[2024-01-25 18:11:35,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:11:35,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:11:35,647] [INFO] DQC Reference Directory: /var/lib/cwl/stgecfa9f2c-d3b2-4d55-9c41-f006778ed328/dqc_reference
[2024-01-25 18:11:36,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:11:36,803] [INFO] Task started: Prodigal
[2024-01-25 18:11:36,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg597df29f-2d72-466a-adfc-fdc961cbf5a9/GCF_003337495.1_ASM333749v1_genomic.fna.gz | prodigal -d GCF_003337495.1_ASM333749v1_genomic.fna/cds.fna -a GCF_003337495.1_ASM333749v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:11:51,327] [INFO] Task succeeded: Prodigal
[2024-01-25 18:11:51,327] [INFO] Task started: HMMsearch
[2024-01-25 18:11:51,327] [INFO] Running command: hmmsearch --tblout GCF_003337495.1_ASM333749v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecfa9f2c-d3b2-4d55-9c41-f006778ed328/dqc_reference/reference_markers.hmm GCF_003337495.1_ASM333749v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:11:51,595] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:11:51,596] [INFO] Found 6/6 markers.
[2024-01-25 18:11:51,637] [INFO] Query marker FASTA was written to GCF_003337495.1_ASM333749v1_genomic.fna/markers.fasta
[2024-01-25 18:11:51,638] [INFO] Task started: Blastn
[2024-01-25 18:11:51,638] [INFO] Running command: blastn -query GCF_003337495.1_ASM333749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecfa9f2c-d3b2-4d55-9c41-f006778ed328/dqc_reference/reference_markers.fasta -out GCF_003337495.1_ASM333749v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:52,357] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:52,360] [INFO] Selected 21 target genomes.
[2024-01-25 18:11:52,360] [INFO] Target genome list was writen to GCF_003337495.1_ASM333749v1_genomic.fna/target_genomes.txt
[2024-01-25 18:11:52,371] [INFO] Task started: fastANI
[2024-01-25 18:11:52,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg597df29f-2d72-466a-adfc-fdc961cbf5a9/GCF_003337495.1_ASM333749v1_genomic.fna.gz --refList GCF_003337495.1_ASM333749v1_genomic.fna/target_genomes.txt --output GCF_003337495.1_ASM333749v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:08,450] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:08,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecfa9f2c-d3b2-4d55-9c41-f006778ed328/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:08,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecfa9f2c-d3b2-4d55-9c41-f006778ed328/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:08,463] [INFO] Found 21 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:12:08,464] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:08,464] [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
Yoonia sediminilitoris	strain=CECT 8284	GCA_003337495.1	1286148	1286148	type	True	100.0	1530	1531	95	conclusive
Yoonia sediminilitoris	strain=DSM 29955	GCA_003058085.1	1286148	1286148	type	True	99.9994	1529	1531	95	conclusive
Yoonia rosea	strain=DSM 29591	GCA_900156505.1	287098	287098	type	True	78.2841	394	1531	95	below_threshold
Yoonia vestfoldensis	strain=DSM 16212	GCA_000382265.1	245188	245188	type	True	78.1247	406	1531	95	below_threshold
Yoonia maricola	strain=DSM 29128	GCA_002797915.1	420999	420999	type	True	77.8981	370	1531	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	77.8027	357	1531	95	below_threshold
Yoonia litorea	strain=DSM 29433	GCA_900114675.1	1123755	1123755	type	True	77.6577	286	1531	95	below_threshold
Loktanella salsilacus	strain=DSM 16199	GCA_900114485.1	195913	195913	type	True	77.0186	251	1531	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.8059	203	1531	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.784	158	1531	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.7466	208	1531	95	below_threshold
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	76.7007	135	1531	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	76.6752	174	1531	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.5657	184	1531	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	76.5471	123	1531	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	76.5274	160	1531	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	76.4357	141	1531	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.2986	153	1531	95	below_threshold
Mameliella sediminis	strain=DP3N28-2	GCA_019218285.1	2836866	2836866	type	True	76.226	192	1531	95	below_threshold
Marivivens niveibacter	strain=MCCC 1A06712	GCA_002150005.2	1930667	1930667	type	True	76.202	126	1531	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	75.8075	111	1531	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:08,465] [INFO] DFAST Taxonomy check result was written to GCF_003337495.1_ASM333749v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:08,465] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:08,466] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:08,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecfa9f2c-d3b2-4d55-9c41-f006778ed328/dqc_reference/checkm_data
[2024-01-25 18:12:08,467] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:08,512] [INFO] Task started: CheckM
[2024-01-25 18:12:08,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003337495.1_ASM333749v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003337495.1_ASM333749v1_genomic.fna/checkm_input GCF_003337495.1_ASM333749v1_genomic.fna/checkm_result
[2024-01-25 18:12:53,594] [INFO] Task succeeded: CheckM
[2024-01-25 18:12:53,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:12:53,624] [INFO] ===== Completeness check finished =====
[2024-01-25 18:12:53,624] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:12:53,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003337495.1_ASM333749v1_genomic.fna/markers.fasta)
[2024-01-25 18:12:53,625] [INFO] Task started: Blastn
[2024-01-25 18:12:53,625] [INFO] Running command: blastn -query GCF_003337495.1_ASM333749v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecfa9f2c-d3b2-4d55-9c41-f006778ed328/dqc_reference/reference_markers_gtdb.fasta -out GCF_003337495.1_ASM333749v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:54,939] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:54,942] [INFO] Selected 19 target genomes.
[2024-01-25 18:12:54,942] [INFO] Target genome list was writen to GCF_003337495.1_ASM333749v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:12:54,959] [INFO] Task started: fastANI
[2024-01-25 18:12:54,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg597df29f-2d72-466a-adfc-fdc961cbf5a9/GCF_003337495.1_ASM333749v1_genomic.fna.gz --refList GCF_003337495.1_ASM333749v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003337495.1_ASM333749v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:09,131] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:09,142] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:09,143] [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_003058085.1	s__Yoonia sediminilitoris	99.9994	1529	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003201935.1	s__Yoonia sp003201935	78.28	428	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156505.1	s__Yoonia rosea	78.2709	396	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	96.70	96.70	0.95	0.95	2	-
GCA_014859355.1	s__Yoonia sp014859355	78.15	383	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001419985.1	s__Yoonia sp001419985	78.1327	416	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002158905.1	s__Yoonia vestfoldensis_B	78.0533	410	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143545.1	s__Yoonia sp900143545	77.9553	390	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402175.1	s__Yoonia sp018402175	77.9433	381	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	95.02	95.02	0.81	0.81	2	-
GCF_002797915.1	s__Yoonia maricola	77.8981	370	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152785.1	s__Yoonia vestfoldensis_A	77.8247	396	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	77.7931	360	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854565.1	s__Yoonia sp017854565	77.7029	390	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854415.1	s__Yoonia sp017854415	77.5008	262	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262635.1	s__Aestuariivita boseongensis	76.7263	211	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100005.1	s__Lutimaribacter saemankumensis	76.6629	176	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	76.5302	124	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	76.465	139	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	76.4528	192	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002708925.1	s__Thalassobius sp002708925	75.9663	140	1531	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.91	99.91	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:09,144] [INFO] GTDB search result was written to GCF_003337495.1_ASM333749v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:09,145] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:09,149] [INFO] DFAST_QC result json was written to GCF_003337495.1_ASM333749v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:09,149] [INFO] DFAST_QC completed!
[2024-01-25 18:13:09,149] [INFO] Total running time: 0h1m34s