[2024-01-24 13:40:41,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:41,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:41,678] [INFO] DQC Reference Directory: /var/lib/cwl/stgd842812b-aa22-4a94-bdb0-7bfe46ebd50b/dqc_reference
[2024-01-24 13:40:43,064] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:43,065] [INFO] Task started: Prodigal
[2024-01-24 13:40:43,065] [INFO] Running command: gunzip -c /var/lib/cwl/stgc93525a9-992b-495e-96c1-757f3acffd2a/GCF_003583365.1_ASM358336v1_genomic.fna.gz | prodigal -d GCF_003583365.1_ASM358336v1_genomic.fna/cds.fna -a GCF_003583365.1_ASM358336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:23,269] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:23,269] [INFO] Task started: HMMsearch
[2024-01-24 13:41:23,269] [INFO] Running command: hmmsearch --tblout GCF_003583365.1_ASM358336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd842812b-aa22-4a94-bdb0-7bfe46ebd50b/dqc_reference/reference_markers.hmm GCF_003583365.1_ASM358336v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:23,639] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:23,640] [INFO] Found 6/6 markers.
[2024-01-24 13:41:23,706] [INFO] Query marker FASTA was written to GCF_003583365.1_ASM358336v1_genomic.fna/markers.fasta
[2024-01-24 13:41:23,706] [INFO] Task started: Blastn
[2024-01-24 13:41:23,707] [INFO] Running command: blastn -query GCF_003583365.1_ASM358336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd842812b-aa22-4a94-bdb0-7bfe46ebd50b/dqc_reference/reference_markers.fasta -out GCF_003583365.1_ASM358336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:24,368] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:24,371] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:24,371] [INFO] Target genome list was writen to GCF_003583365.1_ASM358336v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:24,386] [INFO] Task started: fastANI
[2024-01-24 13:41:24,387] [INFO] Running command: fastANI --query /var/lib/cwl/stgc93525a9-992b-495e-96c1-757f3acffd2a/GCF_003583365.1_ASM358336v1_genomic.fna.gz --refList GCF_003583365.1_ASM358336v1_genomic.fna/target_genomes.txt --output GCF_003583365.1_ASM358336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:45,985] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:45,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd842812b-aa22-4a94-bdb0-7bfe46ebd50b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:45,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd842812b-aa22-4a94-bdb0-7bfe46ebd50b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:46,002] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:46,002] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:46,003] [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
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	100.0	2584	2585	95	conclusive
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	85.4757	1981	2585	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.5115	588	2585	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.4026	536	2585	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.385	515	2585	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.1175	448	2585	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	76.9375	434	2585	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	76.9182	429	2585	95	below_threshold
Fibrella aestuarina	strain=BUZ 2	GCA_000331105.1	651143	651143	type	True	76.9045	371	2585	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	76.7047	371	2585	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	76.6641	346	2585	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	76.6048	324	2585	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	76.3517	273	2585	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	76.2898	245	2585	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:46,004] [INFO] DFAST Taxonomy check result was written to GCF_003583365.1_ASM358336v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:46,005] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:46,005] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:46,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd842812b-aa22-4a94-bdb0-7bfe46ebd50b/dqc_reference/checkm_data
[2024-01-24 13:41:46,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:46,078] [INFO] Task started: CheckM
[2024-01-24 13:41:46,079] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003583365.1_ASM358336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003583365.1_ASM358336v1_genomic.fna/checkm_input GCF_003583365.1_ASM358336v1_genomic.fna/checkm_result
[2024-01-24 13:43:26,983] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:26,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:27,013] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:27,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:27,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003583365.1_ASM358336v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:27,015] [INFO] Task started: Blastn
[2024-01-24 13:43:27,015] [INFO] Running command: blastn -query GCF_003583365.1_ASM358336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd842812b-aa22-4a94-bdb0-7bfe46ebd50b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003583365.1_ASM358336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:27,861] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:27,866] [INFO] Selected 17 target genomes.
[2024-01-24 13:43:27,866] [INFO] Target genome list was writen to GCF_003583365.1_ASM358336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:27,961] [INFO] Task started: fastANI
[2024-01-24 13:43:27,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgc93525a9-992b-495e-96c1-757f3acffd2a/GCF_003583365.1_ASM358336v1_genomic.fna.gz --refList GCF_003583365.1_ASM358336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003583365.1_ASM358336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:47,741] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:47,754] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:47,754] [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_003583365.1	s__Fibrisoma montanum	100.0	2584	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000296815.2	s__Fibrisoma limi	85.4661	1983	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.5025	589	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCF_013127955.1	s__Spirosoma taeanense	77.4123	534	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005870035.1	s__Spirosoma lacussanchae	77.3797	516	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012849055.1	s__Spirosoma sp012849055	77.221	437	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002067135.1	s__Spirosoma rigui	77.123	447	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002825.1	s__Spirosoma oryzae	77.0759	411	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898575.1	s__Spirosoma sp001898575	77.0629	321	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001988955.1	s__Spirosoma montaniterrae	76.9182	429	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	76.8983	408	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331105.1	s__Fibrella aestuarina	76.879	375	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010233585.1	s__Spirosoma endbachense	76.6984	372	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010747415.1	s__Spirosoma agri	76.6466	349	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974425.1	s__Spirosoma radiotolerans	76.611	323	2585	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:47,756] [INFO] GTDB search result was written to GCF_003583365.1_ASM358336v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:47,757] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:47,760] [INFO] DFAST_QC result json was written to GCF_003583365.1_ASM358336v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:47,760] [INFO] DFAST_QC completed!
[2024-01-24 13:43:47,760] [INFO] Total running time: 0h3m6s