[2024-01-24 11:13:04,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,595] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1e91e46-90e0-4a88-8bfe-327c43342ae8/dqc_reference
[2024-01-24 11:13:05,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,783] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,784] [INFO] Running command: gunzip -c /var/lib/cwl/stg337cf223-bc56-4d1d-85f3-38ac7061527f/GCF_016123485.1_ASM1612348v1_genomic.fna.gz | prodigal -d GCF_016123485.1_ASM1612348v1_genomic.fna/cds.fna -a GCF_016123485.1_ASM1612348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:17,066] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:17,067] [INFO] Task started: HMMsearch
[2024-01-24 11:13:17,067] [INFO] Running command: hmmsearch --tblout GCF_016123485.1_ASM1612348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1e91e46-90e0-4a88-8bfe-327c43342ae8/dqc_reference/reference_markers.hmm GCF_016123485.1_ASM1612348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:17,369] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:17,370] [INFO] Found 6/6 markers.
[2024-01-24 11:13:17,406] [INFO] Query marker FASTA was written to GCF_016123485.1_ASM1612348v1_genomic.fna/markers.fasta
[2024-01-24 11:13:17,406] [INFO] Task started: Blastn
[2024-01-24 11:13:17,406] [INFO] Running command: blastn -query GCF_016123485.1_ASM1612348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e91e46-90e0-4a88-8bfe-327c43342ae8/dqc_reference/reference_markers.fasta -out GCF_016123485.1_ASM1612348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:18,075] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:18,079] [INFO] Selected 31 target genomes.
[2024-01-24 11:13:18,080] [INFO] Target genome list was writen to GCF_016123485.1_ASM1612348v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:18,296] [INFO] Task started: fastANI
[2024-01-24 11:13:18,297] [INFO] Running command: fastANI --query /var/lib/cwl/stg337cf223-bc56-4d1d-85f3-38ac7061527f/GCF_016123485.1_ASM1612348v1_genomic.fna.gz --refList GCF_016123485.1_ASM1612348v1_genomic.fna/target_genomes.txt --output GCF_016123485.1_ASM1612348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:37,509] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:37,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1e91e46-90e0-4a88-8bfe-327c43342ae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:37,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1e91e46-90e0-4a88-8bfe-327c43342ae8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:37,536] [INFO] Found 31 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:13:37,536] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:13:37,537] [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
Cochlodiniinecator piscidefendens	strain=M26A2M	GCA_011326755.1	2715756	2715756	type	True	77.4943	161	1221	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	77.2976	127	1221	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	77.1974	146	1221	95	below_threshold
Thalassobius mediterraneus	strain=DSM 16398	GCA_900156595.1	340021	340021	type	True	77.1305	217	1221	95	below_threshold
Shimia marina	strain=DSM 26895	GCA_900112745.1	321267	321267	type	True	77.0124	208	1221	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	77.005	243	1221	95	below_threshold
Shimia marina	strain=CECT 7688	GCA_001458175.1	321267	321267	type	True	76.9969	208	1221	95	below_threshold
Shimia haliotis	strain=DSM 28453	GCA_900114415.1	1280847	1280847	type	True	76.9932	171	1221	95	below_threshold
Phaeobacter inhibens	strain=DSM 16374	GCA_000473105.1	221822	221822	type	True	76.9356	188	1221	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	76.8039	235	1221	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	76.7705	233	1221	95	below_threshold
Aliiroseovarius crassostreae	strain=CV919-312	GCA_001307765.1	154981	154981	type	True	76.6834	198	1221	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.6565	147	1221	95	below_threshold
Profundibacter amoris	strain=BAR1	GCA_003544895.1	2171755	2171755	type	True	76.641	211	1221	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	76.6334	116	1221	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	76.6235	174	1221	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	76.5949	191	1221	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	76.5869	194	1221	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.546	95	1221	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.4902	170	1221	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.4503	189	1221	95	below_threshold
Roseovarius aestuarii	strain=KCTC 22174	GCA_019966515.1	475083	475083	type	True	76.4337	138	1221	95	below_threshold
Litoreibacter roseus	strain=K6	GCA_009811795.1	2601869	2601869	type	True	76.4123	91	1221	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	76.4076	185	1221	95	below_threshold
Shimia isoporae	strain=DSM 26433	GCA_004346865.1	647720	647720	type	True	76.3418	125	1221	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	76.3337	98	1221	95	below_threshold
