[2024-01-25 19:02:35,800] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:35,801] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:35,801] [INFO] DQC Reference Directory: /var/lib/cwl/stg503ca5a0-9358-4d45-a3d8-a627f626fdca/dqc_reference
[2024-01-25 19:02:36,931] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:36,932] [INFO] Task started: Prodigal
[2024-01-25 19:02:36,932] [INFO] Running command: gunzip -c /var/lib/cwl/stgb68485d2-bdaf-4727-aef3-076a8137e0d4/GCF_018139625.1_ASM1813962v1_genomic.fna.gz | prodigal -d GCF_018139625.1_ASM1813962v1_genomic.fna/cds.fna -a GCF_018139625.1_ASM1813962v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:54,329] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:54,330] [INFO] Task started: HMMsearch
[2024-01-25 19:02:54,330] [INFO] Running command: hmmsearch --tblout GCF_018139625.1_ASM1813962v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg503ca5a0-9358-4d45-a3d8-a627f626fdca/dqc_reference/reference_markers.hmm GCF_018139625.1_ASM1813962v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:54,653] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:54,654] [INFO] Found 6/6 markers.
[2024-01-25 19:02:54,712] [INFO] Query marker FASTA was written to GCF_018139625.1_ASM1813962v1_genomic.fna/markers.fasta
[2024-01-25 19:02:54,712] [INFO] Task started: Blastn
[2024-01-25 19:02:54,712] [INFO] Running command: blastn -query GCF_018139625.1_ASM1813962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg503ca5a0-9358-4d45-a3d8-a627f626fdca/dqc_reference/reference_markers.fasta -out GCF_018139625.1_ASM1813962v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:55,981] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:55,984] [INFO] Selected 24 target genomes.
[2024-01-25 19:02:55,984] [INFO] Target genome list was writen to GCF_018139625.1_ASM1813962v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:56,011] [INFO] Task started: fastANI
[2024-01-25 19:02:56,011] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68485d2-bdaf-4727-aef3-076a8137e0d4/GCF_018139625.1_ASM1813962v1_genomic.fna.gz --refList GCF_018139625.1_ASM1813962v1_genomic.fna/target_genomes.txt --output GCF_018139625.1_ASM1813962v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:29,879] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:29,879] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg503ca5a0-9358-4d45-a3d8-a627f626fdca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:29,879] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg503ca5a0-9358-4d45-a3d8-a627f626fdca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:29,893] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:03:29,893] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:03:29,893] [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
Actinospica durhamensis	strain=CSCA 57	GCA_018139695.1	1508375	1508375	type	True	82.769	1305	2466	95	below_threshold
Actinospica robiniae	strain=DSM 44927	GCA_000504285.1	304901	304901	type	True	82.4436	1392	2466	95	below_threshold
Actinocrinis puniceicyclus	strain=DSM 45618	GCA_018283645.1	977794	977794	type	True	79.3253	856	2466	95	below_threshold
Catenulispora rubra	strain=DSM 44948	GCA_015356825.1	280293	280293	type	True	78.0787	892	2466	95	below_threshold
Streptomyces parmotrematis	strain=Ptm05	GCA_019890615.1	2873249	2873249	type	True	77.7594	680	2466	95	below_threshold
Streptomyces radiopugnans	strain=CGMCC 4.3519	GCA_900110735.1	403935	403935	type	True	77.6871	593	2466	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	77.6628	602	2466	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	77.6484	533	2466	95	below_threshold
Streptomyces thermodiastaticus	strain=JCM 4840	GCA_014656135.1	44061	44061	type	True	77.6385	595	2466	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	77.6282	566	2466	95	below_threshold
Kitasatospora paracochleata	strain=DSM 41656	GCA_024172095.1	58354	58354	type	True	77.5977	791	2466	95	below_threshold
Kitasatospora cheerisanensis	strain=KCTC 2395	GCA_000696185.1	81942	81942	type	True	77.5887	789	2466	95	below_threshold
Streptomyces megasporus	strain=NRRL B-16372	GCA_000718985.1	44060	44060	type	True	77.5678	534	2466	95	below_threshold
Streptomyces rubellomurinus	strain=ATCC 31215	GCA_000961885.1	359131	359131	type	True	77.5381	825	2466	95	below_threshold
Allostreptomyces psammosilenae	strain=DSM 42178	GCA_013407765.1	1892865	1892865	type	True	77.3971	648	2466	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	77.3861	537	2466	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	77.3394	594	2466	95	below_threshold
Streptomyces chumphonensis	strain=KK1-2	GCA_014779715.1	1214925	1214925	type	True	77.3068	527	2466	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	77.3027	708	2466	95	below_threshold
Streptomyces toxytricini	strain=JCM 4421	GCA_014649915.1	67369	67369	type	True	77.2685	674	2466	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	77.2513	641	2466	95	below_threshold
