[2024-01-24 11:43:35,341] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:35,342] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:35,342] [INFO] DQC Reference Directory: /var/lib/cwl/stg438c0c2f-9524-4c6e-ab19-c32219dbb545/dqc_reference
[2024-01-24 11:43:36,516] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:36,517] [INFO] Task started: Prodigal
[2024-01-24 11:43:36,517] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d703f99-a7bd-429a-8299-992d051ba422/GCF_015163075.1_ASM1516307v1_genomic.fna.gz | prodigal -d GCF_015163075.1_ASM1516307v1_genomic.fna/cds.fna -a GCF_015163075.1_ASM1516307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:05,550] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:05,550] [INFO] Task started: HMMsearch
[2024-01-24 11:44:05,551] [INFO] Running command: hmmsearch --tblout GCF_015163075.1_ASM1516307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg438c0c2f-9524-4c6e-ab19-c32219dbb545/dqc_reference/reference_markers.hmm GCF_015163075.1_ASM1516307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:05,952] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:05,953] [INFO] Found 6/6 markers.
[2024-01-24 11:44:06,061] [INFO] Query marker FASTA was written to GCF_015163075.1_ASM1516307v1_genomic.fna/markers.fasta
[2024-01-24 11:44:06,062] [INFO] Task started: Blastn
[2024-01-24 11:44:06,062] [INFO] Running command: blastn -query GCF_015163075.1_ASM1516307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg438c0c2f-9524-4c6e-ab19-c32219dbb545/dqc_reference/reference_markers.fasta -out GCF_015163075.1_ASM1516307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:07,373] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:07,377] [INFO] Selected 17 target genomes.
[2024-01-24 11:44:07,377] [INFO] Target genome list was writen to GCF_015163075.1_ASM1516307v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:07,384] [INFO] Task started: fastANI
[2024-01-24 11:44:07,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d703f99-a7bd-429a-8299-992d051ba422/GCF_015163075.1_ASM1516307v1_genomic.fna.gz --refList GCF_015163075.1_ASM1516307v1_genomic.fna/target_genomes.txt --output GCF_015163075.1_ASM1516307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:51,950] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:51,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg438c0c2f-9524-4c6e-ab19-c32219dbb545/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:51,951] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg438c0c2f-9524-4c6e-ab19-c32219dbb545/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:51,966] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:51,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:51,967] [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 justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	100.0	3460	3460	95	conclusive
Streptomyces aquilus	strain=GGCR-6	GCA_003955715.1	2548456	2548456	type	True	94.6027	2737	3460	95	below_threshold
Streptomyces antibioticus	strain=DSM 40234	GCA_001514065.1	1890	1890	suspected-type	True	94.3383	2667	3460	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	86.4753	2060	3460	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	86.4356	2111	3460	95	below_threshold
Streptomyces griseorubiginosus	strain=DSM 40469	GCA_001514195.1	67304	67304	type	True	86.4163	2216	3460	95	below_threshold
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	86.1195	2074	3460	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	86.06	2214	3460	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	85.8312	1952	3460	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.8064	1872	3460	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.8015	2030	3460	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.5087	1693	3460	95	below_threshold
Streptomyces griseoruber	strain=DSM 40281	GCA_001514205.1	1943	1943	type	True	85.5062	2087	3460	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.6109	1855	3460	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.4451	2007	3460	95	below_threshold
Streptomyces tailanensis	strain=TRM68348	GCA_008386495.1	2569858	2569858	type	True	84.3586	1891	3460	95	below_threshold
Streptomyces stelliscabiei	strain=DSM 41803	GCA_014873495.1	146820	146820	type	True	84.0647	2019	3460	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:51,969] [INFO] DFAST Taxonomy check result was written to GCF_015163075.1_ASM1516307v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:51,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:51,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:51,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg438c0c2f-9524-4c6e-ab19-c32219dbb545/dqc_reference/checkm_data
[2024-01-24 11:44:51,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:52,064] [INFO] Task started: CheckM
[2024-01-24 11:44:52,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015163075.1_ASM1516307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015163075.1_ASM1516307v1_genomic.fna/checkm_input GCF_015163075.1_ASM1516307v1_genomic.fna/checkm_result
[2024-01-24 11:47:12,877] [INFO] Task succeeded: CheckM
[2024-01-24 11:47:12,879] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.21%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:47:12,909] [INFO] ===== Completeness check finished =====
[2024-01-24 11:47:12,909] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:47:12,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015163075.1_ASM1516307v1_genomic.fna/markers.fasta)
[2024-01-24 11:47:12,910] [INFO] Task started: Blastn
[2024-01-24 11:47:12,910] [INFO] Running command: blastn -query GCF_015163075.1_ASM1516307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg438c0c2f-9524-4c6e-ab19-c32219dbb545/dqc_reference/reference_markers_gtdb.fasta -out GCF_015163075.1_ASM1516307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:47:15,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:47:15,028] [INFO] Selected 6 target genomes.
[2024-01-24 11:47:15,028] [INFO] Target genome list was writen to GCF_015163075.1_ASM1516307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:47:15,033] [INFO] Task started: fastANI
[2024-01-24 11:47:15,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d703f99-a7bd-429a-8299-992d051ba422/GCF_015163075.1_ASM1516307v1_genomic.fna.gz --refList GCF_015163075.1_ASM1516307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015163075.1_ASM1516307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:47:32,209] [INFO] Task succeeded: fastANI
[2024-01-24 11:47:32,219] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:47:32,219] [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_015163075.1	s__Streptomyces sp015163075	100.0	3460	3460	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_003955715.1	s__Streptomyces aquilus	94.5954	2738	3460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	97.56	95.79	0.89	0.84	3	-
GCF_001514065.1	s__Streptomyces antibioticus	94.3465	2666	3460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	N/A	N/A	N/A	N/A	1	-
GCA_002027195.1	s__Streptomyces sp002027195	94.1391	2205	3460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_003143935.1	s__Streptomyces sp003143935	92.3518	2607	3460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001484565.1	s__Streptomyces sp001484565	85.9809	2194	3460	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 11:47:32,221] [INFO] GTDB search result was written to GCF_015163075.1_ASM1516307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:47:32,222] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:47:32,225] [INFO] DFAST_QC result json was written to GCF_015163075.1_ASM1516307v1_genomic.fna/dqc_result.json
[2024-01-24 11:47:32,225] [INFO] DFAST_QC completed!
[2024-01-24 11:47:32,225] [INFO] Total running time: 0h3m57s