[2024-01-24 13:13:03,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:03,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:03,056] [INFO] DQC Reference Directory: /var/lib/cwl/stgcde8eca8-f8e9-478b-9f2d-754907cd5fdb/dqc_reference
[2024-01-24 13:13:04,239] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:04,240] [INFO] Task started: Prodigal
[2024-01-24 13:13:04,240] [INFO] Running command: gunzip -c /var/lib/cwl/stgfed46bb2-02e9-47b7-87e1-92ca5041831a/GCF_004358675.1_ASM435867v1_genomic.fna.gz | prodigal -d GCF_004358675.1_ASM435867v1_genomic.fna/cds.fna -a GCF_004358675.1_ASM435867v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:18,601] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:18,602] [INFO] Task started: HMMsearch
[2024-01-24 13:13:18,602] [INFO] Running command: hmmsearch --tblout GCF_004358675.1_ASM435867v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcde8eca8-f8e9-478b-9f2d-754907cd5fdb/dqc_reference/reference_markers.hmm GCF_004358675.1_ASM435867v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:18,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:18,878] [INFO] Found 6/6 markers.
[2024-01-24 13:13:18,923] [INFO] Query marker FASTA was written to GCF_004358675.1_ASM435867v1_genomic.fna/markers.fasta
[2024-01-24 13:13:18,923] [INFO] Task started: Blastn
[2024-01-24 13:13:18,923] [INFO] Running command: blastn -query GCF_004358675.1_ASM435867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde8eca8-f8e9-478b-9f2d-754907cd5fdb/dqc_reference/reference_markers.fasta -out GCF_004358675.1_ASM435867v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:19,701] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:19,704] [INFO] Selected 34 target genomes.
[2024-01-24 13:13:19,705] [INFO] Target genome list was writen to GCF_004358675.1_ASM435867v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:19,814] [INFO] Task started: fastANI
[2024-01-24 13:13:19,815] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed46bb2-02e9-47b7-87e1-92ca5041831a/GCF_004358675.1_ASM435867v1_genomic.fna.gz --refList GCF_004358675.1_ASM435867v1_genomic.fna/target_genomes.txt --output GCF_004358675.1_ASM435867v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:40,789] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:40,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcde8eca8-f8e9-478b-9f2d-754907cd5fdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:40,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcde8eca8-f8e9-478b-9f2d-754907cd5fdb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:40,813] [INFO] Found 34 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:40,813] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:40,814] [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
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	78.9252	160	1346	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.3926	206	1346	95	below_threshold
Pseudooceanicola nitratireducens	strain=DSM 29619	GCA_900112545.1	517719	517719	type	True	78.3063	180	1346	95	below_threshold
Pseudooceanicola nitratireducens	strain=CGMCC 1.7292	GCA_900109195.1	517719	517719	type	True	78.2833	181	1346	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1827	207	1346	95	below_threshold
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	78.0328	159	1346	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	77.9721	139	1346	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.8826	181	1346	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	77.841	184	1346	95	below_threshold
Phaeobacter italicus	strain=DSM 26436	GCA_900113345.1	481446	481446	type	True	77.7492	140	1346	95	below_threshold
Marivita geojedonensis	strain=DSM 29432	GCA_003002975.1	1123756	1123756	type	True	77.739	176	1346	95	below_threshold
Marivita geojedonensis	strain=DPG-138	GCA_002115805.1	1123756	1123756	type	True	77.7217	171	1346	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001404195.1	481446	481446	type	True	77.7199	136	1346	95	below_threshold
Phaeobacter italicus	strain=CECT 7645	GCA_001258055.1	481446	481446	type	True	77.7199	136	1346	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	77.592	177	1346	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.5153	173	1346	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	77.3273	152	1346	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	77.2265	119	1346	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	77.1879	152	1346	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	77.1872	121	1346	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.1294	169	1346	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.0756	173	1346	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.0119	167	1346	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.8872	161	1346	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	76.8488	104	1346	95	below_threshold
Chachezhania sediminis	strain=CAU 1508	GCA_009765275.1	2599291	2599291	type	True	76.8328	145	1346	95	below_threshold
Aliiroseovarius pelagivivens	strain=CECT 8811	GCA_900302485.1	1639690	1639690	type	True	76.8063	130	1346	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	76.7182	162	1346	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.7172	154	1346	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.651	141	1346	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	76.5305	139	1346	95	below_threshold
