[2024-01-24 12:15:04,031] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,033] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,033] [INFO] DQC Reference Directory: /var/lib/cwl/stg774196e1-7e2a-4b8f-ad97-c000e52fb3eb/dqc_reference
[2024-01-24 12:15:05,352] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,353] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,353] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b5acb5a-816e-471b-ad34-815e889954b3/GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/cds.fna -a GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:40,322] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:40,323] [INFO] Task started: HMMsearch
[2024-01-24 12:15:40,323] [INFO] Running command: hmmsearch --tblout GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg774196e1-7e2a-4b8f-ad97-c000e52fb3eb/dqc_reference/reference_markers.hmm GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:40,732] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:40,733] [INFO] Found 6/6 markers.
[2024-01-24 12:15:40,803] [INFO] Query marker FASTA was written to GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:15:40,803] [INFO] Task started: Blastn
[2024-01-24 12:15:40,804] [INFO] Running command: blastn -query GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg774196e1-7e2a-4b8f-ad97-c000e52fb3eb/dqc_reference/reference_markers.fasta -out GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:42,184] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:42,187] [INFO] Selected 18 target genomes.
[2024-01-24 12:15:42,187] [INFO] Target genome list was writen to GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:15:42,195] [INFO] Task started: fastANI
[2024-01-24 12:15:42,195] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5acb5a-816e-471b-ad34-815e889954b3/GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna.gz --refList GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:16:23,323] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:23,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg774196e1-7e2a-4b8f-ad97-c000e52fb3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:16:23,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg774196e1-7e2a-4b8f-ad97-c000e52fb3eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:16:23,338] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:16:23,338] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:16:23,338] [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
Lentzea jiangxiensis	strain=CGMCC 4.6609	GCA_900104175.1	641025	641025	type	True	100.0	2828	2831	95	conclusive
Lentzea albida	strain=DSM 44437	GCA_900111005.1	65499	65499	type	True	89.5127	2166	2831	95	below_threshold
Lentzea cavernae	strain=CGMCC 4.7367	GCA_014653695.1	2020703	2020703	type	True	89.4795	2153	2831	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	89.2404	2173	2831	95	below_threshold
Lentzea flaviverrucosa	strain=DSM 44664	GCA_003350445.1	200379	200379	type	True	89.2367	2178	2831	95	below_threshold
Lentzea albidocapillata subsp. violacea	strain=DSM 44796	GCA_900100275.1	128104	40571	type	True	89.157	1976	2831	95	below_threshold
Lentzea pudingi	strain=CGMCC 4.7319	GCA_014646255.1	1789439	1789439	type	True	89.1408	2083	2831	95	below_threshold
Lentzea albidocapillata	strain=NRRL B-24057	GCA_000719115.1	40571	40571	type	True	89.1382	1998	2831	95	below_threshold
Lentzea waywayandensis	strain=DSM 44232	GCA_900115955.1	84724	84724	type	True	88.9634	2105	2831	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	88.0144	1974	2831	95	below_threshold
Lentzea alba	strain=NEAU-D13	GCA_011067745.1	2714351	2714351	type	True	87.9896	2027	2831	95	below_threshold
Lentzea kentuckyensis	strain=NRRL B-24416	GCA_002150765.1	360086	360086	type	True	87.793	1896	2831	95	below_threshold
Lentzea atacamensis	strain=DSM 45479	GCA_003269295.1	531938	531938	type	True	87.5712	2004	2831	95	below_threshold
Lentzea flava	strain=DSM 43885	GCA_024171845.1	103732	103732	type	True	87.4838	1976	2831	95	below_threshold
Lentzea terrae	strain=NEAU-LZS 42	GCA_003265345.1	2200761	2200761	type	True	87.3209	2013	2831	95	below_threshold
Lentzea guizhouensis	strain=DHS C013	GCA_001701025.1	1586287	1586287	type	True	87.0017	2068	2831	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	82.5155	1517	2831	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.1902	1061	2831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:16:23,340] [INFO] DFAST Taxonomy check result was written to GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:16:23,340] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:16:23,340] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:16:23,340] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg774196e1-7e2a-4b8f-ad97-c000e52fb3eb/dqc_reference/checkm_data
[2024-01-24 12:16:23,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:16:23,417] [INFO] Task started: CheckM
[2024-01-24 12:16:23,418] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/checkm_input GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:18:41,454] [INFO] Task succeeded: CheckM
[2024-01-24 12:18:41,456] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:18:41,484] [INFO] ===== Completeness check finished =====
[2024-01-24 12:18:41,484] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:18:41,485] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:18:41,485] [INFO] Task started: Blastn
[2024-01-24 12:18:41,485] [INFO] Running command: blastn -query GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg774196e1-7e2a-4b8f-ad97-c000e52fb3eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:18:43,515] [INFO] Task succeeded: Blastn
[2024-01-24 12:18:43,519] [INFO] Selected 16 target genomes.
[2024-01-24 12:18:43,520] [INFO] Target genome list was writen to GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:18:43,556] [INFO] Task started: fastANI
[2024-01-24 12:18:43,557] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b5acb5a-816e-471b-ad34-815e889954b3/GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna.gz --refList GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:19:20,302] [INFO] Task succeeded: fastANI
[2024-01-24 12:19:20,320] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:19:20,320] [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_900104175.1	s__Lentzea jiangxiensis	100.0	2826	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900111005.1	s__Lentzea albida	89.509	2167	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653695.1	s__Lentzea cavernae	89.4864	2152	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350445.1	s__Lentzea flaviverrucosa	89.2565	2174	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900100275.1	s__Lentzea violacea	89.1449	1978	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	N/A	N/A	N/A	N/A	1	-
GCF_014646255.1	s__Lentzea pudingi	89.1303	2084	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719115.1	s__Lentzea albidocapillata	89.0902	2005	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	96.6655	99.99	99.99	1.00	1.00	2	-
GCF_900115955.1	s__Lentzea waywayandensis	88.9788	2103	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110955.1	s__Lentzea xinjiangensis	88.4312	2069	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011067745.1	s__Lentzea alba	88.0062	2024	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269295.1	s__Lentzea atacamensis	87.5449	2008	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	98.63	98.63	0.90	0.90	2	-
GCF_003265345.1	s__Lentzea terrae	87.3385	2011	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907955.1	s__Lentzea nigeriaca	87.2853	1919	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279525.1	s__Lentzea sp001279525	87.0081	2045	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001701025.1	s__Lentzea guizhouensis	86.9932	2069	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000955955.1	s__Lentzea aerocolonigenes_A	86.9708	1856	2831	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Lentzea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:19:20,322] [INFO] GTDB search result was written to GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:19:20,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:19:20,329] [INFO] DFAST_QC result json was written to GCF_900104175.1_IMG-taxon_2675903132_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:19:20,330] [INFO] DFAST_QC completed!
[2024-01-24 12:19:20,330] [INFO] Total running time: 0h4m16s