Aliiruegeria haliotis	strain=DSM 29328	GCA_003003255.1	1280846	1280846	type	True	76.1646	79	1221	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.0832	147	1221	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	76.0144	76	1221	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	75.8043	101	1221	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	75.7905	100	1221	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:37,539] [INFO] DFAST Taxonomy check result was written to GCF_016123485.1_ASM1612348v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:37,540] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:37,540] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:37,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1e91e46-90e0-4a88-8bfe-327c43342ae8/dqc_reference/checkm_data
[2024-01-24 11:13:37,541] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:37,578] [INFO] Task started: CheckM
[2024-01-24 11:13:37,578] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016123485.1_ASM1612348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016123485.1_ASM1612348v1_genomic.fna/checkm_input GCF_016123485.1_ASM1612348v1_genomic.fna/checkm_result
[2024-01-24 11:14:15,660] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:15,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:15,682] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:15,683] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:15,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016123485.1_ASM1612348v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:15,683] [INFO] Task started: Blastn
[2024-01-24 11:14:15,683] [INFO] Running command: blastn -query GCF_016123485.1_ASM1612348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1e91e46-90e0-4a88-8bfe-327c43342ae8/dqc_reference/reference_markers_gtdb.fasta -out GCF_016123485.1_ASM1612348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:16,646] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:16,651] [INFO] Selected 20 target genomes.
[2024-01-24 11:14:16,651] [INFO] Target genome list was writen to GCF_016123485.1_ASM1612348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:16,667] [INFO] Task started: fastANI
[2024-01-24 11:14:16,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg337cf223-bc56-4d1d-85f3-38ac7061527f/GCF_016123485.1_ASM1612348v1_genomic.fna.gz --refList GCF_016123485.1_ASM1612348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016123485.1_ASM1612348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:31,008] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:31,031] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:31,031] [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
GCA_016123485.1	s__Halocynthiibacter sp016123485	100.0	1221	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003031585.1	s__Halocynthiibacter sp003031585	94.306	1047	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000812685.1	s__Halocynthiibacter namhaensis	80.426	556	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326755.1	s__Halocynthiibacter sp011326755	77.4943	161	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Halocynthiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	77.0029	244	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001458175.1	s__Shimia marina	76.9966	209	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_900114415.1	s__Shimia haliotis	76.9931	171	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001294455.1	s__Pseudophaeobacter sp001294455	76.9665	200	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudophaeobacter	95.0	98.13	98.13	0.97	0.97	2	-
GCF_001458415.1	s__Epibacterium multivorans	76.8039	235	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_009496005.1	s__Epibacterium litoralis	76.7835	182	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003544895.1	s__Profundibacter amoris	76.6533	211	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Profundibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	76.5668	138	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.4902	170	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857745.1	s__Thalassobius mangrovi	76.4216	185	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888515.1	s__Shimia_A biformata	76.3858	163	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003255.1	s__Tropicimonas haliotis	76.1646	79	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tropicimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473225.1	s__Sedimentitalea nanhaiensis	76.114	133	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	76.0991	129	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCA_018500075.1	s__Lentibacter sp018500075	76.0589	96	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328815.1	s__UBA1943 sp013328815	75.8879	108	1221	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	97.27	97.27	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:31,033] [INFO] GTDB search result was written to GCF_016123485.1_ASM1612348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:31,034] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:31,042] [INFO] DFAST_QC result json was written to GCF_016123485.1_ASM1612348v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:31,042] [INFO] DFAST_QC completed!
[2024-01-24 11:14:31,042] [INFO] Total running time: 0h1m26s