[2024-01-24 10:47:10,152] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,162] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,162] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa5ef696-4862-4a2d-9971-9fbf52dcf857/dqc_reference
[2024-01-24 10:47:12,197] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,198] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,198] [INFO] Running command: gunzip -c /var/lib/cwl/stg29229f92-93d4-487e-963d-5ad2741f2700/GCF_012849055.1_ASM1284905v1_genomic.fna.gz | prodigal -d GCF_012849055.1_ASM1284905v1_genomic.fna/cds.fna -a GCF_012849055.1_ASM1284905v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:41,866] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:41,867] [INFO] Task started: HMMsearch
[2024-01-24 10:47:41,867] [INFO] Running command: hmmsearch --tblout GCF_012849055.1_ASM1284905v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa5ef696-4862-4a2d-9971-9fbf52dcf857/dqc_reference/reference_markers.hmm GCF_012849055.1_ASM1284905v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:42,183] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:42,185] [INFO] Found 6/6 markers.
[2024-01-24 10:47:42,247] [INFO] Query marker FASTA was written to GCF_012849055.1_ASM1284905v1_genomic.fna/markers.fasta
[2024-01-24 10:47:42,248] [INFO] Task started: Blastn
[2024-01-24 10:47:42,248] [INFO] Running command: blastn -query GCF_012849055.1_ASM1284905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5ef696-4862-4a2d-9971-9fbf52dcf857/dqc_reference/reference_markers.fasta -out GCF_012849055.1_ASM1284905v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:42,936] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:42,942] [INFO] Selected 21 target genomes.
[2024-01-24 10:47:42,943] [INFO] Target genome list was writen to GCF_012849055.1_ASM1284905v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:43,172] [INFO] Task started: fastANI
[2024-01-24 10:47:43,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg29229f92-93d4-487e-963d-5ad2741f2700/GCF_012849055.1_ASM1284905v1_genomic.fna.gz --refList GCF_012849055.1_ASM1284905v1_genomic.fna/target_genomes.txt --output GCF_012849055.1_ASM1284905v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:08,812] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:08,813] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa5ef696-4862-4a2d-9971-9fbf52dcf857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:08,814] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa5ef696-4862-4a2d-9971-9fbf52dcf857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:08,836] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:08,836] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:08,836] [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 oryzae	strain=DSM 28354	GCA_003002825.1	1469603	1469603	type	True	81.9769	1336	2015	95	below_threshold
Spirosoma montaniterrae	strain=DY10	GCA_001988955.1	1178516	1178516	type	True	77.5829	497	2015	95	below_threshold
Spirosoma taeanense	strain=TS118	GCA_013127955.1	2735870	2735870	type	True	77.5546	490	2015	95	below_threshold
Spirosoma lacussanchae	strain=CPCC 100624	GCA_005870035.1	1884249	1884249	type	True	77.4854	484	2015	95	below_threshold
Spirosoma rigui	strain=KCTC 12531	GCA_002067135.1	564064	564064	type	True	77.4639	475	2015	95	below_threshold
Spirosoma sordidisoli	strain=TY50	GCA_004138325.1	2502893	2502893	type	True	77.3877	533	2015	95	below_threshold
Fibrisoma limi	strain=BUZ 3	GCA_000296815.2	663275	663275	type	True	77.2307	403	2015	95	below_threshold
Spirosoma agri	strain=KCTC 52727	GCA_010747415.1	1987381	1987381	type	True	77.1985	406	2015	95	below_threshold
Spirosoma fluviale	strain=DSM 29961	GCA_900230225.1	1597977	1597977	type	True	77.1477	418	2015	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	77.1458	341	2015	95	below_threshold
Fibrisoma montanum	strain=HYT19	GCA_003583365.1	2305895	2305895	type	True	77.1084	446	2015	95	below_threshold
Spirosoma panaciterrae	strain=DSM 21099	GCA_000374025.1	496058	496058	type	True	77.0248	356	2015	95	below_threshold
Spirosoma endbachense	strain=I-24	GCA_010233585.1	2666025	2666025	type	True	77.0244	320	2015	95	below_threshold
Spirosoma validum	strain=BT704	GCA_014699035.1	2771355	2771355	type	True	76.966	329	2015	95	below_threshold
Spirosoma profusum	strain=BT702	GCA_014699005.1	2771354	2771354	type	True	76.9451	357	2015	95	below_threshold
Spirosoma luteum	strain=DSM 19990	GCA_000374065.1	431553	431553	type	True	76.8497	380	2015	95	below_threshold
Fibrella aquatilis	strain=HMF5036	GCA_017353255.1	2817059	2817059	type	True	76.6964	360	2015	95	below_threshold
