[2024-01-24 12:52:25,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:25,383] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:25,383] [INFO] DQC Reference Directory: /var/lib/cwl/stg681c58be-961f-4b17-bcc0-f358204a035b/dqc_reference
[2024-01-24 12:52:26,694] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:26,695] [INFO] Task started: Prodigal
[2024-01-24 12:52:26,695] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ae1d0f3-8637-4c49-9a9a-29c9bfd58340/GCF_018531495.1_ASM1853149v1_genomic.fna.gz | prodigal -d GCF_018531495.1_ASM1853149v1_genomic.fna/cds.fna -a GCF_018531495.1_ASM1853149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:01,644] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:01,644] [INFO] Task started: HMMsearch
[2024-01-24 12:53:01,645] [INFO] Running command: hmmsearch --tblout GCF_018531495.1_ASM1853149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg681c58be-961f-4b17-bcc0-f358204a035b/dqc_reference/reference_markers.hmm GCF_018531495.1_ASM1853149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:02,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:02,172] [INFO] Found 6/6 markers.
[2024-01-24 12:53:02,281] [INFO] Query marker FASTA was written to GCF_018531495.1_ASM1853149v1_genomic.fna/markers.fasta
[2024-01-24 12:53:02,282] [INFO] Task started: Blastn
[2024-01-24 12:53:02,282] [INFO] Running command: blastn -query GCF_018531495.1_ASM1853149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg681c58be-961f-4b17-bcc0-f358204a035b/dqc_reference/reference_markers.fasta -out GCF_018531495.1_ASM1853149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:03,623] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:03,628] [INFO] Selected 24 target genomes.
[2024-01-24 12:53:03,629] [INFO] Target genome list was writen to GCF_018531495.1_ASM1853149v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:03,658] [INFO] Task started: fastANI
[2024-01-24 12:53:03,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae1d0f3-8637-4c49-9a9a-29c9bfd58340/GCF_018531495.1_ASM1853149v1_genomic.fna.gz --refList GCF_018531495.1_ASM1853149v1_genomic.fna/target_genomes.txt --output GCF_018531495.1_ASM1853149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:04,271] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:04,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg681c58be-961f-4b17-bcc0-f358204a035b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:04,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg681c58be-961f-4b17-bcc0-f358204a035b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:04,294] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:54:04,294] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:54:04,294] [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 rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	83.2002	1240	4011	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	82.7083	1943	4011	95	below_threshold
Nonomuraea aurantiaca	strain=NEAU-L178	GCA_020215705.1	2878562	2878562	type	True	82.6734	2074	4011	95	below_threshold
Nonomuraea guangzhouensis	strain=CGMCC 4.7101	GCA_019396345.1	1291555	1291555	type	True	82.6546	2182	4011	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	82.6397	1976	4011	95	below_threshold
Nonomuraea cavernae	strain=SYSU K10005	GCA_020215905.1	2045107	2045107	type	True	82.5858	1642	4011	95	below_threshold
Nonomuraea cavernae	strain=CGMCC 4.7368	GCA_014646355.1	2045107	2045107	type	True	82.5508	1645	4011	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	82.5144	1966	4011	95	below_threshold
Nonomuraea indica	strain=DRQ-2	GCA_002850745.1	1581193	1581193	type	True	82.506	1715	4011	95	below_threshold
Nonomuraea spiralis	strain=JCM 3286	GCA_014648435.1	46182	46182	type	True	82.4865	2130	4011	95	below_threshold
Nonomuraea muscovyensis	strain=DSM 45913	GCA_014207745.1	1124761	1124761	type	True	82.423	1854	4011	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	82.2799	1971	4011	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	82.2148	2087	4011	95	below_threshold
Nonomuraea glycinis	strain=NEAU-BB2C19	GCA_020215885.1	2047744	2047744	type	True	82.1258	1726	4011	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	82.1177	1649	4011	95	below_threshold
Nonomuraea glycinis	strain=CGMCC 4.7430	GCA_014646515.1	2047744	2047744	type	True	82.1043	1718	4011	95	below_threshold
Nonomuraea africana	strain=DSM 43748	GCA_014873535.1	46171	46171	type	True	82.0606	1883	4011	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	82.0451	1892	4011	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	82.0362	2061	4011	95	below_threshold
Nonomuraea harbinensis	strain=CGMCC 4.7106	GCA_019396385.1	1286938	1286938	type	True	81.9479	1692	4011	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	81.8969	1996	4011	95	below_threshold
Nonomuraea dietziae	strain=DSM 44320	GCA_014195505.1	65515	65515	type	True	81.8591	1922	4011	95	below_threshold
