[2024-01-24 13:25:46,511] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:46,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:46,523] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6215a8f-4fbb-44ce-90db-f70e473944f2/dqc_reference
[2024-01-24 13:25:47,905] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:47,906] [INFO] Task started: Prodigal
[2024-01-24 13:25:47,906] [INFO] Running command: gunzip -c /var/lib/cwl/stg37aba066-ac69-43f9-a2d6-173f16f4e621/GCF_003047285.1_ASM304728v1_genomic.fna.gz | prodigal -d GCF_003047285.1_ASM304728v1_genomic.fna/cds.fna -a GCF_003047285.1_ASM304728v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:59,566] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:59,566] [INFO] Task started: HMMsearch
[2024-01-24 13:25:59,567] [INFO] Running command: hmmsearch --tblout GCF_003047285.1_ASM304728v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6215a8f-4fbb-44ce-90db-f70e473944f2/dqc_reference/reference_markers.hmm GCF_003047285.1_ASM304728v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:59,858] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:59,859] [INFO] Found 6/6 markers.
[2024-01-24 13:25:59,899] [INFO] Query marker FASTA was written to GCF_003047285.1_ASM304728v1_genomic.fna/markers.fasta
[2024-01-24 13:25:59,899] [INFO] Task started: Blastn
[2024-01-24 13:25:59,899] [INFO] Running command: blastn -query GCF_003047285.1_ASM304728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6215a8f-4fbb-44ce-90db-f70e473944f2/dqc_reference/reference_markers.fasta -out GCF_003047285.1_ASM304728v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:01,163] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:01,167] [INFO] Selected 22 target genomes.
[2024-01-24 13:26:01,167] [INFO] Target genome list was writen to GCF_003047285.1_ASM304728v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:01,174] [INFO] Task started: fastANI
[2024-01-24 13:26:01,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg37aba066-ac69-43f9-a2d6-173f16f4e621/GCF_003047285.1_ASM304728v1_genomic.fna.gz --refList GCF_003047285.1_ASM304728v1_genomic.fna/target_genomes.txt --output GCF_003047285.1_ASM304728v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:20,242] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:20,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6215a8f-4fbb-44ce-90db-f70e473944f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:20,243] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6215a8f-4fbb-44ce-90db-f70e473944f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:20,257] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:20,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:20,257] [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 allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	100.0	1292	1292	95	conclusive
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	85.6458	910	1292	95	below_threshold
Nocardioides piscis	strain=HDW12A	GCA_011300215.1	2714938	2714938	type	True	83.6466	846	1292	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	83.4505	834	1292	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	83.0944	827	1292	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	82.3403	776	1292	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	82.0879	773	1292	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	82.0579	753	1292	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	82.0303	769	1292	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	81.9845	776	1292	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	81.9759	778	1292	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	81.9646	785	1292	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	81.8424	755	1292	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	81.6849	773	1292	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	81.5708	728	1292	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.7831	671	1292	95	below_threshold
Nocardioides houyundeii	strain=78	GCA_002865585.1	2045452	2045452	type	True	80.5378	611	1292	95	below_threshold
Nocardioides speluncae	strain=YIM ART13	GCA_003121585.1	2670337	2670337	type	True	80.5246	659	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:20,259] [INFO] DFAST Taxonomy check result was written to GCF_003047285.1_ASM304728v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:20,260] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:20,260] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:20,260] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6215a8f-4fbb-44ce-90db-f70e473944f2/dqc_reference/checkm_data
[2024-01-24 13:26:20,261] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:20,301] [INFO] Task started: CheckM
[2024-01-24 13:26:20,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003047285.1_ASM304728v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003047285.1_ASM304728v1_genomic.fna/checkm_input GCF_003047285.1_ASM304728v1_genomic.fna/checkm_result
[2024-01-24 13:27:17,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:17,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:17,254] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:17,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:17,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003047285.1_ASM304728v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:17,255] [INFO] Task started: Blastn
[2024-01-24 13:27:17,255] [INFO] Running command: blastn -query GCF_003047285.1_ASM304728v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6215a8f-4fbb-44ce-90db-f70e473944f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003047285.1_ASM304728v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:19,186] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:19,191] [INFO] Selected 20 target genomes.
[2024-01-24 13:27:19,191] [INFO] Target genome list was writen to GCF_003047285.1_ASM304728v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:19,222] [INFO] Task started: fastANI
[2024-01-24 13:27:19,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg37aba066-ac69-43f9-a2d6-173f16f4e621/GCF_003047285.1_ASM304728v1_genomic.fna.gz --refList GCF_003047285.1_ASM304728v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003047285.1_ASM304728v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:37,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:37,719] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:37,719] [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_003047285.1	s__Nocardioides allogilvus	100.0	1292	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.72	98.72	0.92	0.92	2	conclusive
GCF_003057875.1	s__Nocardioides currus	85.6334	911	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011300215.1	s__Nocardioides piscis	83.6466	846	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047265.1	s__Nocardioides terrigena	83.4293	836	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	95.44	95.44	0.86	0.86	2	-
GCF_001429625.1	s__Nocardioides sp001429625	83.3057	842	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047295.1	s__Nocardioides sediminis	83.1015	826	1292	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	82.366	740	1292	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	82.3007	779	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	82.031	767	1292	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	82.0289	755	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872795.1	s__Nocardioides sp017872795	81.9951	758	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112035.1	s__Nocardioides alpinus	81.9693	779	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900105585.1	s__Nocardioides exalbidus	81.9283	785	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805925.1	s__Nocardioides sp902805925	81.6005	577	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013815725.1	s__Nocardioides sp013815725	81.1621	425	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117935.1	s__Nocardioides sp002117935	81.132	695	1292	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:37,721] [INFO] GTDB search result was written to GCF_003047285.1_ASM304728v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:37,721] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:37,725] [INFO] DFAST_QC result json was written to GCF_003047285.1_ASM304728v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:37,725] [INFO] DFAST_QC completed!
[2024-01-24 13:27:37,725] [INFO] Total running time: 0h1m51s