Pseudophaeobacter leonis	strain=306	GCA_002087335.1	1144477	1144477	type	True	76.5041	102	1346	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.3791	74	1346	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	76.3156	106	1346	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:40,816] [INFO] DFAST Taxonomy check result was written to GCF_004358675.1_ASM435867v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:40,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:40,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:40,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcde8eca8-f8e9-478b-9f2d-754907cd5fdb/dqc_reference/checkm_data
[2024-01-24 13:13:40,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:40,858] [INFO] Task started: CheckM
[2024-01-24 13:13:40,858] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004358675.1_ASM435867v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004358675.1_ASM435867v1_genomic.fna/checkm_input GCF_004358675.1_ASM435867v1_genomic.fna/checkm_result
[2024-01-24 13:14:25,691] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:25,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:25,715] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:25,715] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:25,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004358675.1_ASM435867v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:25,716] [INFO] Task started: Blastn
[2024-01-24 13:14:25,716] [INFO] Running command: blastn -query GCF_004358675.1_ASM435867v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcde8eca8-f8e9-478b-9f2d-754907cd5fdb/dqc_reference/reference_markers_gtdb.fasta -out GCF_004358675.1_ASM435867v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:27,173] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:27,177] [INFO] Selected 19 target genomes.
[2024-01-24 13:14:27,177] [INFO] Target genome list was writen to GCF_004358675.1_ASM435867v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:27,295] [INFO] Task started: fastANI
[2024-01-24 13:14:27,295] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed46bb2-02e9-47b7-87e1-92ca5041831a/GCF_004358675.1_ASM435867v1_genomic.fna.gz --refList GCF_004358675.1_ASM435867v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004358675.1_ASM435867v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:43,500] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:43,520] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:43,521] [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_004358675.1	s__Fluviibacterium aquatile	100.0	1335	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	98.47	98.47	0.90	0.90	2	conclusive
GCA_003172915.1	s__Fluviibacterium sp003172915	78.6709	482	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.5626	183	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003254465.1	s__Fluviibacterium sp003254465	78.0919	349	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518015.1	s__Epibacterium horizontis	78.0589	166	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014901205.1	s__Fluviibacterium sp014901205	77.8935	270	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fluviibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	77.8635	184	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003646465.1	s__Chachezhania antarctica	77.7914	172	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Chachezhania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115805.1	s__Marivita geojedonensis	77.6973	173	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.6139	195	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_004803475.1	s__Aliishimia ponticola	77.5105	174	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188425.1	s__Antarctobacter heliothermus	77.2745	173	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarctobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003697785.1	s__Paracoccus alkanivorans	76.9238	116	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.8828	128	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176475.1	s__Tropicibacter naphthalenivorans	76.7672	176	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicibacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013184745.1	s__Mangrovicoccus sp013184745	76.6906	170	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016938875.1	s__Rhodovulum sp016938875	76.5153	169	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007735.2	s__Paracoccus marinus_A	76.2615	129	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156835.1	s__Paracoccus saliphilus	76.1631	104	1346	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:43,522] [INFO] GTDB search result was written to GCF_004358675.1_ASM435867v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:43,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:43,529] [INFO] DFAST_QC result json was written to GCF_004358675.1_ASM435867v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:43,529] [INFO] DFAST_QC completed!
[2024-01-24 13:14:43,529] [INFO] Total running time: 0h1m40s