[2024-01-24 12:22:26,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:26,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:26,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg10b37898-e5bd-42fa-95db-b38f861f260b/dqc_reference
[2024-01-24 12:22:27,968] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:27,969] [INFO] Task started: Prodigal
[2024-01-24 12:22:27,969] [INFO] Running command: gunzip -c /var/lib/cwl/stg964f890e-6a1b-4e4f-af69-6d8293831e93/GCF_003194385.1_ASM319438v1_genomic.fna.gz | prodigal -d GCF_003194385.1_ASM319438v1_genomic.fna/cds.fna -a GCF_003194385.1_ASM319438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:44,164] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:44,165] [INFO] Task started: HMMsearch
[2024-01-24 12:22:44,165] [INFO] Running command: hmmsearch --tblout GCF_003194385.1_ASM319438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg10b37898-e5bd-42fa-95db-b38f861f260b/dqc_reference/reference_markers.hmm GCF_003194385.1_ASM319438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:44,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:44,511] [INFO] Found 6/6 markers.
[2024-01-24 12:22:44,564] [INFO] Query marker FASTA was written to GCF_003194385.1_ASM319438v1_genomic.fna/markers.fasta
[2024-01-24 12:22:44,565] [INFO] Task started: Blastn
[2024-01-24 12:22:44,565] [INFO] Running command: blastn -query GCF_003194385.1_ASM319438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10b37898-e5bd-42fa-95db-b38f861f260b/dqc_reference/reference_markers.fasta -out GCF_003194385.1_ASM319438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:45,234] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:45,237] [INFO] Selected 33 target genomes.
[2024-01-24 12:22:45,238] [INFO] Target genome list was writen to GCF_003194385.1_ASM319438v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:45,250] [INFO] Task started: fastANI
[2024-01-24 12:22:45,251] [INFO] Running command: fastANI --query /var/lib/cwl/stg964f890e-6a1b-4e4f-af69-6d8293831e93/GCF_003194385.1_ASM319438v1_genomic.fna.gz --refList GCF_003194385.1_ASM319438v1_genomic.fna/target_genomes.txt --output GCF_003194385.1_ASM319438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:13,844] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:13,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg10b37898-e5bd-42fa-95db-b38f861f260b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:13,845] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg10b37898-e5bd-42fa-95db-b38f861f260b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:13,866] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:13,866] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:13,866] [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
Pokkaliibacter plantistimulans	strain=L1E11	GCA_003194385.1	1635171	1635171	type	True	100.0	1814	1826	95	conclusive
Marinobacterium lutimaris	strain=DSM 22012	GCA_900108065.1	568106	568106	type	True	76.4916	145	1826	95	below_threshold
Marinobacterium mangrovicola	strain=DSM 27697	GCA_004339595.1	1476959	1476959	type	True	76.4859	126	1826	95	below_threshold
Nitrincola iocasae	strain=KXZD1103	GCA_008727795.1	2614693	2614693	type	True	76.4223	51	1826	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	76.3275	120	1826	95	below_threshold
Marinobacterium zhoushanense	strain=CGMCC 1.15341	GCA_014641945.1	1679163	1679163	type	True	76.3195	119	1826	95	below_threshold
Marinobacterium aestuarii	strain=ST58-10	GCA_001651805.1	1821621	1821621	type	True	76.3195	137	1826	95	below_threshold
Endozoicomonas montiporae	strain=CL-33	GCA_001583435.1	1027273	1027273	type	True	76.2542	50	1826	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	76.2179	55	1826	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	76.1904	56	1826	95	below_threshold
Amphritea atlantica	strain=DSM 18887	GCA_900111095.1	355243	355243	type	True	76.1739	58	1826	95	below_threshold
Endozoicomonas montiporae	strain=LMG 24815	GCA_000722565.1	1027273	1027273	type	True	76.1568	51	1826	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	76.1108	89	1826	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	76.1017	102	1826	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	76.0847	102	1826	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	76.0658	51	1826	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	76.0257	111	1826	95	below_threshold
Marinobacterium rhizophilum	strain=DSM 18822	GCA_000378045.1	420402	420402	type	True	75.9616	128	1826	95	below_threshold
Marinobacterium jannaschii	strain=DSM 6295	GCA_000620085.1	64970	64970	type	True	75.945	123	1826	95	below_threshold
Pseudomonas jessenii	strain=DSM 17150	GCA_002236115.1	77298	77298	suspected-type	True	75.9378	112	1826	95	below_threshold
Nitrincola lacisaponensis	strain=4CA	GCA_000691225.1	267850	267850	type	True	75.9324	75	1826	95	below_threshold
Amphritea pacifica	strain=ZJ14W	GCA_016924145.1	2811233	2811233	type	True	75.9245	68	1826	95	below_threshold
Pseudomonas caricapapayae	strain=ICMP2855	GCA_001400735.1	46678	46678	type	True	75.9199	86	1826	95	below_threshold
Pseudomonas caricapapayae	strain=CCUG 32775T	GCA_008692855.1	46678	46678	type	True	75.8965	86	1826	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	75.8608	85	1826	95	below_threshold
Pseudomonas typographi	strain=CA3A	GCA_014694385.1	2715964	2715964	type	True	75.7769	65	1826	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	75.7575	114	1826	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	75.7234	64	1826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:13,868] [INFO] DFAST Taxonomy check result was written to GCF_003194385.1_ASM319438v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:13,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:13,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:13,871] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg10b37898-e5bd-42fa-95db-b38f861f260b/dqc_reference/checkm_data
