[2024-01-24 11:44:38,167] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,168] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,168] [INFO] DQC Reference Directory: /var/lib/cwl/stgcef83ac1-d9ac-4453-85e6-b19109d8bf17/dqc_reference
[2024-01-24 11:44:41,488] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,489] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,490] [INFO] Running command: gunzip -c /var/lib/cwl/stgef3b90af-3e72-4fa1-ac8b-b2cce5f8fbcf/GCF_003696235.1_ASM369623v1_genomic.fna.gz | prodigal -d GCF_003696235.1_ASM369623v1_genomic.fna/cds.fna -a GCF_003696235.1_ASM369623v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:57,708] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:57,709] [INFO] Task started: HMMsearch
[2024-01-24 11:44:57,709] [INFO] Running command: hmmsearch --tblout GCF_003696235.1_ASM369623v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcef83ac1-d9ac-4453-85e6-b19109d8bf17/dqc_reference/reference_markers.hmm GCF_003696235.1_ASM369623v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:58,011] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:58,012] [INFO] Found 6/6 markers.
[2024-01-24 11:44:58,068] [INFO] Query marker FASTA was written to GCF_003696235.1_ASM369623v1_genomic.fna/markers.fasta
[2024-01-24 11:44:58,069] [INFO] Task started: Blastn
[2024-01-24 11:44:58,069] [INFO] Running command: blastn -query GCF_003696235.1_ASM369623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcef83ac1-d9ac-4453-85e6-b19109d8bf17/dqc_reference/reference_markers.fasta -out GCF_003696235.1_ASM369623v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:59,447] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:59,451] [INFO] Selected 14 target genomes.
[2024-01-24 11:44:59,451] [INFO] Target genome list was writen to GCF_003696235.1_ASM369623v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:59,458] [INFO] Task started: fastANI
[2024-01-24 11:44:59,458] [INFO] Running command: fastANI --query /var/lib/cwl/stgef3b90af-3e72-4fa1-ac8b-b2cce5f8fbcf/GCF_003696235.1_ASM369623v1_genomic.fna.gz --refList GCF_003696235.1_ASM369623v1_genomic.fna/target_genomes.txt --output GCF_003696235.1_ASM369623v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:22,463] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:22,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcef83ac1-d9ac-4453-85e6-b19109d8bf17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:22,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcef83ac1-d9ac-4453-85e6-b19109d8bf17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:22,478] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:45:22,478] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:45:22,479] [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 triticirhizae	strain=NEAU-YY642	GCA_003696235.1	2483353	2483353	type	True	100.0	1951	1978	95	inconclusive
Streptomyces mimosae	strain=3MP-10	GCA_006334995.2	2586635	2586635	type	True	95.3661	1758	1978	95	inconclusive
Streptomyces zhaozhouensis	strain=CGMCC 4.7095	GCA_900230195.1	1300267	1300267	type	True	87.5162	1413	1978	95	below_threshold
Streptomyces sedi	strain=JCM 16909	GCA_006335015.1	555059	555059	type	True	87.3535	1421	1978	95	below_threshold
Streptomyces hainanensis	strain=DSM 41900	GCA_004348415.1	402648	402648	type	True	81.6656	1063	1978	95	below_threshold
Streptomyces radicis	strain=DS1-2	GCA_003626575.1	1750517	1750517	type	True	81.3327	1163	1978	95	below_threshold
Streptomyces marincola	strain=SCSIO 64649	GCA_020410765.1	2878388	2878388	type	True	81.2084	1122	1978	95	below_threshold
Streptomyces hoynatensis	strain=KCTC 29097	GCA_003626535.1	1141874	1141874	type	True	81.1549	1150	1978	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	79.758	762	1978	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	79.3881	907	1978	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	79.2852	721	1978	95	below_threshold
Streptomyces thermodiastaticus	strain=DSM 40573	GCA_021394575.1	44061	44061	type	True	79.1984	807	1978	95	below_threshold
Streptomyces clavuligerus	strain=ATCC 27064	GCA_015912925.1	1901	1901	type	True	78.9702	657	1978	95	below_threshold
Streptomyces spinosus	strain=SBTS01	GCA_020400655.1	2872623	2872623	type	True	78.7532	903	1978	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:22,480] [INFO] DFAST Taxonomy check result was written to GCF_003696235.1_ASM369623v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:22,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:22,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:22,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcef83ac1-d9ac-4453-85e6-b19109d8bf17/dqc_reference/checkm_data
[2024-01-24 11:45:22,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:22,543] [INFO] Task started: CheckM
[2024-01-24 11:45:22,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003696235.1_ASM369623v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003696235.1_ASM369623v1_genomic.fna/checkm_input GCF_003696235.1_ASM369623v1_genomic.fna/checkm_result
[2024-01-24 11:46:19,132] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:19,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:19,162] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:19,163] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:19,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003696235.1_ASM369623v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:19,164] [INFO] Task started: Blastn
[2024-01-24 11:46:19,164] [INFO] Running command: blastn -query GCF_003696235.1_ASM369623v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcef83ac1-d9ac-4453-85e6-b19109d8bf17/dqc_reference/reference_markers_gtdb.fasta -out GCF_003696235.1_ASM369623v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:21,629] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:21,634] [INFO] Selected 13 target genomes.
[2024-01-24 11:46:21,634] [INFO] Target genome list was writen to GCF_003696235.1_ASM369623v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:21,660] [INFO] Task started: fastANI
[2024-01-24 11:46:21,660] [INFO] Running command: fastANI --query /var/lib/cwl/stgef3b90af-3e72-4fa1-ac8b-b2cce5f8fbcf/GCF_003696235.1_ASM369623v1_genomic.fna.gz --refList GCF_003696235.1_ASM369623v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003696235.1_ASM369623v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:43,701] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:43,714] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:43,715] [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_003696235.1	s__Streptomyces triticirhizae	100.0	1949	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.35	0.89	0.89	3	conclusive
GCF_900230195.1	s__Streptomyces zhaozhouensis	87.542	1411	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006335015.1	s__Streptomyces sedi	87.3656	1419	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974485.1	s__Streptomyces sp000974485	84.822	1434	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348315.1	s__Streptomyces sp004348315	81.7328	1061	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001493375.1	s__Streptomyces specialis	81.6516	963	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348415.1	s__Streptomyces hainanensis	81.649	1065	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083795.1	s__Streptomyces sp001083795	81.5219	1109	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003311645.1	s__Streptomyces sp003311645	81.3834	1106	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626575.1	s__Streptomyces sp003626575	81.303	1168	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003626535.1	s__Streptomyces hoynatensis	81.0908	1161	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719135.1	s__Streptomyces avicenniae	80.9205	1039	1978	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004684805.1	s__Streptomyces palmae	79.6849	773	1978	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 11:46:43,716] [INFO] GTDB search result was written to GCF_003696235.1_ASM369623v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:43,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:43,721] [INFO] DFAST_QC result json was written to GCF_003696235.1_ASM369623v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:43,721] [INFO] DFAST_QC completed!
[2024-01-24 11:46:43,721] [INFO] Total running time: 0h2m6s