[2024-01-24 13:22:16,817] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:16,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:16,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg0508fe45-2b8b-48ce-978d-518cc4f475b0/dqc_reference
[2024-01-24 13:22:18,169] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:18,170] [INFO] Task started: Prodigal
[2024-01-24 13:22:18,171] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a5f77a9-de6f-4653-8d6e-9da3202f1a66/GCF_009760925.1_ASM976092v1_genomic.fna.gz | prodigal -d GCF_009760925.1_ASM976092v1_genomic.fna/cds.fna -a GCF_009760925.1_ASM976092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:52,398] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:52,399] [INFO] Task started: HMMsearch
[2024-01-24 13:22:52,399] [INFO] Running command: hmmsearch --tblout GCF_009760925.1_ASM976092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0508fe45-2b8b-48ce-978d-518cc4f475b0/dqc_reference/reference_markers.hmm GCF_009760925.1_ASM976092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:53,096] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:53,097] [INFO] Found 6/6 markers.
[2024-01-24 13:22:53,192] [INFO] Query marker FASTA was written to GCF_009760925.1_ASM976092v1_genomic.fna/markers.fasta
[2024-01-24 13:22:53,192] [INFO] Task started: Blastn
[2024-01-24 13:22:53,193] [INFO] Running command: blastn -query GCF_009760925.1_ASM976092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0508fe45-2b8b-48ce-978d-518cc4f475b0/dqc_reference/reference_markers.fasta -out GCF_009760925.1_ASM976092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:54,740] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:54,743] [INFO] Selected 18 target genomes.
[2024-01-24 13:22:54,744] [INFO] Target genome list was writen to GCF_009760925.1_ASM976092v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:54,760] [INFO] Task started: fastANI
[2024-01-24 13:22:54,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a5f77a9-de6f-4653-8d6e-9da3202f1a66/GCF_009760925.1_ASM976092v1_genomic.fna.gz --refList GCF_009760925.1_ASM976092v1_genomic.fna/target_genomes.txt --output GCF_009760925.1_ASM976092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:45,044] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:45,045] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0508fe45-2b8b-48ce-978d-518cc4f475b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:45,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0508fe45-2b8b-48ce-978d-518cc4f475b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:45,060] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:45,060] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:45,061] [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 typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	100.0	3744	3768	95	conclusive
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	86.9505	2652	3768	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	82.3201	1206	3768	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	81.9222	1936	3768	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	81.8457	1590	3768	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	81.8281	1615	3768	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	81.8061	1682	3768	95	below_threshold
Nonomuraea ceibae	strain=KCTC 39826	GCA_019396325.1	1935170	1935170	type	True	81.792	1842	3768	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	81.7582	1856	3768	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	81.5957	1875	3768	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_000379885.1	404386	404386	type	True	81.5883	1739	3768	95	below_threshold
Nonomuraea coxensis	strain=DSM 45129	GCA_019397265.1	404386	404386	type	True	81.5824	1750	3768	95	below_threshold
Nonomuraea pusilla	strain=DSM 43357	GCA_900109355.1	46177	46177	type	True	81.5145	1738	3768	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	81.4762	1930	3768	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	81.3396	1860	3768	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	81.3271	2018	3768	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	81.2678	1996	3768	95	below_threshold
Nonomuraea polychroma	strain=DSM 43925	GCA_004011505.1	46176	46176	type	True	81.2677	1856	3768	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:45,063] [INFO] DFAST Taxonomy check result was written to GCF_009760925.1_ASM976092v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:45,067] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:45,067] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:45,067] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0508fe45-2b8b-48ce-978d-518cc4f475b0/dqc_reference/checkm_data
[2024-01-24 13:23:45,068] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:45,178] [INFO] Task started: CheckM
[2024-01-24 13:23:45,179] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009760925.1_ASM976092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009760925.1_ASM976092v1_genomic.fna/checkm_input GCF_009760925.1_ASM976092v1_genomic.fna/checkm_result
[2024-01-24 13:25:32,034] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:32,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.15%
Strain heterogeneity: 60.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:32,081] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:32,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:32,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009760925.1_ASM976092v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:32,082] [INFO] Task started: Blastn
[2024-01-24 13:25:32,083] [INFO] Running command: blastn -query GCF_009760925.1_ASM976092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0508fe45-2b8b-48ce-978d-518cc4f475b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_009760925.1_ASM976092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:34,462] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:34,467] [INFO] Selected 17 target genomes.
[2024-01-24 13:25:34,467] [INFO] Target genome list was writen to GCF_009760925.1_ASM976092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:34,514] [INFO] Task started: fastANI
[2024-01-24 13:25:34,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a5f77a9-de6f-4653-8d6e-9da3202f1a66/GCF_009760925.1_ASM976092v1_genomic.fna.gz --refList GCF_009760925.1_ASM976092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009760925.1_ASM976092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:23,482] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:23,497] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:23,497] [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_009760925.1	s__Nonomuraea typhae	100.0	3742	3768	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_014203235.1	s__Nonomuraea endophytica	86.9041	2663	3768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018531495.1	s__Nonomuraea sp018531495	82.1466	2043	3768	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	81.8894	1947	3768	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	81.885	1785	3768	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	81.8602	1607	3768	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	81.8077	1681	3768	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	81.742	1818	3768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	81.7327	1793	3768	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	81.6354	1865	3768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379885.1	s__Nonomuraea coxensis	81.5912	1738	3768	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	81.445	1912	3768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002093975.1	s__Nonomuraea rubra_A	81.3645	1624	3768	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	81.3595	2005	3768	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	81.3374	1862	3768	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004011505.1	s__Nonomuraea polychroma	81.2712	1851	3768	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	81.2622	2007	3768	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 13:26:23,499] [INFO] GTDB search result was written to GCF_009760925.1_ASM976092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:23,499] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:23,503] [INFO] DFAST_QC result json was written to GCF_009760925.1_ASM976092v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:23,503] [INFO] DFAST_QC completed!
[2024-01-24 13:26:23,503] [INFO] Total running time: 0h4m7s