[2024-01-24 11:59:35,283] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:35,286] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:35,286] [INFO] DQC Reference Directory: /var/lib/cwl/stg924a2963-f135-4df4-874a-17b9ff11c3a1/dqc_reference
[2024-01-24 11:59:36,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:36,514] [INFO] Task started: Prodigal
[2024-01-24 11:59:36,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg29194ec2-3642-4fa0-93f9-3b967394bb85/GCF_021083185.1_ASM2108318v1_genomic.fna.gz | prodigal -d GCF_021083185.1_ASM2108318v1_genomic.fna/cds.fna -a GCF_021083185.1_ASM2108318v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:48,084] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:48,084] [INFO] Task started: HMMsearch
[2024-01-24 11:59:48,084] [INFO] Running command: hmmsearch --tblout GCF_021083185.1_ASM2108318v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg924a2963-f135-4df4-874a-17b9ff11c3a1/dqc_reference/reference_markers.hmm GCF_021083185.1_ASM2108318v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:48,405] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:48,407] [INFO] Found 6/6 markers.
[2024-01-24 11:59:48,448] [INFO] Query marker FASTA was written to GCF_021083185.1_ASM2108318v1_genomic.fna/markers.fasta
[2024-01-24 11:59:48,449] [INFO] Task started: Blastn
[2024-01-24 11:59:48,449] [INFO] Running command: blastn -query GCF_021083185.1_ASM2108318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg924a2963-f135-4df4-874a-17b9ff11c3a1/dqc_reference/reference_markers.fasta -out GCF_021083185.1_ASM2108318v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:49,616] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:49,620] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:49,621] [INFO] Target genome list was writen to GCF_021083185.1_ASM2108318v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:49,636] [INFO] Task started: fastANI
[2024-01-24 11:59:49,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg29194ec2-3642-4fa0-93f9-3b967394bb85/GCF_021083185.1_ASM2108318v1_genomic.fna.gz --refList GCF_021083185.1_ASM2108318v1_genomic.fna/target_genomes.txt --output GCF_021083185.1_ASM2108318v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:02,624] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:02,624] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg924a2963-f135-4df4-874a-17b9ff11c3a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:02,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg924a2963-f135-4df4-874a-17b9ff11c3a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:02,635] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:02,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:02,635] [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
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	100.0	1352	1353	95	conclusive
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	93.1481	1080	1353	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	86.6478	1017	1353	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	86.3154	1003	1353	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	86.2123	977	1353	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	85.8998	965	1353	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	85.799	952	1353	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.7865	973	1353	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.6874	965	1353	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	85.5305	958	1353	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	85.3091	932	1353	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	79.7196	665	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:02,637] [INFO] DFAST Taxonomy check result was written to GCF_021083185.1_ASM2108318v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:02,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:02,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:02,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg924a2963-f135-4df4-874a-17b9ff11c3a1/dqc_reference/checkm_data
[2024-01-24 12:00:02,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:02,691] [INFO] Task started: CheckM
[2024-01-24 12:00:02,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021083185.1_ASM2108318v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021083185.1_ASM2108318v1_genomic.fna/checkm_input GCF_021083185.1_ASM2108318v1_genomic.fna/checkm_result
[2024-01-24 12:01:03,996] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:03,997] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:04,022] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:04,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:04,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021083185.1_ASM2108318v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:04,023] [INFO] Task started: Blastn
[2024-01-24 12:01:04,024] [INFO] Running command: blastn -query GCF_021083185.1_ASM2108318v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg924a2963-f135-4df4-874a-17b9ff11c3a1/dqc_reference/reference_markers_gtdb.fasta -out GCF_021083185.1_ASM2108318v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:05,919] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:05,923] [INFO] Selected 17 target genomes.
[2024-01-24 12:01:05,924] [INFO] Target genome list was writen to GCF_021083185.1_ASM2108318v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:05,938] [INFO] Task started: fastANI
[2024-01-24 12:01:05,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg29194ec2-3642-4fa0-93f9-3b967394bb85/GCF_021083185.1_ASM2108318v1_genomic.fna.gz --refList GCF_021083185.1_ASM2108318v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021083185.1_ASM2108318v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:23,305] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:23,332] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:01:23,333] [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_017310035.1	s__Nocardioides sp017310035	93.5623	1103	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699265.1	s__Nocardioides sp009699265	93.3178	1032	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428125.1	s__Nocardioides sp001428125	87.2238	945	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	86.6717	1015	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004785795.1	s__Nocardioides eburneiflavus	86.3152	1003	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653115.1	s__Nocardioides flavus	86.2095	977	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155335.1	s__Nocardioides sp013155335	85.8956	978	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137245.1	s__Nocardioides glacieisoli	85.8791	967	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	85.8725	967	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	85.784	973	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137345.1	s__Nocardioides sp004137345	85.7749	954	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	85.7253	974	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	85.554	956	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779665.1	s__Nocardioides hwasunensis	85.3517	927	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916455.1	s__Nocardioides sp017916455	85.2868	875	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_017916425.1	s__Nocardioides sp017916425	84.9875	892	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213595.1	s__Fen-668 sp016213595	78.1953	177	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:23,334] [INFO] GTDB search result was written to GCF_021083185.1_ASM2108318v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:23,335] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:23,339] [INFO] DFAST_QC result json was written to GCF_021083185.1_ASM2108318v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:23,339] [INFO] DFAST_QC completed!
[2024-01-24 12:01:23,339] [INFO] Total running time: 0h1m48s