[2024-01-24 13:19:26,677] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:26,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:26,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bec5e5e-ab24-4ad1-8288-991ac17338b5/dqc_reference
[2024-01-24 13:19:27,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:27,916] [INFO] Task started: Prodigal
[2024-01-24 13:19:27,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg7748dbd2-f4ba-4906-9337-f420aabb93be/GCF_009762775.1_ASM976277v1_genomic.fna.gz | prodigal -d GCF_009762775.1_ASM976277v1_genomic.fna/cds.fna -a GCF_009762775.1_ASM976277v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:20:01,162] [INFO] Task succeeded: Prodigal
[2024-01-24 13:20:01,162] [INFO] Task started: HMMsearch
[2024-01-24 13:20:01,163] [INFO] Running command: hmmsearch --tblout GCF_009762775.1_ASM976277v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bec5e5e-ab24-4ad1-8288-991ac17338b5/dqc_reference/reference_markers.hmm GCF_009762775.1_ASM976277v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:20:01,536] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:20:01,539] [INFO] Found 6/6 markers.
[2024-01-24 13:20:01,609] [INFO] Query marker FASTA was written to GCF_009762775.1_ASM976277v1_genomic.fna/markers.fasta
[2024-01-24 13:20:01,609] [INFO] Task started: Blastn
[2024-01-24 13:20:01,609] [INFO] Running command: blastn -query GCF_009762775.1_ASM976277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bec5e5e-ab24-4ad1-8288-991ac17338b5/dqc_reference/reference_markers.fasta -out GCF_009762775.1_ASM976277v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:02,199] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:02,203] [INFO] Selected 17 target genomes.
[2024-01-24 13:20:02,204] [INFO] Target genome list was writen to GCF_009762775.1_ASM976277v1_genomic.fna/target_genomes.txt
[2024-01-24 13:20:02,411] [INFO] Task started: fastANI
[2024-01-24 13:20:02,412] [INFO] Running command: fastANI --query /var/lib/cwl/stg7748dbd2-f4ba-4906-9337-f420aabb93be/GCF_009762775.1_ASM976277v1_genomic.fna.gz --refList GCF_009762775.1_ASM976277v1_genomic.fna/target_genomes.txt --output GCF_009762775.1_ASM976277v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:20:17,528] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:17,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bec5e5e-ab24-4ad1-8288-991ac17338b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:20:17,529] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bec5e5e-ab24-4ad1-8288-991ac17338b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:20:17,543] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:20:17,543] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:20:17,543] [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
Maribellus comscasis	strain=WC007	GCA_009762775.1	2681766	2681766	type	True	100.0	2589	2603	95	conclusive
Maribellus maritimus	strain=5E3	GCA_022267315.1	2870838	2870838	type	True	93.0359	1923	2603	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	77.6332	278	2603	95	below_threshold
Mariniphaga anaerophila	strain=DSM 26910	GCA_900129025.1	1484053	1484053	type	True	77.4591	248	2603	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	77.2365	268	2603	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	77.0888	232	2603	95	below_threshold
Draconibacterium halophilum	strain=M1	GCA_010448835.1	2706887	2706887	type	True	76.995	262	2603	95	below_threshold
Maribellus luteus	strain=XSD2	GCA_003576475.1	2305463	2305463	type	True	76.9529	247	2603	95	below_threshold
Mariniphaga sediminis	strain=SY21	GCA_003573545.1	1628158	1628158	type	True	76.7397	248	2603	95	below_threshold
Mangrovibacterium diazotrophicum	strain=DSM 27148	GCA_003610535.1	1261403	1261403	type	True	76.1154	67	2603	95	below_threshold
Marinifilum caeruleilacunae	strain=JC070	GCA_013141825.1	2499076	2499076	type	True	75.5682	61	2603	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:20:17,545] [INFO] DFAST Taxonomy check result was written to GCF_009762775.1_ASM976277v1_genomic.fna/tc_result.tsv
[2024-01-24 13:20:17,546] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:20:17,546] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:20:17,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bec5e5e-ab24-4ad1-8288-991ac17338b5/dqc_reference/checkm_data
[2024-01-24 13:20:17,549] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:20:17,622] [INFO] Task started: CheckM
[2024-01-24 13:20:17,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009762775.1_ASM976277v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009762775.1_ASM976277v1_genomic.fna/checkm_input GCF_009762775.1_ASM976277v1_genomic.fna/checkm_result
[2024-01-24 13:21:50,957] [INFO] Task succeeded: CheckM
[2024-01-24 13:21:50,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:21:50,984] [INFO] ===== Completeness check finished =====
[2024-01-24 13:21:50,985] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:21:50,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009762775.1_ASM976277v1_genomic.fna/markers.fasta)
[2024-01-24 13:21:50,986] [INFO] Task started: Blastn
[2024-01-24 13:21:50,986] [INFO] Running command: blastn -query GCF_009762775.1_ASM976277v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bec5e5e-ab24-4ad1-8288-991ac17338b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_009762775.1_ASM976277v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:21:51,845] [INFO] Task succeeded: Blastn
[2024-01-24 13:21:51,849] [INFO] Selected 21 target genomes.
[2024-01-24 13:21:51,850] [INFO] Target genome list was writen to GCF_009762775.1_ASM976277v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:21:51,972] [INFO] Task started: fastANI
[2024-01-24 13:21:51,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg7748dbd2-f4ba-4906-9337-f420aabb93be/GCF_009762775.1_ASM976277v1_genomic.fna.gz --refList GCF_009762775.1_ASM976277v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009762775.1_ASM976277v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:09,116] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:09,135] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:09,135] [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_009762775.1	s__Draconibacterium comscasis	100.0	2590	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016931875.1	s__Draconibacterium sp016931875	78.9442	459	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626635.1	s__Draconibacterium orientale	77.526	276	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_011620585.1	s__Draconibacterium sp011620585	77.3126	206	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011799805.1	s__Draconibacterium sp011799805	77.0777	236	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	96.71	96.71	0.85	0.85	2	-
GCF_003576475.1	s__Draconibacterium luteum	76.9707	249	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010448835.1	s__Draconibacterium halophilum	76.8896	261	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000949475.1	s__Draconibacterium sediminis	76.7747	291	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003573545.1	s__Mariniphaga sediminis	76.716	252	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018648265.1	s__Draconibacterium sp018648265	76.6632	293	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.94	99.92	0.96	0.95	4	-
GCA_009773765.1	s__Draconibacterium sp009773765	76.5974	185	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016705335.1	s__Draconibacterium sp016705335	76.5912	252	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493625.1	s__Draconibacterium sp015493625	76.323	135	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013203755.1	s__Draconibacterium sp013203755	76.1573	209	2603	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:09,137] [INFO] GTDB search result was written to GCF_009762775.1_ASM976277v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:09,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:09,142] [INFO] DFAST_QC result json was written to GCF_009762775.1_ASM976277v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:09,142] [INFO] DFAST_QC completed!
[2024-01-24 13:22:09,142] [INFO] Total running time: 0h2m42s