[2024-01-25 20:23:50,841] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:23:50,844] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:23:50,844] [INFO] DQC Reference Directory: /var/lib/cwl/stg5d912ff7-05cd-4311-9e2c-3a5244d48a56/dqc_reference
[2024-01-25 20:23:51,969] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:23:51,970] [INFO] Task started: Prodigal
[2024-01-25 20:23:51,970] [INFO] Running command: gunzip -c /var/lib/cwl/stgc17b7388-d80c-4ff4-bf55-bbe9d44b2809/GCF_014636255.1_ASM1463625v1_genomic.fna.gz | prodigal -d GCF_014636255.1_ASM1463625v1_genomic.fna/cds.fna -a GCF_014636255.1_ASM1463625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:00,909] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:00,910] [INFO] Task started: HMMsearch
[2024-01-25 20:24:00,910] [INFO] Running command: hmmsearch --tblout GCF_014636255.1_ASM1463625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5d912ff7-05cd-4311-9e2c-3a5244d48a56/dqc_reference/reference_markers.hmm GCF_014636255.1_ASM1463625v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:01,163] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:01,164] [INFO] Found 6/6 markers.
[2024-01-25 20:24:01,195] [INFO] Query marker FASTA was written to GCF_014636255.1_ASM1463625v1_genomic.fna/markers.fasta
[2024-01-25 20:24:01,195] [INFO] Task started: Blastn
[2024-01-25 20:24:01,195] [INFO] Running command: blastn -query GCF_014636255.1_ASM1463625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d912ff7-05cd-4311-9e2c-3a5244d48a56/dqc_reference/reference_markers.fasta -out GCF_014636255.1_ASM1463625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:02,365] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:02,368] [INFO] Selected 12 target genomes.
[2024-01-25 20:24:02,368] [INFO] Target genome list was writen to GCF_014636255.1_ASM1463625v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:02,374] [INFO] Task started: fastANI
[2024-01-25 20:24:02,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgc17b7388-d80c-4ff4-bf55-bbe9d44b2809/GCF_014636255.1_ASM1463625v1_genomic.fna.gz --refList GCF_014636255.1_ASM1463625v1_genomic.fna/target_genomes.txt --output GCF_014636255.1_ASM1463625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:12,410] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:12,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5d912ff7-05cd-4311-9e2c-3a5244d48a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:12,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5d912ff7-05cd-4311-9e2c-3a5244d48a56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:12,418] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:24:12,419] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:12,419] [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 flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	100.0	1183	1185	95	conclusive
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	99.9551	1132	1185	95	conclusive
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	85.3408	862	1185	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	84.4314	812	1185	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	84.4229	864	1185	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	83.7735	831	1185	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	80.6889	621	1185	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	80.4125	582	1185	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	80.3889	518	1185	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.0947	441	1185	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	79.0686	434	1185	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.9989	461	1185	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:12,420] [INFO] DFAST Taxonomy check result was written to GCF_014636255.1_ASM1463625v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:12,421] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:12,421] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:12,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5d912ff7-05cd-4311-9e2c-3a5244d48a56/dqc_reference/checkm_data
[2024-01-25 20:24:12,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:12,457] [INFO] Task started: CheckM
[2024-01-25 20:24:12,457] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014636255.1_ASM1463625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014636255.1_ASM1463625v1_genomic.fna/checkm_input GCF_014636255.1_ASM1463625v1_genomic.fna/checkm_result
[2024-01-25 20:25:07,920] [INFO] Task succeeded: CheckM
[2024-01-25 20:25:07,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:25:07,949] [INFO] ===== Completeness check finished =====
[2024-01-25 20:25:07,949] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:25:07,950] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014636255.1_ASM1463625v1_genomic.fna/markers.fasta)
[2024-01-25 20:25:07,950] [INFO] Task started: Blastn
[2024-01-25 20:25:07,950] [INFO] Running command: blastn -query GCF_014636255.1_ASM1463625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5d912ff7-05cd-4311-9e2c-3a5244d48a56/dqc_reference/reference_markers_gtdb.fasta -out GCF_014636255.1_ASM1463625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:25:09,922] [INFO] Task succeeded: Blastn
[2024-01-25 20:25:09,925] [INFO] Selected 9 target genomes.
[2024-01-25 20:25:09,925] [INFO] Target genome list was writen to GCF_014636255.1_ASM1463625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:25:09,953] [INFO] Task started: fastANI
[2024-01-25 20:25:09,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgc17b7388-d80c-4ff4-bf55-bbe9d44b2809/GCF_014636255.1_ASM1463625v1_genomic.fna.gz --refList GCF_014636255.1_ASM1463625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014636255.1_ASM1463625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:17,883] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:17,890] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:17,890] [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_000768675.1	s__Knoellia flava	99.9551	1132	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_007992835.1	s__Knoellia locipacati	87.8994	975	1185	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	85.3485	862	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768685.1	s__Knoellia subterranea	84.4345	863	1185	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	84.3829	816	1185	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	84.2229	846	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768705.1	s__Knoellia sinensis	83.7844	830	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	81.1371	506	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858245.1	s__Ornithinibacter aureus	80.8028	599	1185	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:17,891] [INFO] GTDB search result was written to GCF_014636255.1_ASM1463625v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:17,892] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:17,894] [INFO] DFAST_QC result json was written to GCF_014636255.1_ASM1463625v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:17,894] [INFO] DFAST_QC completed!
[2024-01-25 20:25:17,894] [INFO] Total running time: 0h1m27s