[2024-01-24 12:16:08,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:16:08,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:16:08,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg1cb72236-8161-4982-89be-a7fe0c4a28d1/dqc_reference
[2024-01-24 12:16:09,778] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:16:09,779] [INFO] Task started: Prodigal
[2024-01-24 12:16:09,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg826501f8-6bfe-42f9-aa5d-72a43050aa02/GCF_002723995.1_ASM272399v1_genomic.fna.gz | prodigal -d GCF_002723995.1_ASM272399v1_genomic.fna/cds.fna -a GCF_002723995.1_ASM272399v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:16:19,148] [INFO] Task succeeded: Prodigal
[2024-01-24 12:16:19,149] [INFO] Task started: HMMsearch
[2024-01-24 12:16:19,149] [INFO] Running command: hmmsearch --tblout GCF_002723995.1_ASM272399v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1cb72236-8161-4982-89be-a7fe0c4a28d1/dqc_reference/reference_markers.hmm GCF_002723995.1_ASM272399v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:16:19,421] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:16:19,422] [INFO] Found 6/6 markers.
[2024-01-24 12:16:19,457] [INFO] Query marker FASTA was written to GCF_002723995.1_ASM272399v1_genomic.fna/markers.fasta
[2024-01-24 12:16:19,458] [INFO] Task started: Blastn
[2024-01-24 12:16:19,458] [INFO] Running command: blastn -query GCF_002723995.1_ASM272399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cb72236-8161-4982-89be-a7fe0c4a28d1/dqc_reference/reference_markers.fasta -out GCF_002723995.1_ASM272399v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:20,213] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:20,217] [INFO] Selected 12 target genomes.
[2024-01-24 12:16:20,217] [INFO] Target genome list was writen to GCF_002723995.1_ASM272399v1_genomic.fna/target_genomes.txt
[2024-01-24 12:16:20,220] [INFO] Task started: fastANI
[2024-01-24 12:16:20,220] [INFO] Running command: fastANI --query /var/lib/cwl/stg826501f8-6bfe-42f9-aa5d-72a43050aa02/GCF_002723995.1_ASM272399v1_genomic.fna.gz --refList GCF_002723995.1_ASM272399v1_genomic.fna/target_genomes.txt --output GCF_002723995.1_ASM272399v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:28,439] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:28,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1cb72236-8161-4982-89be-a7fe0c4a28d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:28,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1cb72236-8161-4982-89be-a7fe0c4a28d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:28,450] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:28,450] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:28,450] [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
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	100.0	1063	1064	95	conclusive
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	93.9867	869	1064	95	below_threshold
Gluconobacter cerevisiae	strain=LMG 27748	GCA_015244675.1	1379734	1379734	type	True	91.3405	820	1064	95	below_threshold
Gluconobacter cerevisiae	strain=DSM 27644	GCA_018811965.1	1379734	1379734	type	True	91.3353	822	1064	95	below_threshold
Gluconobacter albidus	strain=NBRC 3250	GCA_002723915.1	318683	318683	type	True	90.7535	841	1064	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	86.6486	742	1064	95	below_threshold
Gluconobacter oxydans	strain=DSM 3503	GCA_004346605.1	442	442	type	True	86.2767	734	1064	95	below_threshold
Gluconobacter oxydans	strain=NBRC 14819	GCA_006539685.1	442	442	type	True	85.9792	695	1064	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	85.9476	725	1064	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	78.0376	163	1064	95	below_threshold
Neokomagataea anthophila	strain=TBRC 2177	GCA_018122595.1	2826925	2826925	type	True	77.7449	119	1064	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.0519	55	1064	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:28,451] [INFO] DFAST Taxonomy check result was written to GCF_002723995.1_ASM272399v1_genomic.fna/tc_result.tsv
[2024-01-24 12:16:28,452] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:28,452] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:28,452] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1cb72236-8161-4982-89be-a7fe0c4a28d1/dqc_reference/checkm_data
[2024-01-24 12:16:28,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:28,486] [INFO] Task started: CheckM
[2024-01-24 12:16:28,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002723995.1_ASM272399v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002723995.1_ASM272399v1_genomic.fna/checkm_input GCF_002723995.1_ASM272399v1_genomic.fna/checkm_result
[2024-01-24 12:17:00,259] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:00,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:00,285] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:00,285] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:00,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002723995.1_ASM272399v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:00,286] [INFO] Task started: Blastn
[2024-01-24 12:17:00,286] [INFO] Running command: blastn -query GCF_002723995.1_ASM272399v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1cb72236-8161-4982-89be-a7fe0c4a28d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002723995.1_ASM272399v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:01,478] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:01,482] [INFO] Selected 9 target genomes.
[2024-01-24 12:17:01,482] [INFO] Target genome list was writen to GCF_002723995.1_ASM272399v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:01,485] [INFO] Task started: fastANI
[2024-01-24 12:17:01,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg826501f8-6bfe-42f9-aa5d-72a43050aa02/GCF_002723995.1_ASM272399v1_genomic.fna.gz --refList GCF_002723995.1_ASM272399v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002723995.1_ASM272399v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:08,047] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:08,060] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:08,060] [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_002723995.1	s__Gluconobacter kondonii	100.0	1063	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	97.23	97.04	0.89	0.87	8	conclusive
GCF_015244745.1	s__Gluconobacter cadivus	93.9867	869	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
GCF_015244675.1	s__Gluconobacter cerevisiae	91.3202	821	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002723915.1	s__Gluconobacter albidus	90.7567	841	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.35	97.61	0.92	0.87	6	-
GCF_009547075.1	s__Gluconobacter sp009547075	86.6645	741	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018256155.1	s__Gluconobacter sp018256155	86.6362	765	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539125.1	s__Gluconobacter sphaericus	86.1288	710	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.91	98.17	0.94	0.92	6	-
GCF_006539685.1	s__Gluconobacter oxydans	85.9977	693	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	98.14	96.18	0.93	0.85	13	-
GCF_015244565.1	s__Gluconobacter vitians	85.8185	746	1064	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:17:08,062] [INFO] GTDB search result was written to GCF_002723995.1_ASM272399v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:08,062] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:08,066] [INFO] DFAST_QC result json was written to GCF_002723995.1_ASM272399v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:08,066] [INFO] DFAST_QC completed!
[2024-01-24 12:17:08,067] [INFO] Total running time: 0h0m60s