[2024-01-24 15:19:04,558] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:04,560] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:04,560] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a75aff3-a2a3-40e4-9c9f-62d10708df56/dqc_reference
[2024-01-24 15:19:05,809] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:05,810] [INFO] Task started: Prodigal
[2024-01-24 15:19:05,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg5eba884a-7d9a-414f-ab1a-0af9287e4e9f/GCF_006716675.1_ASM671667v1_genomic.fna.gz | prodigal -d GCF_006716675.1_ASM671667v1_genomic.fna/cds.fna -a GCF_006716675.1_ASM671667v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:21,175] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:21,176] [INFO] Task started: HMMsearch
[2024-01-24 15:19:21,176] [INFO] Running command: hmmsearch --tblout GCF_006716675.1_ASM671667v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a75aff3-a2a3-40e4-9c9f-62d10708df56/dqc_reference/reference_markers.hmm GCF_006716675.1_ASM671667v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:21,474] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:21,476] [INFO] Found 6/6 markers.
[2024-01-24 15:19:21,525] [INFO] Query marker FASTA was written to GCF_006716675.1_ASM671667v1_genomic.fna/markers.fasta
[2024-01-24 15:19:21,526] [INFO] Task started: Blastn
[2024-01-24 15:19:21,526] [INFO] Running command: blastn -query GCF_006716675.1_ASM671667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a75aff3-a2a3-40e4-9c9f-62d10708df56/dqc_reference/reference_markers.fasta -out GCF_006716675.1_ASM671667v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:22,767] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:22,770] [INFO] Selected 21 target genomes.
[2024-01-24 15:19:22,771] [INFO] Target genome list was writen to GCF_006716675.1_ASM671667v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:22,780] [INFO] Task started: fastANI
[2024-01-24 15:19:22,780] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eba884a-7d9a-414f-ab1a-0af9287e4e9f/GCF_006716675.1_ASM671667v1_genomic.fna.gz --refList GCF_006716675.1_ASM671667v1_genomic.fna/target_genomes.txt --output GCF_006716675.1_ASM671667v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:39,143] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:39,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a75aff3-a2a3-40e4-9c9f-62d10708df56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:39,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a75aff3-a2a3-40e4-9c9f-62d10708df56/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:39,164] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:39,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:39,165] [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
Intrasporangium calvum	strain=DSM 43043	GCA_000184685.1	53358	53358	type	True	81.1838	776	1752	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	80.9723	673	1752	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	79.9158	605	1752	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	79.8846	599	1752	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.7557	657	1752	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	79.6247	525	1752	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.4726	608	1752	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	79.3897	495	1752	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.3643	691	1752	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.3316	499	1752	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.3072	573	1752	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.2932	585	1752	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	79.1248	520	1752	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	79.0892	491	1752	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_004025845.1	364298	364298	type	True	79.0735	506	1752	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	78.8452	476	1752	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.7804	511	1752	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.769	458	1752	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.739	488	1752	95	below_threshold
Luteipulveratus mongoliensis	strain=MN07-A0370	GCA_001190945.1	571913	571913	type	True	78.4202	438	1752	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	77.8597	424	1752	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:39,166] [INFO] DFAST Taxonomy check result was written to GCF_006716675.1_ASM671667v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:39,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:39,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:39,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a75aff3-a2a3-40e4-9c9f-62d10708df56/dqc_reference/checkm_data
[2024-01-24 15:19:39,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:39,222] [INFO] Task started: CheckM
[2024-01-24 15:19:39,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716675.1_ASM671667v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716675.1_ASM671667v1_genomic.fna/checkm_input GCF_006716675.1_ASM671667v1_genomic.fna/checkm_result
[2024-01-24 15:21:08,400] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:08,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:08,424] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:08,425] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:08,425] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716675.1_ASM671667v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:08,426] [INFO] Task started: Blastn
[2024-01-24 15:21:08,426] [INFO] Running command: blastn -query GCF_006716675.1_ASM671667v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a75aff3-a2a3-40e4-9c9f-62d10708df56/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716675.1_ASM671667v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:10,376] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:10,380] [INFO] Selected 11 target genomes.
[2024-01-24 15:21:10,381] [INFO] Target genome list was writen to GCF_006716675.1_ASM671667v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:10,389] [INFO] Task started: fastANI
[2024-01-24 15:21:10,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg5eba884a-7d9a-414f-ab1a-0af9287e4e9f/GCF_006716675.1_ASM671667v1_genomic.fna.gz --refList GCF_006716675.1_ASM671667v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716675.1_ASM671667v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:24,365] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:24,379] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:24,379] [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_006716675.1	s__Humibacillus xanthopallidus	100.0	1750	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006717145.1	s__Humibacillus xanthopallidus_A	91.2822	1411	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646815.1	s__Terrabacter tumescens	84.8303	1097	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001429185.1	s__Terrabacter sp001429185	84.7004	1107	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.06	99.06	0.95	0.95	2	-
GCF_000383675.1	s__Terrabacter sp000383675	84.6467	1105	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991735.1	s__Terrabacter aerolatus	84.5396	1033	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000955875.1	s__Terrabacter sp000955875	84.1303	1064	1752	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	83.8712	576	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	98.22	98.02	0.74	0.70	4	-
GCF_014518425.1	s__Terrabacter sp014518425	83.6764	1045	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620545.1	s__Terrabacter sp000620545	83.6597	1035	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956915.1	s__Monashia flava	83.5505	892	1752	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:24,380] [INFO] GTDB search result was written to GCF_006716675.1_ASM671667v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:24,381] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:24,386] [INFO] DFAST_QC result json was written to GCF_006716675.1_ASM671667v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:24,386] [INFO] DFAST_QC completed!
[2024-01-24 15:21:24,387] [INFO] Total running time: 0h2m20s