[2024-01-25 19:47:20,711] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg59a5c301-0ec9-4170-a129-94e093a9d9d9/dqc_reference
[2024-01-25 19:47:21,949] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,950] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,950] [INFO] Running command: gunzip -c /var/lib/cwl/stg268a4a88-7914-44f9-9525-3d44f51f8ec8/GCF_018274385.1_ASM1827438v1_genomic.fna.gz | prodigal -d GCF_018274385.1_ASM1827438v1_genomic.fna/cds.fna -a GCF_018274385.1_ASM1827438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:52,716] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:52,716] [INFO] Task started: HMMsearch
[2024-01-25 19:47:52,717] [INFO] Running command: hmmsearch --tblout GCF_018274385.1_ASM1827438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59a5c301-0ec9-4170-a129-94e093a9d9d9/dqc_reference/reference_markers.hmm GCF_018274385.1_ASM1827438v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:53,175] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:53,177] [INFO] Found 6/6 markers.
[2024-01-25 19:47:53,271] [INFO] Query marker FASTA was written to GCF_018274385.1_ASM1827438v1_genomic.fna/markers.fasta
[2024-01-25 19:47:53,271] [INFO] Task started: Blastn
[2024-01-25 19:47:53,271] [INFO] Running command: blastn -query GCF_018274385.1_ASM1827438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a5c301-0ec9-4170-a129-94e093a9d9d9/dqc_reference/reference_markers.fasta -out GCF_018274385.1_ASM1827438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:54,587] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:54,592] [INFO] Selected 15 target genomes.
[2024-01-25 19:47:54,592] [INFO] Target genome list was writen to GCF_018274385.1_ASM1827438v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:54,603] [INFO] Task started: fastANI
[2024-01-25 19:47:54,603] [INFO] Running command: fastANI --query /var/lib/cwl/stg268a4a88-7914-44f9-9525-3d44f51f8ec8/GCF_018274385.1_ASM1827438v1_genomic.fna.gz --refList GCF_018274385.1_ASM1827438v1_genomic.fna/target_genomes.txt --output GCF_018274385.1_ASM1827438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:27,803] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:27,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59a5c301-0ec9-4170-a129-94e093a9d9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:27,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59a5c301-0ec9-4170-a129-94e093a9d9d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:27,814] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:27,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:27,815] [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
Catenulispora pinistramenti	strain=NL8	GCA_018274385.1	2705254	2705254	type	True	100.0	3517	3544	95	conclusive
Catenulispora pinisilvae	strain=NH11	GCA_015356865.1	2705253	2705253	type	True	94.7934	2791	3544	95	below_threshold
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	86.8331	2173	3544	95	below_threshold
Catenulispora acidiphila	strain=DSM 44928	GCA_000024025.1	304895	304895	type	True	86.4422	2168	3544	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	77.5503	713	3544	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	77.4352	777	3544	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	77.2791	684	3544	95	below_threshold
Kitasatospora setae	strain=KM-6054	GCA_000269985.1	2066	2066	type	True	76.9701	1019	3544	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	76.95	830	3544	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	76.8699	747	3544	95	below_threshold
Streptomyces klenkii	strain=KCTC 29202	GCA_003626645.1	1420899	1420899	type	True	76.8031	753	3544	95	below_threshold
Embleya hyalina	strain=NBRC 13850	GCA_003967355.1	516124	516124	type	True	76.6572	980	3544	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	76.5691	759	3544	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	76.5006	824	3544	95	below_threshold
Actinokineospora enzanensis	strain=DSM 44649	GCA_000374445.1	155975	155975	type	True	76.2775	632	3544	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:27,817] [INFO] DFAST Taxonomy check result was written to GCF_018274385.1_ASM1827438v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:27,817] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:27,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:27,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59a5c301-0ec9-4170-a129-94e093a9d9d9/dqc_reference/checkm_data
[2024-01-25 19:48:27,818] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:27,922] [INFO] Task started: CheckM
[2024-01-25 19:48:27,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018274385.1_ASM1827438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018274385.1_ASM1827438v1_genomic.fna/checkm_input GCF_018274385.1_ASM1827438v1_genomic.fna/checkm_result
[2024-01-25 19:50:02,516] [INFO] Task succeeded: CheckM
[2024-01-25 19:50:02,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:50:02,543] [INFO] ===== Completeness check finished =====
[2024-01-25 19:50:02,543] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:50:02,543] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018274385.1_ASM1827438v1_genomic.fna/markers.fasta)
[2024-01-25 19:50:02,543] [INFO] Task started: Blastn
[2024-01-25 19:50:02,544] [INFO] Running command: blastn -query GCF_018274385.1_ASM1827438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59a5c301-0ec9-4170-a129-94e093a9d9d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_018274385.1_ASM1827438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:04,706] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:04,712] [INFO] Selected 7 target genomes.
[2024-01-25 19:50:04,712] [INFO] Target genome list was writen to GCF_018274385.1_ASM1827438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:50:04,720] [INFO] Task started: fastANI
[2024-01-25 19:50:04,720] [INFO] Running command: fastANI --query /var/lib/cwl/stg268a4a88-7914-44f9-9525-3d44f51f8ec8/GCF_018274385.1_ASM1827438v1_genomic.fna.gz --refList GCF_018274385.1_ASM1827438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018274385.1_ASM1827438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:50:25,826] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:25,832] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:50:25,833] [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_018274385.1	s__Catenulispora sp018274385	100.0	3517	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.51	99.51	0.94	0.94	2	conclusive
GCF_015356865.1	s__Catenulispora pinisilvae	94.7896	2792	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	99.32	99.32	0.94	0.94	2	-
GCF_015356825.1	s__Catenulispora rubra	86.8504	2172	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024025.1	s__Catenulispora acidiphila	86.4393	2168	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361685.1	s__Catenulispora sp013361685	83.6243	1501	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362315.1	s__Catenulispora sp013362315	82.9858	1315	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720175.1	s__Streptomyces sp000720175	76.8197	795	3544	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.69	95.67	0.86	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:50:25,834] [INFO] GTDB search result was written to GCF_018274385.1_ASM1827438v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:50:25,834] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:50:25,840] [INFO] DFAST_QC result json was written to GCF_018274385.1_ASM1827438v1_genomic.fna/dqc_result.json
[2024-01-25 19:50:25,840] [INFO] DFAST_QC completed!
[2024-01-25 19:50:25,840] [INFO] Total running time: 0h3m5s