Sphaerisporangium krabiense	strain=NBRC 107571	GCA_016863355.1	763782	763782	type	True	79.2248	1346	4011	95	below_threshold
Sphaerisporangium krabiense	strain=DSM 45790	GCA_014200435.1	763782	763782	type	True	79.186	1369	4011	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:04,296] [INFO] DFAST Taxonomy check result was written to GCF_018531495.1_ASM1853149v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:04,297] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:04,297] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:04,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg681c58be-961f-4b17-bcc0-f358204a035b/dqc_reference/checkm_data
[2024-01-24 12:54:04,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:04,405] [INFO] Task started: CheckM
[2024-01-24 12:54:04,406] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018531495.1_ASM1853149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018531495.1_ASM1853149v1_genomic.fna/checkm_input GCF_018531495.1_ASM1853149v1_genomic.fna/checkm_result
[2024-01-24 12:55:56,477] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:56,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 7.99%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:56,513] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:56,513] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:56,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018531495.1_ASM1853149v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:56,514] [INFO] Task started: Blastn
[2024-01-24 12:55:56,514] [INFO] Running command: blastn -query GCF_018531495.1_ASM1853149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg681c58be-961f-4b17-bcc0-f358204a035b/dqc_reference/reference_markers_gtdb.fasta -out GCF_018531495.1_ASM1853149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:58,579] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:58,583] [INFO] Selected 21 target genomes.
[2024-01-24 12:55:58,583] [INFO] Target genome list was writen to GCF_018531495.1_ASM1853149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:58,598] [INFO] Task started: fastANI
[2024-01-24 12:55:58,599] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae1d0f3-8637-4c49-9a9a-29c9bfd58340/GCF_018531495.1_ASM1853149v1_genomic.fna.gz --refList GCF_018531495.1_ASM1853149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018531495.1_ASM1853149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:56:53,759] [INFO] Task succeeded: fastANI
[2024-01-24 12:56:53,781] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:56:53,782] [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_018531495.1	s__Nonomuraea sp018531495	100.0	3998	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013362835.1	s__Nonomuraea sp013362835	83.4517	869	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	82.7546	1932	4011	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	82.7255	2117	4011	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	82.6623	1971	4011	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	82.6133	1936	4011	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	82.536	1647	4011	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	82.4892	2130	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.03	98.03	0.91	0.91	2	-
GCF_002850745.1	s__Nonomuraea indica	82.4735	1722	4011	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	82.4657	1843	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203235.1	s__Nonomuraea endophytica	82.2647	2073	4011	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	82.2427	1981	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	82.1292	1647	4011	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	82.0824	1722	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760925.1	s__Nonomuraea typhae	82.0777	2048	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873535.1	s__Nonomuraea africana	82.0006	1898	4011	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	81.9695	2089	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_008017515.1	s__Nonomuraea sp008017515	81.917	1724	4011	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	81.864	1920	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013761175.1	s__Nonomuraea soli	80.8931	1811	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203605.1	s__Planomonospora_A venezuelensis	80.2257	1455	4011	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Planomonospora_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:56:53,783] [INFO] GTDB search result was written to GCF_018531495.1_ASM1853149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:56:53,784] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:56:53,788] [INFO] DFAST_QC result json was written to GCF_018531495.1_ASM1853149v1_genomic.fna/dqc_result.json
[2024-01-24 12:56:53,789] [INFO] DFAST_QC completed!
[2024-01-24 12:56:53,789] [INFO] Total running time: 0h4m28s