[2024-01-24 13:40:46,111] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,113] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c1e4bca-848f-4501-a548-9d8fa8624c8a/dqc_reference
[2024-01-24 13:40:47,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,413] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg4e1d346d-1ef2-472a-82c5-4fb3283c256d/GCF_009707235.1_ASM970723v1_genomic.fna.gz | prodigal -d GCF_009707235.1_ASM970723v1_genomic.fna/cds.fna -a GCF_009707235.1_ASM970723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,819] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,819] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,819] [INFO] Running command: hmmsearch --tblout GCF_009707235.1_ASM970723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c1e4bca-848f-4501-a548-9d8fa8624c8a/dqc_reference/reference_markers.hmm GCF_009707235.1_ASM970723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:59,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:59,125] [INFO] Found 6/6 markers.
[2024-01-24 13:40:59,166] [INFO] Query marker FASTA was written to GCF_009707235.1_ASM970723v1_genomic.fna/markers.fasta
[2024-01-24 13:40:59,167] [INFO] Task started: Blastn
[2024-01-24 13:40:59,167] [INFO] Running command: blastn -query GCF_009707235.1_ASM970723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c1e4bca-848f-4501-a548-9d8fa8624c8a/dqc_reference/reference_markers.fasta -out GCF_009707235.1_ASM970723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:00,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:00,469] [INFO] Selected 21 target genomes.
[2024-01-24 13:41:00,470] [INFO] Target genome list was writen to GCF_009707235.1_ASM970723v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:00,501] [INFO] Task started: fastANI
[2024-01-24 13:41:00,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e1d346d-1ef2-472a-82c5-4fb3283c256d/GCF_009707235.1_ASM970723v1_genomic.fna.gz --refList GCF_009707235.1_ASM970723v1_genomic.fna/target_genomes.txt --output GCF_009707235.1_ASM970723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:22,584] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:22,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c1e4bca-848f-4501-a548-9d8fa8624c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:22,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c1e4bca-848f-4501-a548-9d8fa8624c8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:22,609] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:22,610] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:22,610] [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 deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	88.3488	1073	1445	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	88.254	1080	1445	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	83.6224	921	1445	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	82.5376	835	1445	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.5228	840	1445	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	82.4603	849	1445	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	82.3549	830	1445	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	82.3526	859	1445	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.3504	869	1445	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	82.3028	870	1445	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	82.2709	852	1445	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.1648	779	1445	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	82.0018	785	1445	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.6435	811	1445	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.3308	750	1445	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.9153	648	1445	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.8434	712	1445	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.8074	762	1445	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.5375	765	1445	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.4304	699	1445	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.1016	685	1445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:22,612] [INFO] DFAST Taxonomy check result was written to GCF_009707235.1_ASM970723v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:22,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:22,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:22,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c1e4bca-848f-4501-a548-9d8fa8624c8a/dqc_reference/checkm_data
[2024-01-24 13:41:22,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:22,658] [INFO] Task started: CheckM
[2024-01-24 13:41:22,659] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009707235.1_ASM970723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009707235.1_ASM970723v1_genomic.fna/checkm_input GCF_009707235.1_ASM970723v1_genomic.fna/checkm_result
[2024-01-24 13:42:15,420] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:15,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:15,443] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:15,444] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:15,444] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009707235.1_ASM970723v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:15,444] [INFO] Task started: Blastn
[2024-01-24 13:42:15,445] [INFO] Running command: blastn -query GCF_009707235.1_ASM970723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4c1e4bca-848f-4501-a548-9d8fa8624c8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009707235.1_ASM970723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:17,658] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:17,662] [INFO] Selected 16 target genomes.
[2024-01-24 13:42:17,662] [INFO] Target genome list was writen to GCF_009707235.1_ASM970723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:17,766] [INFO] Task started: fastANI
[2024-01-24 13:42:17,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg4e1d346d-1ef2-472a-82c5-4fb3283c256d/GCF_009707235.1_ASM970723v1_genomic.fna.gz --refList GCF_009707235.1_ASM970723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009707235.1_ASM970723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:35,595] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:35,609] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:35,609] [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_013177455.1	s__Nocardioides sp013177455	99.9962	1444	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	conclusive
GCF_011250565.1	s__Nocardioides sp011250565	88.4373	1069	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014266025.1	s__Nocardioides deserti	88.3509	1072	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014127485.1	s__Nocardioides sp014127485	83.5986	924	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_013155365.1	s__Nocardioides sp013155365	82.8334	882	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466785.1	s__Nocardioides marinisabuli	82.4874	846	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_015070375.1	s__Nocardioides kribbensis	82.3679	829	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_013409645.1	s__Nocardioides panaciterrulae	82.1591	778	1445	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	82.0732	832	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013466985.1	s__Nocardioides ungokensis	81.9878	788	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191495.1	s__Nocardioides soli	81.8315	842	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_001425175.1	s__Nocardioides sp001425175	81.7077	886	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009823805.1	s__Nocardioides sp009823805	81.5866	818	1445	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	81.1344	764	1445	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	80.8345	713	1445	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004919105.1	s__Nocardioides sp004919105	80.8317	720	1445	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 13:42:35,611] [INFO] GTDB search result was written to GCF_009707235.1_ASM970723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:35,611] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:35,616] [INFO] DFAST_QC result json was written to GCF_009707235.1_ASM970723v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:35,616] [INFO] DFAST_QC completed!
[2024-01-24 13:42:35,617] [INFO] Total running time: 0h1m50s