[2024-01-24 12:23:35,301] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:35,305] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:35,305] [INFO] DQC Reference Directory: /var/lib/cwl/stge3a6de5d-089d-4a05-8bb9-522542823500/dqc_reference
[2024-01-24 12:23:36,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:36,678] [INFO] Task started: Prodigal
[2024-01-24 12:23:36,678] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a9a6916-b1c5-4ca5-a4c9-04c408a99474/GCF_004348995.1_ASM434899v1_genomic.fna.gz | prodigal -d GCF_004348995.1_ASM434899v1_genomic.fna/cds.fna -a GCF_004348995.1_ASM434899v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:24:02,479] [INFO] Task succeeded: Prodigal
[2024-01-24 12:24:02,480] [INFO] Task started: HMMsearch
[2024-01-24 12:24:02,480] [INFO] Running command: hmmsearch --tblout GCF_004348995.1_ASM434899v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge3a6de5d-089d-4a05-8bb9-522542823500/dqc_reference/reference_markers.hmm GCF_004348995.1_ASM434899v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:24:02,900] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:24:02,901] [INFO] Found 6/6 markers.
[2024-01-24 12:24:02,977] [INFO] Query marker FASTA was written to GCF_004348995.1_ASM434899v1_genomic.fna/markers.fasta
[2024-01-24 12:24:02,978] [INFO] Task started: Blastn
[2024-01-24 12:24:02,978] [INFO] Running command: blastn -query GCF_004348995.1_ASM434899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3a6de5d-089d-4a05-8bb9-522542823500/dqc_reference/reference_markers.fasta -out GCF_004348995.1_ASM434899v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:04,388] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:04,393] [INFO] Selected 17 target genomes.
[2024-01-24 12:24:04,393] [INFO] Target genome list was writen to GCF_004348995.1_ASM434899v1_genomic.fna/target_genomes.txt
[2024-01-24 12:24:04,402] [INFO] Task started: fastANI
[2024-01-24 12:24:04,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a9a6916-b1c5-4ca5-a4c9-04c408a99474/GCF_004348995.1_ASM434899v1_genomic.fna.gz --refList GCF_004348995.1_ASM434899v1_genomic.fna/target_genomes.txt --output GCF_004348995.1_ASM434899v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:48,638] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:48,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge3a6de5d-089d-4a05-8bb9-522542823500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:48,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge3a6de5d-089d-4a05-8bb9-522542823500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:48,654] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:24:48,654] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:24:48,655] [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
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	100.0	2966	2995	95	conclusive
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	93.9043	2334	2995	95	below_threshold
Nonomuraea maritima	strain=CGMCC 4.5681	GCA_900100395.1	683260	683260	type	True	87.5956	1983	2995	95	below_threshold
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	85.9445	2192	2995	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	85.933	1991	2995	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	85.5813	2092	2995	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	85.4761	2090	2995	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.3074	1991	2995	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.2692	1973	2995	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	85.1453	2086	2995	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	85.1397	2061	2995	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.1223	1970	2995	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	84.9006	1874	2995	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	84.1475	1861	2995	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.4902	1131	2995	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.0202	1710	2995	95	below_threshold
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	81.4756	1589	2995	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:48,656] [INFO] DFAST Taxonomy check result was written to GCF_004348995.1_ASM434899v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:48,657] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:48,657] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:48,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge3a6de5d-089d-4a05-8bb9-522542823500/dqc_reference/checkm_data
[2024-01-24 12:24:48,658] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:48,750] [INFO] Task started: CheckM
[2024-01-24 12:24:48,750] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004348995.1_ASM434899v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004348995.1_ASM434899v1_genomic.fna/checkm_input GCF_004348995.1_ASM434899v1_genomic.fna/checkm_result
[2024-01-24 12:26:06,881] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:06,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.43%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:06,916] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:06,917] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:06,917] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004348995.1_ASM434899v1_genomic.fna/markers.fasta)
[2024-01-24 12:26:06,918] [INFO] Task started: Blastn
[2024-01-24 12:26:06,918] [INFO] Running command: blastn -query GCF_004348995.1_ASM434899v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge3a6de5d-089d-4a05-8bb9-522542823500/dqc_reference/reference_markers_gtdb.fasta -out GCF_004348995.1_ASM434899v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:09,326] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:09,331] [INFO] Selected 16 target genomes.
[2024-01-24 12:26:09,332] [INFO] Target genome list was writen to GCF_004348995.1_ASM434899v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:09,344] [INFO] Task started: fastANI
[2024-01-24 12:26:09,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a9a6916-b1c5-4ca5-a4c9-04c408a99474/GCF_004348995.1_ASM434899v1_genomic.fna.gz --refList GCF_004348995.1_ASM434899v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004348995.1_ASM434899v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:51,386] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:51,404] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:51,405] [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_004348995.1	s__Nonomuraea terrae	100.0	2966	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003236395.1	s__Nonomuraea sp003236395	93.8981	2335	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100395.1	s__Nonomuraea maritima	87.6064	1980	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207985.1	s__Nonomuraea rubra	85.9318	2195	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000725485.1	s__Nonomuraea candida	85.9197	1995	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108335.1	s__Nonomuraea solani	85.571	2094	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	85.4808	2088	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	85.4689	2107	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873145.1	s__Nonomuraea angiospora	85.1919	2078	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	85.1838	2052	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	85.142	1967	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	84.8886	1877	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648435.1	s__Nonomuraea spiralis	84.1225	1865	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	82.9727	1689	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195505.1	s__Nonomuraea dietziae	81.4841	1587	2995	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112355.1	s__Streptomyces aidingensis	76.2915	660	2995	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 12:26:51,406] [INFO] GTDB search result was written to GCF_004348995.1_ASM434899v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:51,407] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:51,411] [INFO] DFAST_QC result json was written to GCF_004348995.1_ASM434899v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:51,412] [INFO] DFAST_QC completed!
[2024-01-24 12:26:51,412] [INFO] Total running time: 0h3m16s