[2024-01-24 14:06:03,015] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:03,017] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:03,017] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a7c2a5-ab21-42af-a2c8-23b492d9211d/dqc_reference
[2024-01-24 14:06:04,236] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:04,237] [INFO] Task started: Prodigal
[2024-01-24 14:06:04,237] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d66c8ba-5187-4af8-81a9-f24fd56a0106/GCF_007995215.1_ASM799521v1_genomic.fna.gz | prodigal -d GCF_007995215.1_ASM799521v1_genomic.fna/cds.fna -a GCF_007995215.1_ASM799521v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:16,734] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:16,735] [INFO] Task started: HMMsearch
[2024-01-24 14:06:16,735] [INFO] Running command: hmmsearch --tblout GCF_007995215.1_ASM799521v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a7c2a5-ab21-42af-a2c8-23b492d9211d/dqc_reference/reference_markers.hmm GCF_007995215.1_ASM799521v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:17,038] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:17,039] [INFO] Found 6/6 markers.
[2024-01-24 14:06:17,073] [INFO] Query marker FASTA was written to GCF_007995215.1_ASM799521v1_genomic.fna/markers.fasta
[2024-01-24 14:06:17,074] [INFO] Task started: Blastn
[2024-01-24 14:06:17,074] [INFO] Running command: blastn -query GCF_007995215.1_ASM799521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a7c2a5-ab21-42af-a2c8-23b492d9211d/dqc_reference/reference_markers.fasta -out GCF_007995215.1_ASM799521v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:17,921] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:17,924] [INFO] Selected 30 target genomes.
[2024-01-24 14:06:17,924] [INFO] Target genome list was writen to GCF_007995215.1_ASM799521v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:17,967] [INFO] Task started: fastANI
[2024-01-24 14:06:17,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d66c8ba-5187-4af8-81a9-f24fd56a0106/GCF_007995215.1_ASM799521v1_genomic.fna.gz --refList GCF_007995215.1_ASM799521v1_genomic.fna/target_genomes.txt --output GCF_007995215.1_ASM799521v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:38,668] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:38,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59a7c2a5-ab21-42af-a2c8-23b492d9211d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:38,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59a7c2a5-ab21-42af-a2c8-23b492d9211d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:38,690] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:38,690] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:38,690] [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
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	77.4419	199	1256	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.4356	232	1256	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	77.409	252	1256	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.3725	243	1256	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.3635	237	1256	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.3475	230	1256	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	77.3329	223	1256	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.3304	216	1256	95	below_threshold
Ruegeria profundi	strain=ZGT108	GCA_001507545.1	1685378	1685378	type	True	77.3207	182	1256	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	77.3096	239	1256	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	77.3037	225	1256	95	below_threshold
Litoreibacter roseus	strain=K6	GCA_009811795.1	2601869	2601869	type	True	77.3024	138	1256	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.2955	228	1256	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.2779	219	1256	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.1605	217	1256	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	77.16	184	1256	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.0778	217	1256	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	77.0627	213	1256	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.0604	178	1256	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	76.9989	165	1256	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	76.9648	199	1256	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.9601	155	1256	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.9555	170	1256	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.8689	201	1256	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.8507	118	1256	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.8052	220	1256	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.6239	161	1256	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	76.573	135	1256	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	76.5078	117	1256	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.4933	164	1256	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:38,693] [INFO] DFAST Taxonomy check result was written to GCF_007995215.1_ASM799521v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:38,693] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:38,694] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:38,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a7c2a5-ab21-42af-a2c8-23b492d9211d/dqc_reference/checkm_data
[2024-01-24 14:06:38,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:38,731] [INFO] Task started: CheckM
[2024-01-24 14:06:38,732] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007995215.1_ASM799521v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007995215.1_ASM799521v1_genomic.fna/checkm_input GCF_007995215.1_ASM799521v1_genomic.fna/checkm_result
[2024-01-24 14:07:20,300] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:20,302] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:20,321] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:20,321] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:20,322] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007995215.1_ASM799521v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:20,323] [INFO] Task started: Blastn
[2024-01-24 14:07:20,323] [INFO] Running command: blastn -query GCF_007995215.1_ASM799521v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a7c2a5-ab21-42af-a2c8-23b492d9211d/dqc_reference/reference_markers_gtdb.fasta -out GCF_007995215.1_ASM799521v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:21,810] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:21,816] [INFO] Selected 28 target genomes.
[2024-01-24 14:07:21,816] [INFO] Target genome list was writen to GCF_007995215.1_ASM799521v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:21,857] [INFO] Task started: fastANI
[2024-01-24 14:07:21,857] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d66c8ba-5187-4af8-81a9-f24fd56a0106/GCF_007995215.1_ASM799521v1_genomic.fna.gz --refList GCF_007995215.1_ASM799521v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007995215.1_ASM799521v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:41,706] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:41,731] [INFO] Found 28 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:41,731] [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_007995215.1	s__WX04 sp007995215	100.0	1256	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__WX04	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001205715.1	s__Pseudaestuariivita atlantica	77.8756	275	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudaestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743995.1	s__Ruegeria sp017743995	77.6392	209	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	77.4917	256	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	77.4735	195	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000814005.1	s__Ruegeria sp000814005	77.4457	186	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219815.1	s__Thalassobius aquimarinus	77.4293	199	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129345.1	s__Ruegeria intermedia	77.4113	250	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	77.4052	233	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184945.1	s__Maliponia aquimaris	77.3391	204	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maliponia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032505.1	s__Ruegeria atlantica_F	77.31	195	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363615.1	s__Ruegeria sp009363615	77.2821	214	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	97.20	96.03	0.88	0.85	16	-
GCF_004803475.1	s__Aliishimia ponticola	77.2798	217	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799325.1	s__Thalassobius vesicularis	77.206	213	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	77.1745	182	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342065.1	s__Primorskyibacter sedentarius	77.1528	215	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008555.2	s__Pukyongiella litopenaei	77.1262	206	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pukyongiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010500245.1	s__Ruegeria_B sp010500245	77.1256	207	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363715.1	s__Roseovarius sp009363715	77.1208	204	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	77.0999	187	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768315.1	s__Pseudooceanicola atlanticus	77.0905	211	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.92	0.92	2	-
GCF_005938225.1	s__Arenibacterium halophilum	77.0216	229	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Arenibacterium	95.0	96.35	96.35	0.87	0.87	2	-
GCA_013215215.1	s__Cognatishimia sp013215215	76.99	176	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cognatishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	76.9777	216	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214715.1	s__JABSSB01 sp013214715	76.902	179	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JABSSB01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	76.7857	220	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018279165.1	s__Falsirhodobacter sp018279165	76.5573	118	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Falsirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013093415.1	s__Halovulum dunhuangense	76.5078	117	1256	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halovulum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:41,733] [INFO] GTDB search result was written to GCF_007995215.1_ASM799521v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:41,733] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:41,739] [INFO] DFAST_QC result json was written to GCF_007995215.1_ASM799521v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:41,739] [INFO] DFAST_QC completed!
[2024-01-24 14:07:41,739] [INFO] Total running time: 0h1m39s