[2024-01-24 13:28:01,357] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:01,360] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:01,360] [INFO] DQC Reference Directory: /var/lib/cwl/stg154955ce-eb3b-4510-ae56-0da9bb28c3de/dqc_reference
[2024-01-24 13:28:02,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:02,775] [INFO] Task started: Prodigal
[2024-01-24 13:28:02,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg78e15c73-bad1-4f1c-98e2-5d6172f73767/GCF_000367365.1_ASM36736v1_genomic.fna.gz | prodigal -d GCF_000367365.1_ASM36736v1_genomic.fna/cds.fna -a GCF_000367365.1_ASM36736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:36,840] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:36,841] [INFO] Task started: HMMsearch
[2024-01-24 13:28:36,841] [INFO] Running command: hmmsearch --tblout GCF_000367365.1_ASM36736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg154955ce-eb3b-4510-ae56-0da9bb28c3de/dqc_reference/reference_markers.hmm GCF_000367365.1_ASM36736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:37,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:37,266] [INFO] Found 6/6 markers.
[2024-01-24 13:28:37,355] [INFO] Query marker FASTA was written to GCF_000367365.1_ASM36736v1_genomic.fna/markers.fasta
[2024-01-24 13:28:37,356] [INFO] Task started: Blastn
[2024-01-24 13:28:37,356] [INFO] Running command: blastn -query GCF_000367365.1_ASM36736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg154955ce-eb3b-4510-ae56-0da9bb28c3de/dqc_reference/reference_markers.fasta -out GCF_000367365.1_ASM36736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:38,630] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:38,633] [INFO] Selected 24 target genomes.
[2024-01-24 13:28:38,634] [INFO] Target genome list was writen to GCF_000367365.1_ASM36736v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:38,657] [INFO] Task started: fastANI
[2024-01-24 13:28:38,657] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e15c73-bad1-4f1c-98e2-5d6172f73767/GCF_000367365.1_ASM36736v1_genomic.fna.gz --refList GCF_000367365.1_ASM36736v1_genomic.fna/target_genomes.txt --output GCF_000367365.1_ASM36736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:34,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:34,499] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg154955ce-eb3b-4510-ae56-0da9bb28c3de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:34,499] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg154955ce-eb3b-4510-ae56-0da9bb28c3de/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:34,516] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:34,516] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:34,516] [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
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	100.0	3800	3815	95	conclusive
Streptomyces hokutonensis	strain=R1-NS-10	GCA_000376565.1	1306990	1306990	type	True	91.2353	2713	3815	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	85.1307	2117	3815	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	84.8545	1927	3815	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	84.7891	1955	3815	95	below_threshold
Streptomyces hyaluromycini	strain=NBRC 110483	GCA_002217755.1	1377993	1377993	type	True	84.7145	2332	3815	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	84.6436	1921	3815	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.6217	1781	3815	95	below_threshold
Streptomyces cyaneochromogenes	strain=MK-45	GCA_003963535.1	2496836	2496836	type	True	84.4241	2094	3815	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	84.4118	1904	3815	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	84.3782	2007	3815	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	84.3381	1879	3815	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.2468	1898	3815	95	below_threshold
Streptomyces violarus	strain=CECT 3237	GCA_014191845.1	67380	67380	type	True	84.2381	1908	3815	95	below_threshold
Streptomyces violarus	strain=JCM 4534	GCA_014650255.1	67380	67380	type	True	84.2346	1905	3815	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.2267	1888	3815	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	84.1762	2043	3815	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.0209	2001	3815	95	below_threshold
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	83.916	1934	3815	95	below_threshold
Streptomyces asoensis	strain=JCM 4185	GCA_014649075.1	249586	249586	type	True	83.8888	1935	3815	95	below_threshold
Streptomyces asoensis	strain=NBRC 13813	GCA_016860545.1	249586	249586	type	True	83.8546	1936	3815	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	83.6356	1675	3815	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.2048	1924	3815	95	below_threshold
Streptomyces bauhiniae	strain=Bv016	GCA_004784475.1	2340725	2340725	type	True	83.0904	1501	3815	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:34,519] [INFO] DFAST Taxonomy check result was written to GCF_000367365.1_ASM36736v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:34,520] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:34,520] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:34,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg154955ce-eb3b-4510-ae56-0da9bb28c3de/dqc_reference/checkm_data
[2024-01-24 13:29:34,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:34,618] [INFO] Task started: CheckM
[2024-01-24 13:29:34,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000367365.1_ASM36736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000367365.1_ASM36736v1_genomic.fna/checkm_input GCF_000367365.1_ASM36736v1_genomic.fna/checkm_result
[2024-01-24 13:31:15,578] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:15,579] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:15,610] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:15,611] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:15,611] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000367365.1_ASM36736v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:15,611] [INFO] Task started: Blastn
[2024-01-24 13:31:15,611] [INFO] Running command: blastn -query GCF_000367365.1_ASM36736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg154955ce-eb3b-4510-ae56-0da9bb28c3de/dqc_reference/reference_markers_gtdb.fasta -out GCF_000367365.1_ASM36736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:17,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:17,485] [INFO] Selected 7 target genomes.
[2024-01-24 13:31:17,485] [INFO] Target genome list was writen to GCF_000367365.1_ASM36736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:17,512] [INFO] Task started: fastANI
[2024-01-24 13:31:17,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg78e15c73-bad1-4f1c-98e2-5d6172f73767/GCF_000367365.1_ASM36736v1_genomic.fna.gz --refList GCF_000367365.1_ASM36736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000367365.1_ASM36736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:38,072] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:38,080] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:31:38,080] [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_000367365.1	s__Streptomyces prunicolor	100.0	3800	3815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000716605.1	s__Streptomyces sp000716605	93.4146	2775	3815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612545.1	s__Streptomyces sp016612545	92.2216	2445	3815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716435.1	s__Streptomyces xylophagus	92.2188	2749	3815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000376565.1	s__Streptomyces hokutonensis	91.2279	2713	3815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.37	96.37	0.82	0.82	2	-
GCF_016654115.1	s__Streptomyces sp016654115	91.0538	2526	3815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.80	0.86	0.86	2	-
GCF_000721105.1	s__Streptomyces cellulosae_A	84.7969	1981	3815	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:38,082] [INFO] GTDB search result was written to GCF_000367365.1_ASM36736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:38,083] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:38,086] [INFO] DFAST_QC result json was written to GCF_000367365.1_ASM36736v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:38,087] [INFO] DFAST_QC completed!
[2024-01-24 13:31:38,087] [INFO] Total running time: 0h3m37s