[2024-01-24 12:23:13,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:13,931] [INFO] Task started: CheckM
[2024-01-24 12:23:13,931] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003194385.1_ASM319438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003194385.1_ASM319438v1_genomic.fna/checkm_input GCF_003194385.1_ASM319438v1_genomic.fna/checkm_result
[2024-01-24 12:24:02,539] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:02,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:02,574] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:02,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:02,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003194385.1_ASM319438v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:02,576] [INFO] Task started: Blastn
[2024-01-24 12:24:02,576] [INFO] Running command: blastn -query GCF_003194385.1_ASM319438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg10b37898-e5bd-42fa-95db-b38f861f260b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003194385.1_ASM319438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:03,439] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:03,444] [INFO] Selected 30 target genomes.
[2024-01-24 12:24:03,444] [INFO] Target genome list was writen to GCF_003194385.1_ASM319438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:03,478] [INFO] Task started: fastANI
[2024-01-24 12:24:03,478] [INFO] Running command: fastANI --query /var/lib/cwl/stg964f890e-6a1b-4e4f-af69-6d8293831e93/GCF_003194385.1_ASM319438v1_genomic.fna.gz --refList GCF_003194385.1_ASM319438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003194385.1_ASM319438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:25,960] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:25,980] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:25,980] [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_003194385.1	s__Pokkaliibacter plantistimulans	100.0	1814	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Pokkaliibacter	95.0	95.60	95.60	0.88	0.88	2	conclusive
GCF_000619885.1	s__Balneatrix alpica	77.5932	194	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Balneatrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003250495.1	s__Marinobacterium sp003250495	76.5422	93	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013868415.1	s__Marinobacterium sp013868415	76.4303	87	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008727795.1	s__Nitrincola sp008727795	76.4223	51	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764495.1	s__Nitrincola sp000764495	76.377	58	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001651805.1	s__Marinobacterium_A aestuarii	76.3143	136	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641945.1	s__Marinobacterium zhoushanense	76.3094	118	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007685.1	s__Marinobacter halophilus	76.2624	53	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002744715.1	s__Marinobacter profundi	76.2274	69	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_014645375.1	s__Marinobacterium_A nitratireducens	76.2236	121	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019084545.1	s__Marinobacterium sp019084545	76.2202	139	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000219605.1	s__Pseudomonas_A stutzeri	76.0954	101	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	-
GCF_008795955.1	s__Marinobacter sp008795955	76.0868	50	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014842265.1	s__Pseudomonas_E sp014842265	76.0354	106	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001902145.1	s__Pseudomonas_E fluorescens_BV	76.0027	111	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.76	95.23	0.87	0.84	22	-
GCF_001655615.1	s__Pseudomonas_E sp001655615	75.9812	102	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.42	96.99	0.93	0.87	27	-
GCF_003935375.1	s__Pseudomonas_A xanthomarina_A	75.9781	92	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0614	97.25	97.14	0.91	0.88	14	-
GCF_013359695.1	s__Pseudomonas_E sp013359695	75.9761	109	1826	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_000378045.1	s__Marinobacterium_A rhizophilum	75.9532	127	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691225.1	s__Nitrincola lacisaponensis	75.9324	75	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Nitrincola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620085.1	s__Marinobacterium_B jannaschii	75.9322	122	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Marinobacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	75.8137	59	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014694385.1	s__Pseudomonas_E typographi	75.7888	64	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.61	99.56	0.95	0.95	3	-
GCF_016924235.1	s__Amphritea sp016924235	75.7519	69	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Nitrincolaceae;g__Amphritea	95.0	99.30	99.30	0.95	0.95	2	-
GCF_900114155.1	s__Marinobacter persicus	75.5126	54	1826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:25,982] [INFO] GTDB search result was written to GCF_003194385.1_ASM319438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:25,983] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:25,989] [INFO] DFAST_QC result json was written to GCF_003194385.1_ASM319438v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:25,989] [INFO] DFAST_QC completed!
[2024-01-24 12:24:25,989] [INFO] Total running time: 0h1m59s