Streptomyces rhizosphaericola	strain=1AS2c	GCA_004794175.1	2564098	2564098	type	True	77.2416	545	2466	95	below_threshold
Embleya scabrispora	strain=DSM 41855	GCA_000372745.1	159449	159449	type	True	77.1343	733	2466	95	below_threshold
Streptomyces kanasensis	strain=ZX01	GCA_001484625.1	936756	936756	type	True	77.0643	630	2466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:29,895] [INFO] DFAST Taxonomy check result was written to GCF_018139625.1_ASM1813962v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:29,895] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:29,895] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:29,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg503ca5a0-9358-4d45-a3d8-a627f626fdca/dqc_reference/checkm_data
[2024-01-25 19:03:29,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:29,969] [INFO] Task started: CheckM
[2024-01-25 19:03:29,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018139625.1_ASM1813962v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018139625.1_ASM1813962v1_genomic.fna/checkm_input GCF_018139625.1_ASM1813962v1_genomic.fna/checkm_result
[2024-01-25 19:04:24,407] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:24,408] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:24,425] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:24,425] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:24,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018139625.1_ASM1813962v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:24,426] [INFO] Task started: Blastn
[2024-01-25 19:04:24,426] [INFO] Running command: blastn -query GCF_018139625.1_ASM1813962v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg503ca5a0-9358-4d45-a3d8-a627f626fdca/dqc_reference/reference_markers_gtdb.fasta -out GCF_018139625.1_ASM1813962v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:26,622] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:26,625] [INFO] Selected 14 target genomes.
[2024-01-25 19:04:26,625] [INFO] Target genome list was writen to GCF_018139625.1_ASM1813962v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:26,644] [INFO] Task started: fastANI
[2024-01-25 19:04:26,644] [INFO] Running command: fastANI --query /var/lib/cwl/stgb68485d2-bdaf-4727-aef3-076a8137e0d4/GCF_018139625.1_ASM1813962v1_genomic.fna.gz --refList GCF_018139625.1_ASM1813962v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018139625.1_ASM1813962v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:49,858] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:49,867] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:49,867] [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_018139625.1	s__Actinospica sp018139625	100.0	2444	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018139695.1	s__Actinospica durhamensis	82.7448	1310	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504285.1	s__Actinospica robiniae	82.4397	1395	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinospica	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018283645.1	s__Actinocrinis puniceicyclus	79.3412	853	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Actinocrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014083985.1	s__SCUT-3 sp014083985	77.8707	622	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__SCUT-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013361685.1	s__Catenulispora sp013361685	77.6707	749	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Catenulisporaceae;g__Catenulispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000696185.1	s__Kitasatospora cheerisanensis	77.5723	794	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Kitasatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900091855.1	s__Streptomyces sp900091855	77.4516	640	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013407765.1	s__Allostreptomyces psammosilenae	77.3927	649	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Allostreptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007280575.1	s__Streptomyces sp007280575	77.3632	541	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654895.1	s__Streptomyces filamentosus	77.3286	721	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.28	96.27	0.93	0.92	4	-
GCF_000424825.1	s__Streptomyces sp000424825	77.0437	582	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484625.1	s__Streptomyces kanasensis	77.0289	639	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362785.1	s__Streptomyces sp013362785	76.7958	506	2466	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:49,868] [INFO] GTDB search result was written to GCF_018139625.1_ASM1813962v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:49,869] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:49,872] [INFO] DFAST_QC result json was written to GCF_018139625.1_ASM1813962v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:49,872] [INFO] DFAST_QC completed!
[2024-01-25 19:04:49,872] [INFO] Total running time: 0h2m14s