[2024-01-24 13:57:56,094] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,096] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a62de22-97b1-4469-bc43-7f69ef31a4bb/dqc_reference
[2024-01-24 13:57:57,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,541] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg3909c30b-93fe-4a3d-9dbc-31e4584f42ca/GCF_019396325.1_ASM1939632v1_genomic.fna.gz | prodigal -d GCF_019396325.1_ASM1939632v1_genomic.fna/cds.fna -a GCF_019396325.1_ASM1939632v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:26,813] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:26,814] [INFO] Task started: HMMsearch
[2024-01-24 13:58:26,814] [INFO] Running command: hmmsearch --tblout GCF_019396325.1_ASM1939632v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a62de22-97b1-4469-bc43-7f69ef31a4bb/dqc_reference/reference_markers.hmm GCF_019396325.1_ASM1939632v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:27,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:27,267] [INFO] Found 6/6 markers.
[2024-01-24 13:58:27,356] [INFO] Query marker FASTA was written to GCF_019396325.1_ASM1939632v1_genomic.fna/markers.fasta
[2024-01-24 13:58:27,357] [INFO] Task started: Blastn
[2024-01-24 13:58:27,357] [INFO] Running command: blastn -query GCF_019396325.1_ASM1939632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a62de22-97b1-4469-bc43-7f69ef31a4bb/dqc_reference/reference_markers.fasta -out GCF_019396325.1_ASM1939632v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:28,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:28,827] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:28,828] [INFO] Target genome list was writen to GCF_019396325.1_ASM1939632v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:28,833] [INFO] Task started: fastANI
[2024-01-24 13:58:28,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg3909c30b-93fe-4a3d-9dbc-31e4584f42ca/GCF_019396325.1_ASM1939632v1_genomic.fna.gz --refList GCF_019396325.1_ASM1939632v1_genomic.fna/target_genomes.txt --output GCF_019396325.1_ASM1939632v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:18,046] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:18,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a62de22-97b1-4469-bc43-7f69ef31a4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:18,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a62de22-97b1-4469-bc43-7f69ef31a4bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:18,066] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:18,066] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:18,066] [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 ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	100.0	3295	3311	95	conclusive
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	85.0623	1929	3311	95	below_threshold
Nonomuraea glycinis	strain=CGMCC 4.7430	GCA_014646515.1	2047744	2047744	type	True	84.9998	1892	3311	95	below_threshold
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	84.8923	1920	3311	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.2236	1183	3311	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	83.9654	1686	3311	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	83.8409	2075	3311	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	83.6983	1749	3311	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	83.671	1986	3311	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.4775	1895	3311	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	83.4286	1991	3311	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	83.4161	2056	3311	95	below_threshold
Nonomuraea wenchangensis	strain=CGMCC 4.5598	GCA_900111685.1	568860	568860	type	True	83.4109	1953	3311	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	83.1824	2035	3311	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	83.0877	2056	3311	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	83.0864	1923	3311	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	82.9941	1953	3311	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	82.8659	1953	3311	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:18,068] [INFO] DFAST Taxonomy check result was written to GCF_019396325.1_ASM1939632v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:18,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:18,069] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:18,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a62de22-97b1-4469-bc43-7f69ef31a4bb/dqc_reference/checkm_data
[2024-01-24 13:59:18,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:18,163] [INFO] Task started: CheckM
[2024-01-24 13:59:18,164] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019396325.1_ASM1939632v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019396325.1_ASM1939632v1_genomic.fna/checkm_input GCF_019396325.1_ASM1939632v1_genomic.fna/checkm_result
[2024-01-24 14:00:55,015] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:55,017] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 7.52%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2024-01-24 14:00:55,062] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:55,063] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:55,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019396325.1_ASM1939632v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:55,064] [INFO] Task started: Blastn
[2024-01-24 14:00:55,064] [INFO] Running command: blastn -query GCF_019396325.1_ASM1939632v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a62de22-97b1-4469-bc43-7f69ef31a4bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_019396325.1_ASM1939632v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:57,485] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:57,490] [INFO] Selected 19 target genomes.
[2024-01-24 14:00:57,490] [INFO] Target genome list was writen to GCF_019396325.1_ASM1939632v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:57,501] [INFO] Task started: fastANI
[2024-01-24 14:00:57,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg3909c30b-93fe-4a3d-9dbc-31e4584f42ca/GCF_019396325.1_ASM1939632v1_genomic.fna.gz --refList GCF_019396325.1_ASM1939632v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019396325.1_ASM1939632v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:01:51,129] [INFO] Task succeeded: fastANI
[2024-01-24 14:01:51,145] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:01:51,145] [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_001083785.1	s__Nonomuraea sp001083785	91.4291	2377	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008017515.1	s__Nonomuraea sp008017515	85.1276	1972	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646515.1	s__Nonomuraea glycinis	84.9601	1901	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646355.1	s__Nonomuraea cavernae	83.9193	1678	3311	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	83.8613	2070	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013283785.1	s__Nonomuraea sp013283785	83.7366	1973	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850745.1	s__Nonomuraea indica	83.7316	1742	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207745.1	s__Nonomuraea muscovyensis	83.6472	1820	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	83.5168	1856	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111685.1	s__Nonomuraea wenchangensis	83.4147	1954	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	83.4024	2142	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_014648435.1	s__Nonomuraea spiralis	83.3944	2061	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_013363975.1	s__Nonomuraea montanisoli	83.335	1858	3311	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	83.3102	2002	3311	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	83.2061	2030	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065375.1	s__Nonomuraea sp008065375	83.1906	1950	3311	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	83.0826	2058	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603905.1	s__Nonomuraea sp018603905	83.0244	1901	3311	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	83.0198	1948	3311	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:01:51,147] [INFO] GTDB search result was written to GCF_019396325.1_ASM1939632v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:01:51,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:01:51,152] [INFO] DFAST_QC result json was written to GCF_019396325.1_ASM1939632v1_genomic.fna/dqc_result.json
[2024-01-24 14:01:51,152] [INFO] DFAST_QC completed!
[2024-01-24 14:01:51,152] [INFO] Total running time: 0h3m55s