[2024-01-24 14:47:19,095] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:19,097] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:19,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg97d7f1a9-6253-4ced-99f7-abf133504100/dqc_reference
[2024-01-24 14:47:20,312] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:20,313] [INFO] Task started: Prodigal
[2024-01-24 14:47:20,313] [INFO] Running command: gunzip -c /var/lib/cwl/stgc70bcc8e-313b-4e54-9772-bc61d803930c/GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/cds.fna -a GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:44,922] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:44,922] [INFO] Task started: HMMsearch
[2024-01-24 14:47:44,922] [INFO] Running command: hmmsearch --tblout GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97d7f1a9-6253-4ced-99f7-abf133504100/dqc_reference/reference_markers.hmm GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:45,237] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:45,239] [INFO] Found 6/6 markers.
[2024-01-24 14:47:45,280] [INFO] Query marker FASTA was written to GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:45,280] [INFO] Task started: Blastn
[2024-01-24 14:47:45,280] [INFO] Running command: blastn -query GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d7f1a9-6253-4ced-99f7-abf133504100/dqc_reference/reference_markers.fasta -out GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:45,920] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:45,925] [INFO] Selected 18 target genomes.
[2024-01-24 14:47:45,926] [INFO] Target genome list was writen to GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:45,937] [INFO] Task started: fastANI
[2024-01-24 14:47:45,937] [INFO] Running command: fastANI --query /var/lib/cwl/stgc70bcc8e-313b-4e54-9772-bc61d803930c/GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna.gz --refList GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:48:02,571] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:02,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97d7f1a9-6253-4ced-99f7-abf133504100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:48:02,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97d7f1a9-6253-4ced-99f7-abf133504100/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:48:02,585] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:48:02,585] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:48:02,586] [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
Sunxiuqinia elliptica	strain=CGMCC 1.9156	GCA_900113005.1	655355	655355	type	True	100.0	1680	1683	95	conclusive
Sunxiuqinia indica	strain=RC1_OXG_1F	GCA_009847015.1	2692584	2692584	type	True	78.0167	363	1683	95	below_threshold
Sunxiuqinia dokdonensis	strain=DH1	GCA_001270965.1	1409788	1409788	type	True	77.7929	349	1683	95	below_threshold
Mangrovibacterium lignilyticum	strain=BM_7	GCA_010882175.1	2668052	2668052	type	True	77.4909	156	1683	95	below_threshold
Mangrovibacterium diazotrophicum	strain=DSM 27148	GCA_003610535.1	1261403	1261403	type	True	77.1324	161	1683	95	below_threshold
Draconibacterium orientale	strain=FH5	GCA_000626635.1	1168034	1168034	type	True	77.069	90	1683	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	76.9406	91	1683	95	below_threshold
Draconibacterium sediminis	strain=JN14CK-3	GCA_000949475.1	1544798	1544798	type	True	76.5446	97	1683	95	below_threshold
Maribellus sediminis	strain=Y2-1-60	GCA_011799805.1	2696285	2696285	type	True	76.3057	90	1683	95	below_threshold
Mariniphaga anaerophila	strain=DSM 26910	GCA_900129025.1	1484053	1484053	type	True	76.2117	86	1683	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:48:02,587] [INFO] DFAST Taxonomy check result was written to GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:48:02,588] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:48:02,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:48:02,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97d7f1a9-6253-4ced-99f7-abf133504100/dqc_reference/checkm_data
[2024-01-24 14:48:02,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:48:02,677] [INFO] Task started: CheckM
[2024-01-24 14:48:02,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/checkm_input GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:49:15,294] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:15,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:15,331] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:15,332] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:15,332] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:49:15,333] [INFO] Task started: Blastn
[2024-01-24 14:49:15,333] [INFO] Running command: blastn -query GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg97d7f1a9-6253-4ced-99f7-abf133504100/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:16,237] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:16,244] [INFO] Selected 18 target genomes.
[2024-01-24 14:49:16,244] [INFO] Target genome list was writen to GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:16,261] [INFO] Task started: fastANI
[2024-01-24 14:49:16,261] [INFO] Running command: fastANI --query /var/lib/cwl/stgc70bcc8e-313b-4e54-9772-bc61d803930c/GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna.gz --refList GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:30,860] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:30,877] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:30,878] [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_900113005.1	s__Sunxiuqinia elliptica	100.0	1680	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	95.76	95.76	0.90	0.90	3	conclusive
GCF_009847015.1	s__Sunxiuqinia indica	78.0167	363	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001270965.1	s__Sunxiuqinia dokdonensis	77.7827	350	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Sunxiuqinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010882175.1	s__Mangrovibacterium sp010882175	77.532	153	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003046625.1	s__Mangrovibacterium marinum	77.1717	147	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610535.1	s__Mangrovibacterium diazotrophicum	77.1483	160	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000626635.1	s__Draconibacterium orientale	77.069	90	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000949475.1	s__Draconibacterium sediminis	76.5446	97	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Draconibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129025.1	s__Mariniphaga anaerophila	76.2307	85	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mariniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506435.1	s__GWE2-42-39 sp003506435	75.889	94	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__GWE2-42-39	95.0	99.97	99.92	0.99	0.98	6	-
GCA_019163175.1	s__UBA6024 sp019163175	75.7355	71	1683	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__UBA6024	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:30,879] [INFO] GTDB search result was written to GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:30,880] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:30,884] [INFO] DFAST_QC result json was written to GCF_900113005.1_IMG-taxon_2663762719_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:49:30,885] [INFO] DFAST_QC completed!
[2024-01-24 14:49:30,885] [INFO] Total running time: 0h2m12s