[2024-01-24 14:12:15,884] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:15,886] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:15,886] [INFO] DQC Reference Directory: /var/lib/cwl/stga76fe3d9-88a5-48e2-850d-83494d81e4c2/dqc_reference
[2024-01-24 14:12:17,308] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:17,309] [INFO] Task started: Prodigal
[2024-01-24 14:12:17,309] [INFO] Running command: gunzip -c /var/lib/cwl/stg577fea06-a7f9-4c63-8c9d-d76e677bb631/GCF_030814815.1_ASM3081481v1_genomic.fna.gz | prodigal -d GCF_030814815.1_ASM3081481v1_genomic.fna/cds.fna -a GCF_030814815.1_ASM3081481v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:32,195] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:32,196] [INFO] Task started: HMMsearch
[2024-01-24 14:12:32,196] [INFO] Running command: hmmsearch --tblout GCF_030814815.1_ASM3081481v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga76fe3d9-88a5-48e2-850d-83494d81e4c2/dqc_reference/reference_markers.hmm GCF_030814815.1_ASM3081481v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:32,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:32,569] [INFO] Found 6/6 markers.
[2024-01-24 14:12:32,615] [INFO] Query marker FASTA was written to GCF_030814815.1_ASM3081481v1_genomic.fna/markers.fasta
[2024-01-24 14:12:32,615] [INFO] Task started: Blastn
[2024-01-24 14:12:32,615] [INFO] Running command: blastn -query GCF_030814815.1_ASM3081481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76fe3d9-88a5-48e2-850d-83494d81e4c2/dqc_reference/reference_markers.fasta -out GCF_030814815.1_ASM3081481v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:33,671] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:33,674] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:33,675] [INFO] Target genome list was writen to GCF_030814815.1_ASM3081481v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:33,679] [INFO] Task started: fastANI
[2024-01-24 14:12:33,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg577fea06-a7f9-4c63-8c9d-d76e677bb631/GCF_030814815.1_ASM3081481v1_genomic.fna.gz --refList GCF_030814815.1_ASM3081481v1_genomic.fna/target_genomes.txt --output GCF_030814815.1_ASM3081481v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:46,203] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:46,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga76fe3d9-88a5-48e2-850d-83494d81e4c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:46,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga76fe3d9-88a5-48e2-850d-83494d81e4c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:46,213] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:46,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:46,214] [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
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	84.4758	936	1590	95	below_threshold
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	84.3499	985	1590	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	84.1328	975	1590	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	84.0191	960	1590	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	83.4471	944	1590	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	83.2901	1008	1590	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	83.2439	1020	1590	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	77.3392	456	1590	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	77.3088	484	1590	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	77.2299	472	1590	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:46,216] [INFO] DFAST Taxonomy check result was written to GCF_030814815.1_ASM3081481v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:46,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:46,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:46,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga76fe3d9-88a5-48e2-850d-83494d81e4c2/dqc_reference/checkm_data
[2024-01-24 14:12:46,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:46,268] [INFO] Task started: CheckM
[2024-01-24 14:12:46,269] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030814815.1_ASM3081481v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030814815.1_ASM3081481v1_genomic.fna/checkm_input GCF_030814815.1_ASM3081481v1_genomic.fna/checkm_result
[2024-01-24 14:13:35,104] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:35,106] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:35,127] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:35,128] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:35,128] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030814815.1_ASM3081481v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:35,128] [INFO] Task started: Blastn
[2024-01-24 14:13:35,129] [INFO] Running command: blastn -query GCF_030814815.1_ASM3081481v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga76fe3d9-88a5-48e2-850d-83494d81e4c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_030814815.1_ASM3081481v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:37,208] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:37,212] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:37,212] [INFO] Target genome list was writen to GCF_030814815.1_ASM3081481v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:37,258] [INFO] Task started: fastANI
[2024-01-24 14:13:37,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg577fea06-a7f9-4c63-8c9d-d76e677bb631/GCF_030814815.1_ASM3081481v1_genomic.fna.gz --refList GCF_030814815.1_ASM3081481v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030814815.1_ASM3081481v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:49,616] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:49,632] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:13:49,632] [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_014195655.1	s__Angulomicrobium tetraedrale	94.5259	1382	1590	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	85.2123	1025	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	84.7311	932	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	84.3654	985	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	84.3607	984	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	84.3161	953	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007559435.1	s__Starkeya sp007559435	84.2814	922	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	84.1645	972	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100155.1	s__Ancylobacter rudongensis	84.0272	959	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCA_000378025.1	s__Ancylobacter sp000378025	83.9433	988	1590	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	83.4562	943	1590	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:49,635] [INFO] GTDB search result was written to GCF_030814815.1_ASM3081481v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:49,635] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:49,639] [INFO] DFAST_QC result json was written to GCF_030814815.1_ASM3081481v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:49,639] [INFO] DFAST_QC completed!
[2024-01-24 14:13:49,639] [INFO] Total running time: 0h1m34s