[2024-01-24 15:10:22,917] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:22,919] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:22,919] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e0443bb-b830-4161-983a-b0bd2a2b9611/dqc_reference
[2024-01-24 15:10:24,496] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,497] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,497] [INFO] Running command: gunzip -c /var/lib/cwl/stgb9e1bf60-ad90-4f7b-ac39-283e302f7bef/GCF_004014875.1_ASM401487v1_genomic.fna.gz | prodigal -d GCF_004014875.1_ASM401487v1_genomic.fna/cds.fna -a GCF_004014875.1_ASM401487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:34,574] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:34,575] [INFO] Task started: HMMsearch
[2024-01-24 15:10:34,575] [INFO] Running command: hmmsearch --tblout GCF_004014875.1_ASM401487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e0443bb-b830-4161-983a-b0bd2a2b9611/dqc_reference/reference_markers.hmm GCF_004014875.1_ASM401487v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:34,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:34,841] [INFO] Found 6/6 markers.
[2024-01-24 15:10:34,876] [INFO] Query marker FASTA was written to GCF_004014875.1_ASM401487v1_genomic.fna/markers.fasta
[2024-01-24 15:10:34,877] [INFO] Task started: Blastn
[2024-01-24 15:10:34,877] [INFO] Running command: blastn -query GCF_004014875.1_ASM401487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e0443bb-b830-4161-983a-b0bd2a2b9611/dqc_reference/reference_markers.fasta -out GCF_004014875.1_ASM401487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:36,135] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:36,139] [INFO] Selected 18 target genomes.
[2024-01-24 15:10:36,139] [INFO] Target genome list was writen to GCF_004014875.1_ASM401487v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:36,173] [INFO] Task started: fastANI
[2024-01-24 15:10:36,173] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9e1bf60-ad90-4f7b-ac39-283e302f7bef/GCF_004014875.1_ASM401487v1_genomic.fna.gz --refList GCF_004014875.1_ASM401487v1_genomic.fna/target_genomes.txt --output GCF_004014875.1_ASM401487v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:50,607] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:50,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e0443bb-b830-4161-983a-b0bd2a2b9611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:50,607] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e0443bb-b830-4161-983a-b0bd2a2b9611/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:50,623] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:10:50,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:50,624] [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 yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	100.0	1106	1107	95	conclusive
Nocardioides daphniae	strain=CCM 7403	GCA_014635145.1	402297	402297	type	True	81.7652	604	1107	95	below_threshold
Nocardioides daphniae	strain=JCM 16608	GCA_004777465.1	402297	402297	type	True	81.7026	626	1107	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	81.3139	635	1107	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	81.1542	568	1107	95	below_threshold
Nocardioides gilvus	strain=XZ17	GCA_003194605.1	1735589	1735589	type	True	80.8143	569	1107	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.9875	498	1107	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.7184	472	1107	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	79.712	467	1107	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.5644	504	1107	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.5326	451	1107	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.3455	463	1107	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.3452	466	1107	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.2644	456	1107	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.1338	509	1107	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	78.9981	505	1107	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	78.7361	470	1107	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	78.6887	455	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:50,627] [INFO] DFAST Taxonomy check result was written to GCF_004014875.1_ASM401487v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:50,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:50,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:50,628] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e0443bb-b830-4161-983a-b0bd2a2b9611/dqc_reference/checkm_data
[2024-01-24 15:10:50,629] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:50,664] [INFO] Task started: CheckM
[2024-01-24 15:10:50,665] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004014875.1_ASM401487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004014875.1_ASM401487v1_genomic.fna/checkm_input GCF_004014875.1_ASM401487v1_genomic.fna/checkm_result
[2024-01-24 15:11:54,785] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:54,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:54,803] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:54,803] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:54,804] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004014875.1_ASM401487v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:54,804] [INFO] Task started: Blastn
[2024-01-24 15:11:54,804] [INFO] Running command: blastn -query GCF_004014875.1_ASM401487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e0443bb-b830-4161-983a-b0bd2a2b9611/dqc_reference/reference_markers_gtdb.fasta -out GCF_004014875.1_ASM401487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:56,544] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:56,547] [INFO] Selected 21 target genomes.
[2024-01-24 15:11:56,548] [INFO] Target genome list was writen to GCF_004014875.1_ASM401487v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:56,561] [INFO] Task started: fastANI
[2024-01-24 15:11:56,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgb9e1bf60-ad90-4f7b-ac39-283e302f7bef/GCF_004014875.1_ASM401487v1_genomic.fna.gz --refList GCF_004014875.1_ASM401487v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004014875.1_ASM401487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:13,830] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:13,847] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:13,847] [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_004014875.1	s__Nocardioides sp004014875	100.0	1106	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_004777465.1	s__Nocardioides daphniae	81.6857	630	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.94	99.94	1.00	1.00	2	-
GCF_006007965.1	s__Nocardioides sp006007965	81.3475	638	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003194605.1	s__Nocardioides gilvus	80.8034	570	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013624435.2	s__Nocardioides sp013624415	80.0673	541	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCF_003194625.1	s__Nocardioides solisilvae	79.9548	501	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011420305.2	s__Nocardioides sp011420305	79.761	535	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_003047265.1	s__Nocardioides terrigena	79.6901	469	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_017310035.1	s__Nocardioides sp017310035	79.6834	472	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627335.1	s__Nocardioides sp001627335	79.6449	399	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_900105585.1	s__Nocardioides exalbidus	79.6278	498	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018275325.1	s__Nocardioides sp018275325	79.4942	508	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778305.1	s__Nocardioides sp013778305	79.4921	466	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410035.1	s__Nocardioides cavernae_A	79.4822	488	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005954645.2	s__Nocardioides dongxiaopingii	79.4455	462	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.98	98.98	0.96	0.96	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	79.3237	454	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710085.1	s__Nocardioides sp003710085	79.2825	504	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_004919105.1	s__Nocardioides sp004919105	79.2273	466	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426525.1	s__Nocardioides alkalitolerans	78.7098	473	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010686755.1	s__Nocardioides zeae	78.7054	419	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046535.1	s__Nocardioides anomalus	78.6708	456	1107	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:13,849] [INFO] GTDB search result was written to GCF_004014875.1_ASM401487v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:13,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:13,854] [INFO] DFAST_QC result json was written to GCF_004014875.1_ASM401487v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:13,854] [INFO] DFAST_QC completed!
[2024-01-24 15:12:13,855] [INFO] Total running time: 0h1m51s