Fibrella rubiginis	strain=HMF5335	GCA_017353185.1	2817060	2817060	type	True	76.5864	302	2015	95	below_threshold
Hymenobacter guriensis	strain=BT594	GCA_015773195.1	2793065	2793065	type	True	75.6752	61	2015	95	below_threshold
Hymenobacter terricola	strain=3F2	GCA_017921975.2	2819236	2819236	type	True	75.3805	71	2015	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:08,838] [INFO] DFAST Taxonomy check result was written to GCF_012849055.1_ASM1284905v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:08,839] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:08,839] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:08,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa5ef696-4862-4a2d-9971-9fbf52dcf857/dqc_reference/checkm_data
[2024-01-24 10:48:08,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:08,901] [INFO] Task started: CheckM
[2024-01-24 10:48:08,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012849055.1_ASM1284905v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012849055.1_ASM1284905v1_genomic.fna/checkm_input GCF_012849055.1_ASM1284905v1_genomic.fna/checkm_result
[2024-01-24 10:49:29,562] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:29,564] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:29,586] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:29,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:29,586] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012849055.1_ASM1284905v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:29,587] [INFO] Task started: Blastn
[2024-01-24 10:49:29,587] [INFO] Running command: blastn -query GCF_012849055.1_ASM1284905v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa5ef696-4862-4a2d-9971-9fbf52dcf857/dqc_reference/reference_markers_gtdb.fasta -out GCF_012849055.1_ASM1284905v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:30,456] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:30,460] [INFO] Selected 17 target genomes.
[2024-01-24 10:49:30,460] [INFO] Target genome list was writen to GCF_012849055.1_ASM1284905v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:30,490] [INFO] Task started: fastANI
[2024-01-24 10:49:30,491] [INFO] Running command: fastANI --query /var/lib/cwl/stg29229f92-93d4-487e-963d-5ad2741f2700/GCF_012849055.1_ASM1284905v1_genomic.fna.gz --refList GCF_012849055.1_ASM1284905v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012849055.1_ASM1284905v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:53,725] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:53,751] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:53,751] [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_012849055.1	s__Spirosoma sp012849055	100.0	2013	2015	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_003002825.1	s__Spirosoma oryzae	81.9903	1333	2015	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	78.2242	488	2015	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	77.5773	486	2015	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	77.5588	496	2015	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	77.4968	484	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138325.1	s__Spirosoma sordidisoli	77.3876	533	2015	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	77.3193	473	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014377625.1	s__Spirosoma sp014377625	77.1993	410	2015	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	77.1918	407	2015	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	77.1477	418	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011604685.1	s__Spirosoma aureum	77.1033	290	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583365.1	s__Fibrisoma montanum	77.1022	448	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Fibrisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010233585.1	s__Spirosoma endbachense	77.0319	319	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374025.1	s__Spirosoma panaciterrae	77.0242	356	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699035.1	s__Spirosoma validum	76.9582	330	2015	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014699005.1	s__Spirosoma profusum	76.9387	358	2015	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 10:49:53,753] [INFO] GTDB search result was written to GCF_012849055.1_ASM1284905v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:53,753] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:53,757] [INFO] DFAST_QC result json was written to GCF_012849055.1_ASM1284905v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:53,758] [INFO] DFAST_QC completed!
[2024-01-24 10:49:53,758] [INFO] Total running time: 0h2m44s