[2024-01-24 12:54:22,581] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:22,585] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:22,585] [INFO] DQC Reference Directory: /var/lib/cwl/stge9912f5a-6fb9-4dc4-9bbf-d65e3b5379a2/dqc_reference
[2024-01-24 12:54:24,145] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:24,146] [INFO] Task started: Prodigal
[2024-01-24 12:54:24,146] [INFO] Running command: gunzip -c /var/lib/cwl/stg99700161-f358-40df-beca-c0c105837afb/GCF_000768705.1_ASM76870v1_genomic.fna.gz | prodigal -d GCF_000768705.1_ASM76870v1_genomic.fna/cds.fna -a GCF_000768705.1_ASM76870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:36,452] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:36,452] [INFO] Task started: HMMsearch
[2024-01-24 12:54:36,452] [INFO] Running command: hmmsearch --tblout GCF_000768705.1_ASM76870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9912f5a-6fb9-4dc4-9bbf-d65e3b5379a2/dqc_reference/reference_markers.hmm GCF_000768705.1_ASM76870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:36,730] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:36,731] [INFO] Found 6/6 markers.
[2024-01-24 12:54:36,782] [INFO] Query marker FASTA was written to GCF_000768705.1_ASM76870v1_genomic.fna/markers.fasta
[2024-01-24 12:54:36,783] [INFO] Task started: Blastn
[2024-01-24 12:54:36,783] [INFO] Running command: blastn -query GCF_000768705.1_ASM76870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9912f5a-6fb9-4dc4-9bbf-d65e3b5379a2/dqc_reference/reference_markers.fasta -out GCF_000768705.1_ASM76870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:37,928] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:37,931] [INFO] Selected 13 target genomes.
[2024-01-24 12:54:37,931] [INFO] Target genome list was writen to GCF_000768705.1_ASM76870v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:37,935] [INFO] Task started: fastANI
[2024-01-24 12:54:37,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg99700161-f358-40df-beca-c0c105837afb/GCF_000768705.1_ASM76870v1_genomic.fna.gz --refList GCF_000768705.1_ASM76870v1_genomic.fna/target_genomes.txt --output GCF_000768705.1_ASM76870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:48,625] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:48,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9912f5a-6fb9-4dc4-9bbf-d65e3b5379a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:48,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9912f5a-6fb9-4dc4-9bbf-d65e3b5379a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:48,642] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:48,642] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:48,642] [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
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	100.0	1298	1299	95	conclusive
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	83.8937	844	1299	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	83.7749	832	1299	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	83.7705	815	1299	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	82.8259	733	1299	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	82.3933	752	1299	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.5376	476	1299	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.3718	410	1299	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.2983	435	1299	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	79.2672	389	1299	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.7206	334	1299	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.636	361	1299	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.6118	338	1299	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:48,644] [INFO] DFAST Taxonomy check result was written to GCF_000768705.1_ASM76870v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:48,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:48,645] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:48,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9912f5a-6fb9-4dc4-9bbf-d65e3b5379a2/dqc_reference/checkm_data
[2024-01-24 12:54:48,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:48,685] [INFO] Task started: CheckM
[2024-01-24 12:54:48,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000768705.1_ASM76870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000768705.1_ASM76870v1_genomic.fna/checkm_input GCF_000768705.1_ASM76870v1_genomic.fna/checkm_result
[2024-01-24 12:55:43,192] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:43,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:43,221] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:43,221] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:43,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000768705.1_ASM76870v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:43,222] [INFO] Task started: Blastn
[2024-01-24 12:55:43,222] [INFO] Running command: blastn -query GCF_000768705.1_ASM76870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9912f5a-6fb9-4dc4-9bbf-d65e3b5379a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000768705.1_ASM76870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:44,972] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:44,977] [INFO] Selected 11 target genomes.
[2024-01-24 12:55:44,977] [INFO] Target genome list was writen to GCF_000768705.1_ASM76870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:44,987] [INFO] Task started: fastANI
[2024-01-24 12:55:44,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg99700161-f358-40df-beca-c0c105837afb/GCF_000768705.1_ASM76870v1_genomic.fna.gz --refList GCF_000768705.1_ASM76870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000768705.1_ASM76870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:54,491] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:54,503] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:54,503] [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_000768705.1	s__Knoellia sinensis	100.0	1298	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000768685.1	s__Knoellia subterranea	83.9042	843	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992835.1	s__Knoellia locipacati	83.8825	840	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768675.1	s__Knoellia flava	83.8004	813	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000152705.1	s__Knoellia sp000152705	83.0908	838	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427985.1	s__Knoellia sp001427985	82.8639	780	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768695.1	s__Knoellia aerolata	82.8208	733	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002895.1	s__Knoellia remsis	82.3689	755	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858245.1	s__Ornithinibacter aureus	79.8675	502	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955875.1	s__Terrabacter sp000955875	79.3081	462	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361975.1	s__Terrabacter sp013361975	78.7437	283	1299	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	98.22	98.02	0.74	0.70	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:54,505] [INFO] GTDB search result was written to GCF_000768705.1_ASM76870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:54,506] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:54,509] [INFO] DFAST_QC result json was written to GCF_000768705.1_ASM76870v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:54,510] [INFO] DFAST_QC completed!
[2024-01-24 12:55:54,510] [INFO] Total running time: 0h1m32s