Task started: CheckM
[2024-01-24 12:07:35,238] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002514725.1_ASM251472v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002514725.1_ASM251472v1_genomic.fna/checkm_input GCF_002514725.1_ASM251472v1_genomic.fna/checkm_result
[2024-01-24 12:08:15,841] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:15,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:15,867] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:15,867] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:15,868] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002514725.1_ASM251472v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:15,868] [INFO] Task started: Blastn
[2024-01-24 12:08:15,868] [INFO] Running command: blastn -query GCF_002514725.1_ASM251472v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68991f9-d386-447c-acc6-94d19978968c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002514725.1_ASM251472v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:17,197] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:17,201] [INFO] Selected 20 target genomes.
[2024-01-24 12:08:17,201] [INFO] Target genome list was writen to GCF_002514725.1_ASM251472v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:17,218] [INFO] Task started: fastANI
[2024-01-24 12:08:17,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fbd3da0-f3dd-4288-ada3-baf48652ba6c/GCF_002514725.1_ASM251472v1_genomic.fna.gz --refList GCF_002514725.1_ASM251472v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002514725.1_ASM251472v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:32,842] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:32,862] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:32,862] [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_002514725.1	s__Mangrovitalea sediminis	100.0	1456	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Mangrovitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003315345.1	s__Marinobacter pelagius_A	77.4722	169	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	77.3677	224	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_900114925.1	s__Marinobacter pelagius	77.3584	175	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005298175.1	s__Marinobacter sp005298175	77.2641	158	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003789045.1	s__Marinobacter_A sp003789045	77.2062	231	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	77.2033	242	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235625.1	s__Marinobacter manganoxydans_A	77.1735	147	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.5877	97.20	96.90	0.83	0.80	5	-
GCF_018424605.1	s__Marinobacter lipolyticus_B	77.158	182	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002933295.1	s__Marinobacter flavimaris	77.1184	143	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	97.80	96.90	0.89	0.83	14	-
GCF_000347775.1	s__Marinobacter santoriniensis	77.1137	160	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001045555.1	s__Marinobacter subterrani	77.1033	192	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.05	97.05	0.84	0.84	2	-
GCF_002934325.1	s__Marinobacter persicus_A	77.1018	146	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_017301335.1	s__Marinobacter sp017301335	77.0662	147	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859525.1	s__Marinobacter sp014859525	77.0173	105	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792665.1	s__Marinobacter orientalis	76.9467	147	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900099645.1	s__Pseudomonas_E peli	76.3844	60	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	76.312	98	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016565.1	s__Pseudomonas_E mendocina_A	76.1996	116	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.76	97.37	0.90	0.88	7	-
GCF_005938625.1	s__Pseudomonas_E fluorescens_BD	75.6061	78	1458	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:32,864] [INFO] GTDB search result was written to GCF_002514725.1_ASM251472v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:32,864] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:32,868] [INFO] DFAST_QC result json was written to GCF_002514725.1_ASM251472v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:32,868] [INFO] DFAST_QC completed!
[2024-01-24 12:08:32,869] [INFO] Total running time: 0h1m29s