[2024-01-24 14:22:15,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:15,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:15,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a0c95a7-009c-4cc3-a352-7e2e166b2352/dqc_reference
[2024-01-24 14:22:17,253] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:17,254] [INFO] Task started: Prodigal
[2024-01-24 14:22:17,254] [INFO] Running command: gunzip -c /var/lib/cwl/stg8690e06b-8c99-4eef-9b91-4fd8d81e8f22/GCF_013166515.1_ASM1316651v1_genomic.fna.gz | prodigal -d GCF_013166515.1_ASM1316651v1_genomic.fna/cds.fna -a GCF_013166515.1_ASM1316651v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:34,872] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:34,873] [INFO] Task started: HMMsearch
[2024-01-24 14:22:34,873] [INFO] Running command: hmmsearch --tblout GCF_013166515.1_ASM1316651v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a0c95a7-009c-4cc3-a352-7e2e166b2352/dqc_reference/reference_markers.hmm GCF_013166515.1_ASM1316651v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:35,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:35,109] [INFO] Found 6/6 markers.
[2024-01-24 14:22:35,144] [INFO] Query marker FASTA was written to GCF_013166515.1_ASM1316651v1_genomic.fna/markers.fasta
[2024-01-24 14:22:35,145] [INFO] Task started: Blastn
[2024-01-24 14:22:35,145] [INFO] Running command: blastn -query GCF_013166515.1_ASM1316651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a0c95a7-009c-4cc3-a352-7e2e166b2352/dqc_reference/reference_markers.fasta -out GCF_013166515.1_ASM1316651v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:35,734] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:35,738] [INFO] Selected 29 target genomes.
[2024-01-24 14:22:35,739] [INFO] Target genome list was writen to GCF_013166515.1_ASM1316651v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:35,761] [INFO] Task started: fastANI
[2024-01-24 14:22:35,762] [INFO] Running command: fastANI --query /var/lib/cwl/stg8690e06b-8c99-4eef-9b91-4fd8d81e8f22/GCF_013166515.1_ASM1316651v1_genomic.fna.gz --refList GCF_013166515.1_ASM1316651v1_genomic.fna/target_genomes.txt --output GCF_013166515.1_ASM1316651v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:51,051] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:51,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a0c95a7-009c-4cc3-a352-7e2e166b2352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:51,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a0c95a7-009c-4cc3-a352-7e2e166b2352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:51,067] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:51,067] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:51,067] [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
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	81.4198	165	1002	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	80.845	67	1002	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	79.8939	170	1002	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	79.3701	121	1002	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	78.8593	114	1002	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	78.242	107	1002	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	77.6551	143	1002	95	below_threshold
Prevotella maculosa	strain=DSM 19339	GCA_000382385.1	439703	439703	type	True	77.0367	63	1002	95	below_threshold
Prevotella enoeca	strain=JCM 12259	GCA_000613405.1	76123	76123	type	True	77.021	53	1002	95	below_threshold
Prevotella maculosa	strain=JCM 15638	GCA_000613965.1	439703	439703	type	True	77.0198	61	1002	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.945	50	1002	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.9026	90	1002	95	below_threshold
Prevotella falsenii	strain=JCM 15124	GCA_000613945.1	515414	515414	type	True	76.8123	52	1002	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_001953955.1	28131	28131	type	True	76.7275	51	1002	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	76.654	71	1002	95	below_threshold
Prevotella intermedia	strain=ATCC 25611	GCA_000519165.1	28131	28131	type	True	76.5581	53	1002	95	below_threshold
Hallella seregens	strain=ATCC 51272	GCA_000518545.1	52229	52229	type	True	76.55	71	1002	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000220215.1	52227	52227	type	True	76.5485	72	1002	95	below_threshold
Prevotella intermedia	strain=DSM 20706	GCA_000439065.1	28131	28131	type	True	76.507	51	1002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,070] [INFO] DFAST Taxonomy check result was written to GCF_013166515.1_ASM1316651v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:51,071] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:51,071] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:51,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a0c95a7-009c-4cc3-a352-7e2e166b2352/dqc_reference/checkm_data
[2024-01-24 14:22:51,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:51,107] [INFO] Task started: CheckM
[2024-01-24 14:22:51,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013166515.1_ASM1316651v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013166515.1_ASM1316651v1_genomic.fna/checkm_input GCF_013166515.1_ASM1316651v1_genomic.fna/checkm_result
[2024-01-24 14:23:41,985] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:41,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:42,010] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:42,011] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:42,011] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013166515.1_ASM1316651v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:42,011] [INFO] Task started: Blastn
[2024-01-24 14:23:42,012] [INFO] Running command: blastn -query GCF_013166515.1_ASM1316651v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a0c95a7-009c-4cc3-a352-7e2e166b2352/dqc_reference/reference_markers_gtdb.fasta -out GCF_013166515.1_ASM1316651v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:42,911] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:42,915] [INFO] Selected 21 target genomes.
[2024-01-24 14:23:42,915] [INFO] Target genome list was writen to GCF_013166515.1_ASM1316651v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:42,933] [INFO] Task started: fastANI
[2024-01-24 14:23:42,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg8690e06b-8c99-4eef-9b91-4fd8d81e8f22/GCF_013166515.1_ASM1316651v1_genomic.fna.gz --refList GCF_013166515.1_ASM1316651v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013166515.1_ASM1316651v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:55,484] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:55,511] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:55,512] [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_013166515.1	s__Prevotella sp013166515	100.0	1001	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	conclusive
GCA_900545525.1	s__Prevotella sp900545525	85.9498	681	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCF_013166545.1	s__Prevotella sp013166545	80.0866	150	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCF_900079775.1	s__Prevotella lascolaii	79.9018	169	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.26	98.20	0.94	0.92	5	-
GCF_001275135.1	s__Prevotella rara	78.8018	212	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCA_905196835.1	s__Prevotella stercoripullorum	78.6934	190	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCF_000834015.1	s__Prevotella pectinovora	77.6529	144	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCA_905214625.1	s__Prevotella sp905214625	77.6522	146	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550365.1	s__Prevotella sp900550365	77.3857	121	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216025.1	s__Prevotella sp905216025	77.3324	141	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	95.83	95.83	0.83	0.83	2	-
GCA_900554695.1	s__Prevotella sp900554695	77.2164	105	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.88	0.84	0.83	3	-
GCA_017415455.1	s__Prevotella sp017415455	77.1618	127	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.11	0.83	0.82	3	-
GCA_000433175.1	s__Prevotella sp000433175	77.1215	169	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCA_002298545.1	s__Prevotella sp002298545	77.0739	107	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002314055.1	s__Prevotella sp002314055	77.0273	139	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.08	98.98	0.90	0.84	9	-
GCA_900314915.1	s__Prevotella sp900314915	76.7558	71	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.86	97.07	0.88	0.81	19	-
GCF_002251435.1	s__Prevotella sp002251435	76.7502	95	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557285.1	s__Prevotella sp004557285	76.4314	98	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	-
GCA_905198745.1	s__Prevotella sp905198745	76.3869	74	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546345.1	s__Prevotella sp900546345	76.3073	62	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900553155.1	s__Prevotella sp900553155	76.1661	62	1002	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.04	96.93	0.80	0.75	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:55,514] [INFO] GTDB search result was written to GCF_013166515.1_ASM1316651v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:55,515] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:55,520] [INFO] DFAST_QC result json was written to GCF_013166515.1_ASM1316651v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:55,521] [INFO] DFAST_QC completed!
[2024-01-24 14:23:55,521] [INFO] Total running time: 0h1m40s