[2024-01-24 13:23:11,162] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:23:11,164] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:23:11,164] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb69d176-f612-4651-8ae7-8870f7868494/dqc_reference
[2024-01-24 13:23:12,494] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:23:12,495] [INFO] Task started: Prodigal
[2024-01-24 13:23:12,495] [INFO] Running command: gunzip -c /var/lib/cwl/stg7b6ba5db-0452-4aac-bc18-12138294a109/GCF_013408925.1_ASM1340892v1_genomic.fna.gz | prodigal -d GCF_013408925.1_ASM1340892v1_genomic.fna/cds.fna -a GCF_013408925.1_ASM1340892v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:23:23,281] [INFO] Task succeeded: Prodigal
[2024-01-24 13:23:23,281] [INFO] Task started: HMMsearch
[2024-01-24 13:23:23,281] [INFO] Running command: hmmsearch --tblout GCF_013408925.1_ASM1340892v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb69d176-f612-4651-8ae7-8870f7868494/dqc_reference/reference_markers.hmm GCF_013408925.1_ASM1340892v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:23:23,559] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:23:23,560] [INFO] Found 6/6 markers.
[2024-01-24 13:23:23,593] [INFO] Query marker FASTA was written to GCF_013408925.1_ASM1340892v1_genomic.fna/markers.fasta
[2024-01-24 13:23:23,594] [INFO] Task started: Blastn
[2024-01-24 13:23:23,594] [INFO] Running command: blastn -query GCF_013408925.1_ASM1340892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb69d176-f612-4651-8ae7-8870f7868494/dqc_reference/reference_markers.fasta -out GCF_013408925.1_ASM1340892v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:24,873] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:24,876] [INFO] Selected 18 target genomes.
[2024-01-24 13:23:24,877] [INFO] Target genome list was writen to GCF_013408925.1_ASM1340892v1_genomic.fna/target_genomes.txt
[2024-01-24 13:23:24,887] [INFO] Task started: fastANI
[2024-01-24 13:23:24,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6ba5db-0452-4aac-bc18-12138294a109/GCF_013408925.1_ASM1340892v1_genomic.fna.gz --refList GCF_013408925.1_ASM1340892v1_genomic.fna/target_genomes.txt --output GCF_013408925.1_ASM1340892v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:36,907] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:36,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb69d176-f612-4651-8ae7-8870f7868494/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:36,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb69d176-f612-4651-8ae7-8870f7868494/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:36,922] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:36,922] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:36,922] [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
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	100.0	1128	1128	95	conclusive
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	84.8253	811	1128	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	81.629	682	1128	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	80.2404	521	1128	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	80.2145	511	1128	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	80.0796	495	1128	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	80.0447	510	1128	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	79.7374	433	1128	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.7052	387	1128	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	79.3938	394	1128	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	79.3654	384	1128	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	79.338	409	1128	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.2085	419	1128	95	below_threshold
Janibacter anophelis	strain=NBRC 107843	GCA_001570945.1	319054	319054	type	True	79.2028	380	1128	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	79.1706	365	1128	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.1451	382	1128	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	79.042	405	1128	95	below_threshold
Dermacoccus abyssi	strain=MT1.1	GCA_003515945.1	322596	322596	type	True	78.4839	272	1128	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:36,924] [INFO] DFAST Taxonomy check result was written to GCF_013408925.1_ASM1340892v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:36,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:36,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:36,925] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb69d176-f612-4651-8ae7-8870f7868494/dqc_reference/checkm_data
[2024-01-24 13:23:36,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:36,965] [INFO] Task started: CheckM
[2024-01-24 13:23:36,965] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013408925.1_ASM1340892v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013408925.1_ASM1340892v1_genomic.fna/checkm_input GCF_013408925.1_ASM1340892v1_genomic.fna/checkm_result
[2024-01-24 13:24:34,190] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:34,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:34,214] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:34,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:34,215] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013408925.1_ASM1340892v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:34,215] [INFO] Task started: Blastn
[2024-01-24 13:24:34,215] [INFO] Running command: blastn -query GCF_013408925.1_ASM1340892v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb69d176-f612-4651-8ae7-8870f7868494/dqc_reference/reference_markers_gtdb.fasta -out GCF_013408925.1_ASM1340892v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:36,219] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:36,222] [INFO] Selected 7 target genomes.
[2024-01-24 13:24:36,223] [INFO] Target genome list was writen to GCF_013408925.1_ASM1340892v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:36,252] [INFO] Task started: fastANI
[2024-01-24 13:24:36,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6ba5db-0452-4aac-bc18-12138294a109/GCF_013408925.1_ASM1340892v1_genomic.fna.gz --refList GCF_013408925.1_ASM1340892v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013408925.1_ASM1340892v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:42,595] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:42,602] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:42,602] [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_013408925.1	s__Pedococcus badiiscoriae	100.0	1128	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006438965.1	s__Pedococcus bigeumensis	86.1699	889	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429605.1	s__Pedococcus sp001429605	85.3727	844	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.23	98.23	0.91	0.91	2	-
GCF_900104525.1	s__Pedococcus dokdonensis	84.8129	812	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428025.1	s__Pedococcus sp001428025	83.2157	771	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426245.1	s__Pedococcus sp001426245	83.1073	799	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	98.80	98.80	0.95	0.95	2	-
GCF_009707485.1	s__Pedococcus sp009707485	83.0435	750	1128	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Pedococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:42,604] [INFO] GTDB search result was written to GCF_013408925.1_ASM1340892v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:42,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:42,608] [INFO] DFAST_QC result json was written to GCF_013408925.1_ASM1340892v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:42,608] [INFO] DFAST_QC completed!
[2024-01-24 13:24:42,608] [INFO] Total running time: 0h1m31s