[2024-01-24 13:49:44,696] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:44,702] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:44,702] [INFO] DQC Reference Directory: /var/lib/cwl/stgea3435cf-22b4-4ffd-9d46-1f2099543957/dqc_reference
[2024-01-24 13:49:46,141] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,142] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,143] [INFO] Running command: gunzip -c /var/lib/cwl/stg63b93f08-f072-4406-ad4f-cab2bc33347f/GCF_007991735.1_ASM799173v1_genomic.fna.gz | prodigal -d GCF_007991735.1_ASM799173v1_genomic.fna/cds.fna -a GCF_007991735.1_ASM799173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:58,559] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:58,560] [INFO] Task started: HMMsearch
[2024-01-24 13:49:58,560] [INFO] Running command: hmmsearch --tblout GCF_007991735.1_ASM799173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea3435cf-22b4-4ffd-9d46-1f2099543957/dqc_reference/reference_markers.hmm GCF_007991735.1_ASM799173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:58,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:58,824] [INFO] Found 6/6 markers.
[2024-01-24 13:49:58,863] [INFO] Query marker FASTA was written to GCF_007991735.1_ASM799173v1_genomic.fna/markers.fasta
[2024-01-24 13:49:58,863] [INFO] Task started: Blastn
[2024-01-24 13:49:58,863] [INFO] Running command: blastn -query GCF_007991735.1_ASM799173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea3435cf-22b4-4ffd-9d46-1f2099543957/dqc_reference/reference_markers.fasta -out GCF_007991735.1_ASM799173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:00,264] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:00,268] [INFO] Selected 24 target genomes.
[2024-01-24 13:50:00,268] [INFO] Target genome list was writen to GCF_007991735.1_ASM799173v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:00,274] [INFO] Task started: fastANI
[2024-01-24 13:50:00,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b93f08-f072-4406-ad4f-cab2bc33347f/GCF_007991735.1_ASM799173v1_genomic.fna.gz --refList GCF_007991735.1_ASM799173v1_genomic.fna/target_genomes.txt --output GCF_007991735.1_ASM799173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:18,890] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:18,891] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea3435cf-22b4-4ffd-9d46-1f2099543957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:18,891] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea3435cf-22b4-4ffd-9d46-1f2099543957/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:18,910] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:18,910] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:18,910] [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	81.3985	755	1442	95	below_threshold
Intrasporangium chromatireducens	strain=Q5-1	GCA_000576575.1	1386088	1386088	type	True	81.094	662	1442	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	79.9903	625	1442	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	79.961	609	1442	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	79.9182	659	1442	95	below_threshold
Pedococcus cremeus	strain=CGMCC 1.6963	GCA_900111375.1	587636	587636	type	True	79.8775	650	1442	95	below_threshold
Pedococcus dokdonensis	strain=DSM 22329	GCA_900104525.1	443156	443156	type	True	79.7716	595	1442	95	below_threshold
Pedococcus badiiscoriae	strain=DSM 23987	GCA_013408925.1	642776	642776	type	True	79.5387	522	1442	95	below_threshold
Janibacter indicus	strain=CGMCC 1.12511	GCA_900176385.1	857417	857417	type	True	79.5025	515	1442	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	79.3857	524	1442	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.3594	480	1442	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.3586	546	1442	95	below_threshold
Janibacter hoylei	strain=PVAS-1	GCA_000297495.1	364298	364298	type	True	79.3255	475	1442	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	79.2326	463	1442	95	below_threshold
Janibacter terrae	strain=NBRC 107853	GCA_001591405.1	103817	103817	type	True	79.1863	506	1442	95	below_threshold
Janibacter limosus	strain=NBRC 16128	GCA_001570985.1	53458	53458	type	True	78.9872	429	1442	95	below_threshold
Luteipulveratus halotolerans	strain=C296001	GCA_001247745.1	1631356	1631356	type	True	78.8432	508	1442	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.7926	504	1442	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.6247	487	1442	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	78.1404	387	1442	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	77.5329	370	1442	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	77.2174	461	1442	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	77.0541	474	1442	95	below_threshold
Cellulomonas telluris	strain=CPCC 204705	GCA_004886325.1	2306636	2306636	type	True	76.9162	419	1442	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:18,912] [INFO] DFAST Taxonomy check result was written to GCF_007991735.1_ASM799173v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:18,912] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:18,912] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:18,912] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea3435cf-22b4-4ffd-9d46-1f2099543957/dqc_reference/checkm_data
[2024-01-24 13:50:18,913] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:18,954] [INFO] Task started: CheckM
[2024-01-24 13:50:18,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991735.1_ASM799173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991735.1_ASM799173v1_genomic.fna/checkm_input GCF_007991735.1_ASM799173v1_genomic.fna/checkm_result
[2024-01-24 13:51:06,368] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:06,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:06,393] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:06,393] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:06,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991735.1_ASM799173v1_genomic.fna/markers.fasta)
[2024-01-24 13:51:06,394] [INFO] Task started: Blastn
[2024-01-24 13:51:06,394] [INFO] Running command: blastn -query GCF_007991735.1_ASM799173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea3435cf-22b4-4ffd-9d46-1f2099543957/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991735.1_ASM799173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:08,478] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:08,483] [INFO] Selected 11 target genomes.
[2024-01-24 13:51:08,483] [INFO] Target genome list was writen to GCF_007991735.1_ASM799173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:08,513] [INFO] Task started: fastANI
[2024-01-24 13:51:08,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg63b93f08-f072-4406-ad4f-cab2bc33347f/GCF_007991735.1_ASM799173v1_genomic.fna.gz --refList GCF_007991735.1_ASM799173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991735.1_ASM799173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:22,396] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:22,410] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:22,411] [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_007991735.1	s__Terrabacter aerolatus	100.0	1440	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646815.1	s__Terrabacter tumescens	88.901	1184	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006716915.1	s__Terrabacter sp006716915	88.7894	1211	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429185.1	s__Terrabacter sp001429185	87.9367	1183	1442	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	87.7739	1186	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428505.1	s__Terrabacter sp001428505	87.7625	1151	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	99.23	99.23	0.97	0.97	2	-
GCA_000620545.1	s__Terrabacter sp000620545	86.4908	1066	1442	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	85.9411	1084	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014518425.1	s__Terrabacter sp014518425	85.3982	1050	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Terrabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717145.1	s__Humibacillus xanthopallidus_A	84.6286	1033	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716675.1	s__Humibacillus xanthopallidus	84.5912	1033	1442	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Humibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:22,412] [INFO] GTDB search result was written to GCF_007991735.1_ASM799173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:22,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:22,417] [INFO] DFAST_QC result json was written to GCF_007991735.1_ASM799173v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:22,417] [INFO] DFAST_QC completed!
[2024-01-24 13:51:22,417] [INFO] Total running time: 0h1m38s