[2024-01-25 19:58:20,662] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:58:20,664] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:58:20,664] [INFO] DQC Reference Directory: /var/lib/cwl/stg73a9f973-82da-4f69-8624-2db69f9689db/dqc_reference
[2024-01-25 19:58:21,797] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:58:21,798] [INFO] Task started: Prodigal
[2024-01-25 19:58:21,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg146bb816-e97a-4e53-835c-475b538e3c63/GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/cds.fna -a GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:33,680] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:33,681] [INFO] Task started: HMMsearch
[2024-01-25 19:58:33,681] [INFO] Running command: hmmsearch --tblout GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73a9f973-82da-4f69-8624-2db69f9689db/dqc_reference/reference_markers.hmm GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:33,936] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:33,937] [INFO] Found 6/6 markers.
[2024-01-25 19:58:33,979] [INFO] Query marker FASTA was written to GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 19:58:33,980] [INFO] Task started: Blastn
[2024-01-25 19:58:33,980] [INFO] Running command: blastn -query GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg73a9f973-82da-4f69-8624-2db69f9689db/dqc_reference/reference_markers.fasta -out GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:35,023] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:35,035] [INFO] Selected 10 target genomes.
[2024-01-25 19:58:35,036] [INFO] Target genome list was writen to GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 19:58:35,057] [INFO] Task started: fastANI
[2024-01-25 19:58:35,057] [INFO] Running command: fastANI --query /var/lib/cwl/stg146bb816-e97a-4e53-835c-475b538e3c63/GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna.gz --refList GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:46,678] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:46,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73a9f973-82da-4f69-8624-2db69f9689db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:46,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73a9f973-82da-4f69-8624-2db69f9689db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:46,686] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:58:46,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:58:46,686] [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
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	100.0	1492	1494	95	conclusive
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	90.3089	1239	1494	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	88.6784	1133	1494	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	85.9486	1005	1494	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	85.3837	1057	1494	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	83.5086	954	1494	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	83.3024	980	1494	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	77.6368	316	1494	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.5923	494	1494	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	77.4186	387	1494	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:46,692] [INFO] DFAST Taxonomy check result was written to GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 19:58:46,692] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:46,692] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:46,692] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73a9f973-82da-4f69-8624-2db69f9689db/dqc_reference/checkm_data
[2024-01-25 19:58:46,693] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:46,735] [INFO] Task started: CheckM
[2024-01-25 19:58:46,736] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/checkm_input GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 19:59:26,454] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:26,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:26,470] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:26,470] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:26,470] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 19:59:26,471] [INFO] Task started: Blastn
[2024-01-25 19:59:26,471] [INFO] Running command: blastn -query GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg73a9f973-82da-4f69-8624-2db69f9689db/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:28,630] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:28,632] [INFO] Selected 8 target genomes.
[2024-01-25 19:59:28,632] [INFO] Target genome list was writen to GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:28,647] [INFO] Task started: fastANI
[2024-01-25 19:59:28,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg146bb816-e97a-4e53-835c-475b538e3c63/GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna.gz --refList GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:37,749] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:37,755] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:59:37,755] [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_900100155.1	s__Ancylobacter rudongensis	100.0	1492	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	conclusive
GCA_000378025.1	s__Ancylobacter sp000378025	92.4444	1301	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004339465.1	s__Ancylobacter aquaticus	90.2961	1240	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	88.6907	1132	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	86.2903	997	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	85.2595	945	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_018449475.1	s__Angulomicrobium sp018449475	84.4923	997	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241485.1	s__Angulomicrobium novellum_A	84.3678	914	1494	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:37,757] [INFO] GTDB search result was written to GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:37,758] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:37,761] [INFO] DFAST_QC result json was written to GCF_900100155.1_IMG-taxon_2596583652_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 19:59:37,761] [INFO] DFAST_QC completed!
[2024-01-25 19:59:37,761] [INFO] Total running time: 0h1m17s