[2024-01-24 13:22:10,832] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,834] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg4aa3af2d-e53e-4925-9488-b05ea587051b/dqc_reference
[2024-01-24 13:22:12,117] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:12,118] [INFO] Task started: Prodigal
[2024-01-24 13:22:12,118] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb870e5d-130a-4aa3-ae7f-7f8ac03b7b0c/GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/cds.fna -a GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:24,008] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:24,008] [INFO] Task started: HMMsearch
[2024-01-24 13:22:24,008] [INFO] Running command: hmmsearch --tblout GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4aa3af2d-e53e-4925-9488-b05ea587051b/dqc_reference/reference_markers.hmm GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:24,298] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:24,299] [INFO] Found 6/6 markers.
[2024-01-24 13:22:24,339] [INFO] Query marker FASTA was written to GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:22:24,339] [INFO] Task started: Blastn
[2024-01-24 13:22:24,339] [INFO] Running command: blastn -query GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aa3af2d-e53e-4925-9488-b05ea587051b/dqc_reference/reference_markers.fasta -out GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:25,729] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:25,732] [INFO] Selected 16 target genomes.
[2024-01-24 13:22:25,733] [INFO] Target genome list was writen to GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:22:25,742] [INFO] Task started: fastANI
[2024-01-24 13:22:25,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb870e5d-130a-4aa3-ae7f-7f8ac03b7b0c/GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna.gz --refList GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:44,759] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:44,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4aa3af2d-e53e-4925-9488-b05ea587051b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:44,760] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4aa3af2d-e53e-4925-9488-b05ea587051b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:44,776] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:22:44,776] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:44,776] [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
Cellulosimicrobium funkei	strain=JCM 14302	GCA_004519295.1	264251	264251	suspected-type	True	98.5494	1332	1432	95	conclusive
Cellulosimicrobium funkei	strain=NBRC 104118	GCA_001570825.1	264251	264251	suspected-type	True	98.5047	1275	1432	95	conclusive
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	85.0176	969	1432	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	83.469	904	1432	95	below_threshold
Oerskovia turbata	strain=JCM3160	GCA_004121315.1	1713	1713	type	True	81.7542	872	1432	95	below_threshold
Oerskovia rustica	strain=Sa4CUA1	GCA_014836555.1	2762237	2762237	type	True	81.716	879	1432	95	below_threshold
Oerskovia jenensis	strain=DSM 46000	GCA_016907235.1	162169	162169	type	True	81.5597	902	1432	95	below_threshold
Oerskovia douganii	strain=Sa1BUA8	GCA_015142735.1	2762210	2762210	type	True	81.5436	855	1432	95	below_threshold
Oerskovia merdavium	strain=Sa2CUA9	GCA_014836755.1	2762227	2762227	type	True	81.5005	892	1432	95	below_threshold
Sediminihabitans luteus	strain=DSM 25478	GCA_002797595.1	1138585	1138585	type	True	81.2521	740	1432	95	below_threshold
Sediminihabitans luteus	strain=NBRC 108568	GCA_016863455.1	1138585	1138585	type	True	81.25	734	1432	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	79.8228	690	1432	95	below_threshold
Actinotalea solisilvae	strain=KACC 19191	GCA_016464425.1	2072922	2072922	type	True	79.3942	719	1432	95	below_threshold
Promicromonospora kroppenstedtii	strain=DSM 19349	GCA_000515355.1	440482	440482	type	True	79.3066	682	1432	95	below_threshold
Promicromonospora sukumoe	strain=DSM 44121	GCA_014137995.1	88382	88382	type	True	79.3016	807	1432	95	below_threshold
Myceligenerans xiligouense	strain=DSM 15700	GCA_003814695.1	253184	253184	type	True	78.9333	611	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:44,778] [INFO] DFAST Taxonomy check result was written to GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:22:44,779] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:44,779] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:44,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4aa3af2d-e53e-4925-9488-b05ea587051b/dqc_reference/checkm_data
[2024-01-24 13:22:44,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:44,826] [INFO] Task started: CheckM
[2024-01-24 13:22:44,826] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/checkm_input GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:23:39,524] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:39,526] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:39,550] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:39,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:39,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:23:39,551] [INFO] Task started: Blastn
[2024-01-24 13:23:39,551] [INFO] Running command: blastn -query GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg4aa3af2d-e53e-4925-9488-b05ea587051b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:41,739] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:41,744] [INFO] Selected 10 target genomes.
[2024-01-24 13:23:41,745] [INFO] Target genome list was writen to GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:41,762] [INFO] Task started: fastANI
[2024-01-24 13:23:41,762] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb870e5d-130a-4aa3-ae7f-7f8ac03b7b0c/GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna.gz --refList GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:56,292] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:56,307] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:56,308] [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_004519295.1	s__Cellulosimicrobium funkei	98.5494	1332	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	98.03	96.84	0.93	0.88	18	conclusive
GCA_003052455.1	s__Cellulosimicrobium cinnabarinum	95.8991	1261	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	96.0261	97.94	97.40	0.92	0.90	4	-
GCF_016921195.1	s__Cellulosimicrobium cellulans_F	90.1233	1198	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001019615.1	s__Cellulosimicrobium cellulans_E	90.0703	1229	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.64	98.58	0.94	0.93	3	-
GCF_006539945.1	s__Cellulosimicrobium cellulans	89.9313	1178	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907755.1	s__Cellulosimicrobium cellulans_D	89.7006	1228	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	99.18	99.18	0.97	0.97	2	-
GCF_009708005.2	s__Cellulosimicrobium sp009708005	89.506	1207	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010287905.1	s__Cellulosimicrobium fucosivorans	89.3271	1124	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulosimicrobium	95.0	98.84	98.55	0.94	0.90	6	-
GCF_014137995.1	s__Promicromonospora sukumoe	79.3024	807	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515355.1	s__Promicromonospora kroppenstedtii	79.2682	689	1432	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Promicromonospora	95.0	97.09	97.09	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:56,311] [INFO] GTDB search result was written to GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:56,312] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:56,315] [INFO] DFAST_QC result json was written to GCF_900155925.1_IMG-taxon_2681812868_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:23:56,316] [INFO] DFAST_QC completed!
[2024-01-24 13:23:56,316] [INFO] Total running time: 0h1m45s