[2024-01-24 15:27:12,676] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,679] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,679] [INFO] DQC Reference Directory: /var/lib/cwl/stg66336c38-2f95-4c52-996a-209cef24ecbc/dqc_reference
[2024-01-24 15:27:14,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:14,069] [INFO] Task started: Prodigal
[2024-01-24 15:27:14,069] [INFO] Running command: gunzip -c /var/lib/cwl/stgbbebe428-c89b-4331-9bfb-471d85af6c03/GCF_014649015.1_ASM1464901v1_genomic.fna.gz | prodigal -d GCF_014649015.1_ASM1464901v1_genomic.fna/cds.fna -a GCF_014649015.1_ASM1464901v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:34,330] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:34,331] [INFO] Task started: HMMsearch
[2024-01-24 15:27:34,331] [INFO] Running command: hmmsearch --tblout GCF_014649015.1_ASM1464901v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66336c38-2f95-4c52-996a-209cef24ecbc/dqc_reference/reference_markers.hmm GCF_014649015.1_ASM1464901v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:34,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:34,783] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbbebe428-c89b-4331-9bfb-471d85af6c03/GCF_014649015.1_ASM1464901v1_genomic.fna.gz]
[2024-01-24 15:27:34,847] [INFO] Query marker FASTA was written to GCF_014649015.1_ASM1464901v1_genomic.fna/markers.fasta
[2024-01-24 15:27:34,848] [INFO] Task started: Blastn
[2024-01-24 15:27:34,848] [INFO] Running command: blastn -query GCF_014649015.1_ASM1464901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66336c38-2f95-4c52-996a-209cef24ecbc/dqc_reference/reference_markers.fasta -out GCF_014649015.1_ASM1464901v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:36,068] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:36,072] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:36,072] [INFO] Target genome list was writen to GCF_014649015.1_ASM1464901v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:36,078] [INFO] Task started: fastANI
[2024-01-24 15:27:36,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbebe428-c89b-4331-9bfb-471d85af6c03/GCF_014649015.1_ASM1464901v1_genomic.fna.gz --refList GCF_014649015.1_ASM1464901v1_genomic.fna/target_genomes.txt --output GCF_014649015.1_ASM1464901v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:12,330] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:12,331] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66336c38-2f95-4c52-996a-209cef24ecbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:12,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66336c38-2f95-4c52-996a-209cef24ecbc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:12,350] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:28:12,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:12,351] [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 narbonensis	strain=JCM 4147	GCA_014649015.1	67333	67333	type	True	100.0	2499	2505	95	conclusive
Streptomyces gardneri	strain=JCM 4375	GCA_014655085.1	66892	66892	type	True	94.2708	2181	2505	95	below_threshold
Streptomyces gardneri	strain=NBRC 12865	GCA_006539185.1	66892	66892	type	True	94.2687	2156	2505	95	below_threshold
Streptomyces tanashiensis	strain=JCM 4086	GCA_014648895.1	67367	67367	type	True	89.5169	1919	2505	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	89.5126	1929	2505	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000718175.1	1905	1905	type	True	89.4262	1858	2505	95	below_threshold
Streptomyces exfoliatus	strain=NRRL B-2924	GCA_000725545.1	1905	1905	type	True	89.4002	1867	2505	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_000253235.1	54571	54571	type	True	89.2869	1921	2505	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_008639165.1	54571	54571	type	True	89.2747	1924	2505	95	below_threshold
Streptomyces vietnamensis	strain=GIM4.0001	GCA_000830005.1	362257	362257	type	True	89.2557	1901	2505	95	below_threshold
Streptomyces venezuelae	strain=ATCC 10712	GCA_021432215.1	54571	54571	type	True	89.2354	1452	2505	95	below_threshold
Streptomyces wedmorensis	strain=NRRL 3426	GCA_000716445.1	43759	43759	type	True	89.1588	1935	2505	95	below_threshold
Streptomyces nymphaeiformis	strain=SFB5A	GCA_014203895.1	2663842	2663842	type	True	89.0834	1891	2505	95	below_threshold
Streptomyces formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	83.2029	1444	2505	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	81.5595	1444	2505	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	81.3632	1236	2505	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:12,352] [INFO] DFAST Taxonomy check result was written to GCF_014649015.1_ASM1464901v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:12,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:12,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:12,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66336c38-2f95-4c52-996a-209cef24ecbc/dqc_reference/checkm_data
[2024-01-24 15:28:12,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:12,428] [INFO] Task started: CheckM
[2024-01-24 15:28:12,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014649015.1_ASM1464901v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014649015.1_ASM1464901v1_genomic.fna/checkm_input GCF_014649015.1_ASM1464901v1_genomic.fna/checkm_result
[2024-01-24 15:29:44,560] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:44,562] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.13%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:29:44,590] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:44,590] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:44,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014649015.1_ASM1464901v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:44,591] [INFO] Task started: Blastn
[2024-01-24 15:29:44,591] [INFO] Running command: blastn -query GCF_014649015.1_ASM1464901v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66336c38-2f95-4c52-996a-209cef24ecbc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014649015.1_ASM1464901v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:46,474] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:46,479] [INFO] Selected 12 target genomes.
[2024-01-24 15:29:46,479] [INFO] Target genome list was writen to GCF_014649015.1_ASM1464901v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:46,498] [INFO] Task started: fastANI
[2024-01-24 15:29:46,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgbbebe428-c89b-4331-9bfb-471d85af6c03/GCF_014649015.1_ASM1464901v1_genomic.fna.gz --refList GCF_014649015.1_ASM1464901v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014649015.1_ASM1464901v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:15,498] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:15,519] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:15,520] [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_014649015.1	s__Streptomyces narbonensis	100.0	2499	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.06	95.06	0.89	0.89	2	conclusive
GCF_006539185.1	s__Streptomyces gardneri	94.2687	2156	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.06	97.41	0.92	0.89	5	-
GCF_001426585.1	s__Streptomyces sp001426585	92.8496	1849	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.07	96.69	0.91	0.88	3	-
GCF_014648895.1	s__Streptomyces tanashiensis	89.5204	1918	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.78	97.78	0.91	0.91	2	-
GCF_000725545.1	s__Streptomyces exfoliatus	89.4184	1865	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCA_000717735.1	s__Streptomyces griseoluteus_A	89.3834	1843	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.3384	N/A	N/A	N/A	N/A	1	-
GCF_001905665.1	s__Streptomyces sp001905665	89.2811	1814	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008639165.1	s__Streptomyces venezuelae	89.2756	1924	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	98.42	0.98	0.95	7	-
GCF_000830005.1	s__Streptomyces vietnamensis	89.2541	1901	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716445.1	s__Streptomyces wedmorensis	89.1824	1933	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.81	97.63	0.94	0.88	3	-
GCF_003386135.1	s__Streptomyces sp003386135	89.0891	1870	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.57	99.57	0.94	0.94	2	-
GCF_001905825.1	s__Streptomyces sp001905825	88.9899	1949	2505	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.90	96.90	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:15,522] [INFO] GTDB search result was written to GCF_014649015.1_ASM1464901v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:15,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:15,531] [INFO] DFAST_QC result json was written to GCF_014649015.1_ASM1464901v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:15,531] [INFO] DFAST_QC completed!
[2024-01-24 15:30:15,531] [INFO] Total running time: 0h3m3s