[2024-01-24 14:39:15,018] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg6c27b77e-207d-4fd0-b803-72553f9f807b/dqc_reference
[2024-01-24 14:39:16,384] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,385] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,386] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5858f66-d218-4eeb-9c6e-786d8e3ce657/GCF_019890635.1_ASM1989063v1_genomic.fna.gz | prodigal -d GCF_019890635.1_ASM1989063v1_genomic.fna/cds.fna -a GCF_019890635.1_ASM1989063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:36,441] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:36,442] [INFO] Task started: HMMsearch
[2024-01-24 14:39:36,442] [INFO] Running command: hmmsearch --tblout GCF_019890635.1_ASM1989063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6c27b77e-207d-4fd0-b803-72553f9f807b/dqc_reference/reference_markers.hmm GCF_019890635.1_ASM1989063v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:36,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:36,794] [INFO] Found 6/6 markers.
[2024-01-24 14:39:36,852] [INFO] Query marker FASTA was written to GCF_019890635.1_ASM1989063v1_genomic.fna/markers.fasta
[2024-01-24 14:39:36,853] [INFO] Task started: Blastn
[2024-01-24 14:39:36,853] [INFO] Running command: blastn -query GCF_019890635.1_ASM1989063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c27b77e-207d-4fd0-b803-72553f9f807b/dqc_reference/reference_markers.fasta -out GCF_019890635.1_ASM1989063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:38,204] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:38,208] [INFO] Selected 19 target genomes.
[2024-01-24 14:39:38,208] [INFO] Target genome list was writen to GCF_019890635.1_ASM1989063v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:38,215] [INFO] Task started: fastANI
[2024-01-24 14:39:38,215] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5858f66-d218-4eeb-9c6e-786d8e3ce657/GCF_019890635.1_ASM1989063v1_genomic.fna.gz --refList GCF_019890635.1_ASM1989063v1_genomic.fna/target_genomes.txt --output GCF_019890635.1_ASM1989063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:17,611] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:17,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6c27b77e-207d-4fd0-b803-72553f9f807b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:17,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6c27b77e-207d-4fd0-b803-72553f9f807b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:17,628] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:40:17,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:17,628] [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 sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	100.0	2375	2381	95	conclusive
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	87.7323	1706	2381	95	below_threshold
Streptomyces carpinensis	strain=NRRL B-16921	GCA_002154505.1	66369	66369	type	True	87.6171	1518	2381	95	below_threshold
Streptomyces naganishii	strain=JCM 4654	GCA_014650575.1	285447	285447	type	True	87.4604	1630	2381	95	below_threshold
Streptomyces anandii	strain=JCM 4720	GCA_014650655.1	285454	285454	type	True	87.3861	1638	2381	95	below_threshold
Streptomyces kebangsaanensis	strain=SUK12	GCA_001906585.1	864058	864058	type	True	87.1588	1515	2381	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	86.2269	1425	2381	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.5254	1605	2381	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	85.357	1603	2381	95	below_threshold
Streptomyces lavenduligriseus	strain=NRRL ISP-5487	GCA_000718625.1	67315	67315	type	True	85.3463	1555	2381	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.3046	1574	2381	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.2638	1564	2381	95	below_threshold
Streptomyces fumigatiscleroticus	strain=JCM 3101	GCA_014647975.1	66371	66371	type	True	85.2629	1587	2381	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.1801	1336	2381	95	below_threshold
Streptomyces puniciscabiei	strain=DSM 41929	GCA_006715785.1	164348	164348	type	True	85.1243	1590	2381	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	84.9991	1519	2381	95	below_threshold
Streptomyces glaucescens	strain=NRRL B-2706	GCA_002154375.1	1907	1907	type	True	84.998	1289	2381	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.9643	1501	2381	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	84.9409	1526	2381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:17,632] [INFO] DFAST Taxonomy check result was written to GCF_019890635.1_ASM1989063v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:17,633] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:17,633] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:17,633] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6c27b77e-207d-4fd0-b803-72553f9f807b/dqc_reference/checkm_data
[2024-01-24 14:40:17,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:17,702] [INFO] Task started: CheckM
[2024-01-24 14:40:17,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019890635.1_ASM1989063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019890635.1_ASM1989063v1_genomic.fna/checkm_input GCF_019890635.1_ASM1989063v1_genomic.fna/checkm_result
[2024-01-24 14:41:44,354] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:44,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:44,383] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:44,383] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:44,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019890635.1_ASM1989063v1_genomic.fna/markers.fasta)
[2024-01-24 14:41:44,384] [INFO] Task started: Blastn
[2024-01-24 14:41:44,384] [INFO] Running command: blastn -query GCF_019890635.1_ASM1989063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6c27b77e-207d-4fd0-b803-72553f9f807b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019890635.1_ASM1989063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:46,552] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:46,555] [INFO] Selected 14 target genomes.
[2024-01-24 14:41:46,556] [INFO] Target genome list was writen to GCF_019890635.1_ASM1989063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:46,566] [INFO] Task started: fastANI
[2024-01-24 14:41:46,566] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5858f66-d218-4eeb-9c6e-786d8e3ce657/GCF_019890635.1_ASM1989063v1_genomic.fna.gz --refList GCF_019890635.1_ASM1989063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019890635.1_ASM1989063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:25,074] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:25,086] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:25,086] [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_000383935.1	s__Streptomyces sp000383935	98.1027	2131	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.62	97.70	0.92	0.84	4	conclusive
GCF_013364255.1	s__Streptomyces seoulensis_A	92.4426	1902	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001654495.1	s__Streptomyces sp001654495	87.8217	1679	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.91	96.91	0.92	0.92	2	-
GCF_000720185.1	s__Streptomyces sp000720185	87.7395	1675	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654675.1	s__Streptomyces spiralis	87.7246	1707	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_002154505.1	s__Streptomyces carpinensis	87.5928	1520	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650575.1	s__Streptomyces naganishii	87.482	1627	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650655.1	s__Streptomyces anandii	87.3383	1644	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647975.1	s__Streptomyces fumigatiscleroticus	85.3265	1578	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650995.1	s__Streptomyces viridiviolaceus	85.3	1575	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002128465.1	s__Streptomyces pharetrae	85.1073	1393	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237655.1	s__Streptomyces sp002237655	85.003	1536	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000761215.1	s__Streptomyces glaucescens	84.9259	1519	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070565.1	s__Streptomyces sp018070565	84.7935	1452	2381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:25,090] [INFO] GTDB search result was written to GCF_019890635.1_ASM1989063v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:25,091] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:25,095] [INFO] DFAST_QC result json was written to GCF_019890635.1_ASM1989063v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:25,095] [INFO] DFAST_QC completed!
[2024-01-24 14:42:25,095] [INFO] Total running time: 0h3m10s