[2024-01-24 11:26:03,004] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:03,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:03,006] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c6e0599-4f2f-4c6b-96dd-fed6ae5f6c8b/dqc_reference
[2024-01-24 11:26:04,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,131] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg138fa919-f74c-43df-b111-995e6aebbf5c/GCF_006717145.1_ASM671714v1_genomic.fna.gz | prodigal -d GCF_006717145.1_ASM671714v1_genomic.fna/cds.fna -a GCF_006717145.1_ASM671714v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:19,364] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:19,365] [INFO] Task started: HMMsearch
[2024-01-24 11:26:19,365] [INFO] Running command: hmmsearch --tblout GCF_006717145.1_ASM671714v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c6e0599-4f2f-4c6b-96dd-fed6ae5f6c8b/dqc_reference/reference_markers.hmm GCF_006717145.1_ASM671714v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:19,603] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:19,604] [INFO] Found 6/6 markers.
[2024-01-24 11:26:19,647] [INFO] Query marker FASTA was written to GCF_006717145.1_ASM671714v1_genomic.fna/markers.fasta
[2024-01-24 11:26:19,648] [INFO] Task started: Blastn
[2024-01-24 11:26:19,648] [INFO] Running command: blastn -query GCF_006717145.1_ASM671714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c6e0599-4f2f-4c6b-96dd-fed6ae5f6c8b/dqc_reference/reference_markers.fasta -out GCF_006717145.1_ASM671714v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:20,787] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:20,790] [INFO] Selected 24 target genomes.
[2024-01-24 11:26:20,791] [INFO] Target genome list was writen to GCF_006717145.1_ASM671714v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:20,799] [INFO] Task started: fastANI
[2024-01-24 11:26:20,799] [INFO] Running command: fastANI --query /var/lib/cwl/stg138fa919-f74c-43df-b111-995e6aebbf5c/GCF_006717145.1_ASM671714v1_genomic.fna.gz --refList GCF_006717145.1_ASM671714v1_genomic.fna/target_genomes.txt --output GCF_006717145.1_ASM671714v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:38,260] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:38,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c6e0599-4f2f-4c6b-96dd-fed6ae5f6c8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:38,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c6e0599-4f2f-4c6b-96dd-fed6ae5f6c8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:38,279] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:38,279] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:38,279] [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	81.008	796	1796	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	80.9003	665	1796	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.7411	652	1796	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	79.7125	539	1796	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	79.6485	621	1796	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	79.6405	612	1796	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	79.5553	521	1796	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.4677	602	1796	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	79.4236	672	1796	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.3067	496	1796	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	79.2623	532	1796	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.2485	581	1796	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	79.2194	507	1796	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	79.0781	605	1796	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	79.0032	503	1796	95	below_threshold
Barrientosiimonas humi	strain=type strain: 39	GCA_910573815.1	999931	999931	type	True	78.8044	534	1796	95	below_threshold
Barrientosiimonas humi	strain=DSM 24617	GCA_006716095.1	999931	999931	type	True	78.768	535	1796	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.7197	502	1796	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.623	481	1796	95	below_threshold
Dermacoccus abyssi	strain=MT1.1	GCA_003515945.1	322596	322596	type	True	78.4707	392	1796	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.3655	438	1796	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	77.1838	398	1796	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	77.1391	401	1796	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	76.9365	478	1796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:38,281] [INFO] DFAST Taxonomy check result was written to GCF_006717145.1_ASM671714v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:38,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:38,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:38,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c6e0599-4f2f-4c6b-96dd-fed6ae5f6c8b/dqc_reference/checkm_data
[2024-01-24 11:26:38,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:38,330] [INFO] Task started: CheckM
[2024-01-24 11:26:38,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006717145.1_ASM671714v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006717145.1_ASM671714v1_genomic.fna/checkm_input GCF_006717145.1_ASM671714v1_genomic.fna/checkm_result
[2024-01-24 11:28:03,630] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:03,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:03,649] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:03,649] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:03,649] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006717145.1_ASM671714v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:03,650] [INFO] Task started: Blastn
[2024-01-24 11:28:03,650] [INFO] Running command: blastn -query GCF_006717145.1_ASM671714v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c6e0599-4f2f-4c6b-96dd-fed6ae5f6c8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006717145.1_ASM671714v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:05,452] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:05,455] [INFO] Selected 13 target genomes.
[2024-01-24 11:28:05,455] [INFO] Target genome list was writen to GCF_006717145.1_ASM671714v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:05,477] [INFO] Task started: fastANI
[2024-01-24 11:28:05,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg138fa919-f74c-43df-b111-995e6aebbf5c/GCF_006717145.1_ASM671714v1_genomic.fna.gz --refList GCF_006717145.1_ASM671714v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006717145.1_ASM671714v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:20,361] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:20,372] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:20,372] [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_006717145.1	s__Humibacillus xanthopallidus_A	100.0	1793	1796	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_006716675.1	s__Humibacillus xanthopallidus	91.149	1438	1796	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	84.8877	1105	1796	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	84.6255	1151	1796	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	84.6139	1129	1796	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	84.4909	1040	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716915.1	s__Terrabacter sp006716915	84.2228	1109	1796	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	84.208	1040	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717025.1	s__Terrabacter lapilli	83.7777	997	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	95.88	95.88	0.91	0.91	2	-
GCA_013361975.1	s__Terrabacter sp013361975	83.7123	588	1796	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	83.6279	1047	1796	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	83.2795	887	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Monashia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576595.1	s__Humihabitans oryzae	83.0478	999	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:20,374] [INFO] GTDB search result was written to GCF_006717145.1_ASM671714v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:20,375] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:20,379] [INFO] DFAST_QC result json was written to GCF_006717145.1_ASM671714v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:20,379] [INFO] DFAST_QC completed!
[2024-01-24 11:28:20,379] [INFO] Total running time: 0h2m17s