[2024-01-24 13:47:11,617] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:11,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:11,619] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb09d7fc-f8b0-4d5b-98d2-3480dba3ca52/dqc_reference
[2024-01-24 13:47:13,003] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:13,004] [INFO] Task started: Prodigal
[2024-01-24 13:47:13,004] [INFO] Running command: gunzip -c /var/lib/cwl/stg32de03f1-e2b0-4853-bedf-8498ad1f2781/GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna.gz | prodigal -d GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/cds.fna -a GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:34,666] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:34,667] [INFO] Task started: HMMsearch
[2024-01-24 13:47:34,667] [INFO] Running command: hmmsearch --tblout GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb09d7fc-f8b0-4d5b-98d2-3480dba3ca52/dqc_reference/reference_markers.hmm GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:35,019] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:35,020] [INFO] Found 6/6 markers.
[2024-01-24 13:47:35,074] [INFO] Query marker FASTA was written to GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta
[2024-01-24 13:47:35,075] [INFO] Task started: Blastn
[2024-01-24 13:47:35,075] [INFO] Running command: blastn -query GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb09d7fc-f8b0-4d5b-98d2-3480dba3ca52/dqc_reference/reference_markers.fasta -out GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:36,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:36,329] [INFO] Selected 20 target genomes.
[2024-01-24 13:47:36,330] [INFO] Target genome list was writen to GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/target_genomes.txt
[2024-01-24 13:47:36,341] [INFO] Task started: fastANI
[2024-01-24 13:47:36,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg32de03f1-e2b0-4853-bedf-8498ad1f2781/GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna.gz --refList GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/target_genomes.txt --output GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:02,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:02,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb09d7fc-f8b0-4d5b-98d2-3480dba3ca52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:02,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb09d7fc-f8b0-4d5b-98d2-3480dba3ca52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:02,946] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:48:02,946] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:02,947] [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
Nocardiopsis ganjiahuensis	strain=DSM 45031	GCA_000341085.1	239984	239984	type	True	100.0	2428	2431	95	conclusive
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	89.3337	1783	2431	95	below_threshold
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	89.2228	1781	2431	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	89.1991	1798	2431	95	below_threshold
Nocardiopsis terrae	strain=DSM 45157	GCA_014874035.1	372655	372655	type	True	88.4215	1620	2431	95	below_threshold
Nocardiopsis terrae	strain=KCTC 19431	GCA_014651695.1	372655	372655	type	True	88.4082	1599	2431	95	below_threshold
Nocardiopsis prasina	strain=DSM 43845	GCA_000341265.1	2015	2015	type	True	87.6218	1508	2431	95	below_threshold
Nocardiopsis listeri	strain=NBRC 13360	GCA_001570765.1	53440	53440	type	True	84.3122	1393	2431	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	83.6096	1409	2431	95	below_threshold
Nocardiopsis alkaliphila	strain=YIM 80379	GCA_000341005.1	225762	225762	type	True	83.5127	1213	2431	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	83.2705	1411	2431	95	below_threshold
Nocardiopsis kunsanensis	strain=DSM 44524	GCA_000340965.1	141693	141693	type	True	81.3732	1045	2431	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	79.4653	755	2431	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.0588	832	2431	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	76.6608	317	2431	95	below_threshold
Streptomyces subrutilus	strain=ATCC 27467	GCA_008704535.1	36818	36818	type	True	76.6443	597	2431	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	76.6017	323	2431	95	below_threshold
Streptomyces subrutilus	strain=JCM 4834	GCA_014650935.1	36818	36818	type	True	76.5865	588	2431	95	below_threshold
Klenkia soli	strain=DSM 45843	GCA_900103975.1	1052260	1052260	type	True	76.3879	456	2431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:02,948] [INFO] DFAST Taxonomy check result was written to GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/tc_result.tsv
[2024-01-24 13:48:02,949] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:02,949] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:02,949] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb09d7fc-f8b0-4d5b-98d2-3480dba3ca52/dqc_reference/checkm_data
[2024-01-24 13:48:02,950] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:03,016] [INFO] Task started: CheckM
[2024-01-24 13:48:03,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/checkm_input GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/checkm_result
[2024-01-24 13:49:43,540] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:43,541] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:43,567] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:43,568] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:43,568] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta)
[2024-01-24 13:49:43,569] [INFO] Task started: Blastn
[2024-01-24 13:49:43,569] [INFO] Running command: blastn -query GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb09d7fc-f8b0-4d5b-98d2-3480dba3ca52/dqc_reference/reference_markers_gtdb.fasta -out GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:45,803] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:45,807] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:45,807] [INFO] Target genome list was writen to GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:45,819] [INFO] Task started: fastANI
[2024-01-24 13:49:45,819] [INFO] Running command: fastANI --query /var/lib/cwl/stg32de03f1-e2b0-4853-bedf-8498ad1f2781/GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna.gz --refList GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/target_genomes_gtdb.txt --output GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:12,723] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:12,737] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:12,737] [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_000341085.1	s__Nocardiopsis ganjiahuensis	100.0	2428	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000340985.1	s__Nocardiopsis valliformis	89.2187	1782	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	89.2156	1796	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651695.1	s__Nocardiopsis terrae	88.4026	1600	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000341265.1	s__Nocardiopsis prasina	87.6031	1511	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	96.74	95.74	0.91	0.87	4	-
GCA_018388625.1	s__Nocardiopsis sp018388625	87.4075	1589	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143625.1	s__Nocardiopsis sp900143625	84.3631	1482	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008638415.1	s__Nocardiopsis sinuspersici	83.7521	1370	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.63	98.89	0.96	0.91	4	-
GCF_013410755.1	s__Nocardiopsis aegyptia	83.2453	1415	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001279585.1	s__Nocardiopsis sp001279585	83.1942	1363	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386285.1	s__Nocardiopsis sp003386285	82.9096	1224	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	79.5829	1077	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083785.1	s__Nonomuraea sp001083785	76.8132	671	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003519485.1	s__Streptomyces sp003519485	76.7773	334	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001700505.1	s__Streptomyces mutomycini	76.719	457	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.53	99.53	0.96	0.96	2	-
GCF_900112035.1	s__Nocardioides alpinus	76.5951	324	2431	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:12,738] [INFO] GTDB search result was written to GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:12,739] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:12,743] [INFO] DFAST_QC result json was written to GCF_000341085.1_SOAPdenovo_v1.06_genomic.fna/dqc_result.json
[2024-01-24 13:50:12,743] [INFO] DFAST_QC completed!
[2024-01-24 13:50:12,743] [INFO] Total running time: 0h3m1s