[2024-01-24 13:13:20,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:20,226] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:20,227] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf833d7f-f6c5-4d48-8779-04ec79dd62b3/dqc_reference
[2024-01-24 13:13:21,437] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:21,437] [INFO] Task started: Prodigal
[2024-01-24 13:13:21,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ba6a36d-f6cc-4b3d-9b8e-7078d57f1a30/GCF_005870035.1_ASM587003v1_genomic.fna.gz | prodigal -d GCF_005870035.1_ASM587003v1_genomic.fna/cds.fna -a GCF_005870035.1_ASM587003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:51,133] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:51,134] [INFO] Task started: HMMsearch
[2024-01-24 13:13:51,134] [INFO] Running command: hmmsearch --tblout GCF_005870035.1_ASM587003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf833d7f-f6c5-4d48-8779-04ec79dd62b3/dqc_reference/reference_markers.hmm GCF_005870035.1_ASM587003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:51,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:51,482] [INFO] Found 6/6 markers.
[2024-01-24 13:13:51,548] [INFO] Query marker FASTA was written to GCF_005870035.1_ASM587003v1_genomic.fna/markers.fasta
[2024-01-24 13:13:51,548] [INFO] Task started: Blastn
[2024-01-24 13:13:51,548] [INFO] Running command: blastn -query GCF_005870035.1_ASM587003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf833d7f-f6c5-4d48-8779-04ec79dd62b3/dqc_reference/reference_markers.fasta -out GCF_005870035.1_ASM587003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:52,238] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:52,242] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:52,242] [INFO] Target genome list was writen to GCF_005870035.1_ASM587003v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:52,365] [INFO] Task started: fastANI
[2024-01-24 13:13:52,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba6a36d-f6cc-4b3d-9b8e-7078d57f1a30/GCF_005870035.1_ASM587003v1_genomic.fna.gz --refList GCF_005870035.1_ASM587003v1_genomic.fna/target_genomes.txt --output GCF_005870035.1_ASM587003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:13,574] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:13,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf833d7f-f6c5-4d48-8779-04ec79dd62b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:13,575] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf833d7f-f6c5-4d48-8779-04ec79dd62b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:13,591] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:13,592] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:13,592] [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
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	100.0	2097	2101	95	conclusive
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	93.2458	1875	2101	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.6894	543	2101	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.6883	594	2101	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	77.677	578	2101	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.6232	497	2101	95	below_threshold
Spirosoma utsteinense	strain=LMG 31447	GCA_014282275.1	2585773	2585773	type	True	77.5349	552	2101	95	below_threshold
Spirosoma oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	77.2583	415	2101	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	77.2558	482	2101	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.2053	410	2101	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.0742	379	2101	95	below_threshold
Spirosoma terrae	strain=KCTC 52035	GCA_010435915.1	1968276	1968276	type	True	76.8776	322	2101	95	below_threshold
Larkinella soli	strain=MIMbqt9	GCA_003703975.1	1770527	1770527	type	True	76.3164	284	2101	95	below_threshold
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.2695	68	2101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:13,594] [INFO] DFAST Taxonomy check result was written to GCF_005870035.1_ASM587003v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:13,594] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:13,595] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:13,595] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf833d7f-f6c5-4d48-8779-04ec79dd62b3/dqc_reference/checkm_data
[2024-01-24 13:14:13,596] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:13,654] [INFO] Task started: CheckM
[2024-01-24 13:14:13,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005870035.1_ASM587003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005870035.1_ASM587003v1_genomic.fna/checkm_input GCF_005870035.1_ASM587003v1_genomic.fna/checkm_result
[2024-01-24 13:15:34,311] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:34,313] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:15:34,336] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:34,337] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:34,337] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005870035.1_ASM587003v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:34,338] [INFO] Task started: Blastn
[2024-01-24 13:15:34,338] [INFO] Running command: blastn -query GCF_005870035.1_ASM587003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf833d7f-f6c5-4d48-8779-04ec79dd62b3/dqc_reference/reference_markers_gtdb.fasta -out GCF_005870035.1_ASM587003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:35,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:35,173] [INFO] Selected 16 target genomes.
[2024-01-24 13:15:35,173] [INFO] Target genome list was writen to GCF_005870035.1_ASM587003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:35,206] [INFO] Task started: fastANI
[2024-01-24 13:15:35,207] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ba6a36d-f6cc-4b3d-9b8e-7078d57f1a30/GCF_005870035.1_ASM587003v1_genomic.fna.gz --refList GCF_005870035.1_ASM587003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005870035.1_ASM587003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:54,370] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:54,385] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:54,385] [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_005870035.1	s__Spirosoma lacussanchae	100.0	2097	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004138325.1	s__Spirosoma sordidisoli	93.2358	1876	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	98.69	98.69	0.94	0.94	2	-
GCA_000024525.1	s__Spirosoma linguale	77.9329	528	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013127955.1	s__Spirosoma taeanense	77.6894	543	2101	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	77.6851	593	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001988955.1	s__Spirosoma montaniterrae	77.677	578	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900230225.1	s__Spirosoma fluviale	77.6111	496	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014282275.1	s__Spirosoma utsteinense	77.5181	555	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	99.94	99.94	0.98	0.98	2	-
GCF_003583365.1	s__Fibrisoma montanum	77.3558	518	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375035.1	s__Spirosoma sp013375035	77.2827	418	2101	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	77.2649	414	2101	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	77.2053	410	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006965485.1	s__Spirosoma sp006965485	77.1877	360	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010435915.1	s__Spirosoma terrae	76.8707	323	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003703975.1	s__Larkinella soli	76.3287	282	2101	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Larkinella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:54,387] [INFO] GTDB search result was written to GCF_005870035.1_ASM587003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:54,387] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:54,391] [INFO] DFAST_QC result json was written to GCF_005870035.1_ASM587003v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:54,391] [INFO] DFAST_QC completed!
[2024-01-24 13:15:54,392] [INFO] Total running time: 0h2m34s