[2024-01-24 12:47:12,403] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,404] [INFO] DQC Reference Directory: /var/lib/cwl/stg597adcee-0597-4587-a478-c6e2edb07575/dqc_reference
[2024-01-24 12:47:13,754] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,755] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,755] [INFO] Running command: gunzip -c /var/lib/cwl/stg70d1684e-abf3-4f05-a02e-2a907c691c5b/GCF_003752505.1_ASM375250v1_genomic.fna.gz | prodigal -d GCF_003752505.1_ASM375250v1_genomic.fna/cds.fna -a GCF_003752505.1_ASM375250v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:25,158] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:25,158] [INFO] Task started: HMMsearch
[2024-01-24 12:47:25,158] [INFO] Running command: hmmsearch --tblout GCF_003752505.1_ASM375250v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg597adcee-0597-4587-a478-c6e2edb07575/dqc_reference/reference_markers.hmm GCF_003752505.1_ASM375250v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:25,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:25,442] [INFO] Found 6/6 markers.
[2024-01-24 12:47:25,488] [INFO] Query marker FASTA was written to GCF_003752505.1_ASM375250v1_genomic.fna/markers.fasta
[2024-01-24 12:47:25,489] [INFO] Task started: Blastn
[2024-01-24 12:47:25,489] [INFO] Running command: blastn -query GCF_003752505.1_ASM375250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg597adcee-0597-4587-a478-c6e2edb07575/dqc_reference/reference_markers.fasta -out GCF_003752505.1_ASM375250v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:27,028] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:27,050] [INFO] Selected 21 target genomes.
[2024-01-24 12:47:27,051] [INFO] Target genome list was writen to GCF_003752505.1_ASM375250v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:27,064] [INFO] Task started: fastANI
[2024-01-24 12:47:27,064] [INFO] Running command: fastANI --query /var/lib/cwl/stg70d1684e-abf3-4f05-a02e-2a907c691c5b/GCF_003752505.1_ASM375250v1_genomic.fna.gz --refList GCF_003752505.1_ASM375250v1_genomic.fna/target_genomes.txt --output GCF_003752505.1_ASM375250v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:48,539] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:48,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg597adcee-0597-4587-a478-c6e2edb07575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:48,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg597adcee-0597-4587-a478-c6e2edb07575/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:48,557] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:48,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:48,558] [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
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	100.0	1353	1353	95	conclusive
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	86.5375	1020	1353	95	below_threshold
Marmoricola aequoreus	strain=NRRL B-24464	GCA_000720335.1	397278	397278	type	True	83.3168	848	1353	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.9442	730	1353	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	80.6961	685	1353	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	80.675	698	1353	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	80.6732	695	1353	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	80.4794	671	1353	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.4003	661	1353	95	below_threshold
Marmoricola solisilvae	strain=KIS18-7	GCA_003725775.1	1542737	1542737	type	True	80.3643	601	1353	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.3621	702	1353	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.2973	587	1353	95	below_threshold
Marmoricola ginsengisoli	strain=Gsoil 097	GCA_003725695.1	661483	661483	type	True	80.272	601	1353	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.1991	635	1353	95	below_threshold
Nocardioides euryhalodurans	strain=MMS17-SY117	GCA_004564375.1	2518370	2518370	type	True	80.1823	632	1353	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.1571	652	1353	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	80.049	662	1353	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.0426	632	1353	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.917	585	1353	95	below_threshold
Nocardioides islandensis	strain=KCTC 19275	GCA_015352455.1	433663	433663	type	True	79.8173	603	1353	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	79.7145	543	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:48,560] [INFO] DFAST Taxonomy check result was written to GCF_003752505.1_ASM375250v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:48,561] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:48,561] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:48,561] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg597adcee-0597-4587-a478-c6e2edb07575/dqc_reference/checkm_data
[2024-01-24 12:47:48,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:48,619] [INFO] Task started: CheckM
[2024-01-24 12:47:48,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003752505.1_ASM375250v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003752505.1_ASM375250v1_genomic.fna/checkm_input GCF_003752505.1_ASM375250v1_genomic.fna/checkm_result
[2024-01-24 12:48:57,446] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:57,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:57,471] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:57,471] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:57,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003752505.1_ASM375250v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:57,472] [INFO] Task started: Blastn
[2024-01-24 12:48:57,472] [INFO] Running command: blastn -query GCF_003752505.1_ASM375250v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg597adcee-0597-4587-a478-c6e2edb07575/dqc_reference/reference_markers_gtdb.fasta -out GCF_003752505.1_ASM375250v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:59,954] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:59,959] [INFO] Selected 9 target genomes.
[2024-01-24 12:48:59,959] [INFO] Target genome list was writen to GCF_003752505.1_ASM375250v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:59,967] [INFO] Task started: fastANI
[2024-01-24 12:48:59,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg70d1684e-abf3-4f05-a02e-2a907c691c5b/GCF_003752505.1_ASM375250v1_genomic.fna.gz --refList GCF_003752505.1_ASM375250v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003752505.1_ASM375250v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:09,424] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:09,440] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:09,441] [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_003752505.1	s__Marmoricola aurantiacus	100.0	1353	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001424755.1	s__Marmoricola sp001424755	93.2638	1091	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104965.1	s__Marmoricola scoriae	86.57	1017	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720335.1	s__Marmoricola aequoreus	83.305	848	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426045.1	s__Marmoricola sp000426045	82.2696	786	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907435.1	s__Nocardioides salarius	80.774	698	1353	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004564375.1	s__Nocardioides euryhalodurans	80.2062	630	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_003194625.1	s__Nocardioides solisilvae	79.9009	587	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_004683965.1	s__Nocardioides seonyuensis	79.7744	539	1353	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 12:49:09,446] [INFO] GTDB search result was written to GCF_003752505.1_ASM375250v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:09,447] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:09,452] [INFO] DFAST_QC result json was written to GCF_003752505.1_ASM375250v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:09,452] [INFO] DFAST_QC completed!
[2024-01-24 12:49:09,453] [INFO] Total running time: 0h1m57s