[2024-01-24 14:05:48,853] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:48,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:48,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg46c86af8-b730-4078-8931-51061448f30a/dqc_reference
[2024-01-24 14:05:50,174] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:50,174] [INFO] Task started: Prodigal
[2024-01-24 14:05:50,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c0ca2a6-fec3-45d2-acd6-b75613ed28e6/GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/cds.fna -a GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:00,320] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:00,321] [INFO] Task started: HMMsearch
[2024-01-24 14:06:00,321] [INFO] Running command: hmmsearch --tblout GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46c86af8-b730-4078-8931-51061448f30a/dqc_reference/reference_markers.hmm GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:00,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:00,595] [INFO] Found 6/6 markers.
[2024-01-24 14:06:00,624] [INFO] Query marker FASTA was written to GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:06:00,625] [INFO] Task started: Blastn
[2024-01-24 14:06:00,625] [INFO] Running command: blastn -query GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c86af8-b730-4078-8931-51061448f30a/dqc_reference/reference_markers.fasta -out GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:01,965] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:01,969] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:01,969] [INFO] Target genome list was writen to GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:01,972] [INFO] Task started: fastANI
[2024-01-24 14:06:01,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0ca2a6-fec3-45d2-acd6-b75613ed28e6/GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna.gz --refList GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:12,315] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:12,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46c86af8-b730-4078-8931-51061448f30a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:12,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46c86af8-b730-4078-8931-51061448f30a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:12,328] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:12,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:12,328] [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
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	100.0	1121	1122	95	conclusive
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	88.8591	875	1122	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	88.7997	843	1122	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	86.9434	827	1122	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	86.5675	837	1122	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	85.2803	797	1122	95	below_threshold
Janibacter corallicola	strain=NBRC 107790	GCA_001570965.1	415212	415212	type	True	82.7982	670	1122	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	82.0936	618	1122	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	81.9215	704	1122	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.9236	398	1122	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.9102	430	1122	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.0197	361	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:12,330] [INFO] DFAST Taxonomy check result was written to GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:12,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:12,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:12,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46c86af8-b730-4078-8931-51061448f30a/dqc_reference/checkm_data
[2024-01-24 14:06:12,333] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:12,369] [INFO] Task started: CheckM
[2024-01-24 14:06:12,369] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/checkm_input GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:03,084] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:03,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:03,109] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:03,109] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:03,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:03,110] [INFO] Task started: Blastn
[2024-01-24 14:07:03,110] [INFO] Running command: blastn -query GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg46c86af8-b730-4078-8931-51061448f30a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:05,238] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:05,241] [INFO] Selected 9 target genomes.
[2024-01-24 14:07:05,241] [INFO] Target genome list was writen to GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:05,247] [INFO] Task started: fastANI
[2024-01-24 14:07:05,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c0ca2a6-fec3-45d2-acd6-b75613ed28e6/GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna.gz --refList GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:12,784] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:12,795] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:12,795] [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_900176385.1	s__Janibacter indicus	100.0	1121	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	97.60	97.16	0.90	0.88	4	conclusive
GCF_000297495.1	s__Janibacter hoylei	88.8237	841	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	99.95	99.95	0.99	0.99	2	-
GCF_001570945.1	s__Janibacter anophelis	86.9481	827	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	96.19	96.19	0.85	0.85	2	-
GCF_001591405.1	s__Janibacter terrae	86.5676	837	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	98.98	98.88	0.95	0.93	4	-
GCF_004295485.1	s__Janibacter limosus_A	85.7538	877	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428305.1	s__Janibacter sp001428305	85.2691	848	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116945.1	s__Janibacter merdipullorum	84.9743	714	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001570965.1	s__Janibacter corallicola	82.798	670	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Janibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016888335.1	s__Marihabitans sp016888335	82.0936	618	1122	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Marihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:12,797] [INFO] GTDB search result was written to GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:12,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:12,800] [INFO] DFAST_QC result json was written to GCF_900176385.1_IMG-taxon_2718217638_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:07:12,800] [INFO] DFAST_QC completed!
[2024-01-24 14:07:12,800] [INFO] Total running time: 0h1m24s