[2024-01-24 12:14:48,600] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,602] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3119c75-44f1-4fd9-82b6-e36e0b353818/dqc_reference
[2024-01-24 12:14:50,014] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,015] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,016] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3cf95e5-9f6b-493d-8cce-7edf714b8d4f/GCF_010686755.1_ASM1068675v1_genomic.fna.gz | prodigal -d GCF_010686755.1_ASM1068675v1_genomic.fna/cds.fna -a GCF_010686755.1_ASM1068675v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:02,280] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:02,281] [INFO] Task started: HMMsearch
[2024-01-24 12:15:02,281] [INFO] Running command: hmmsearch --tblout GCF_010686755.1_ASM1068675v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3119c75-44f1-4fd9-82b6-e36e0b353818/dqc_reference/reference_markers.hmm GCF_010686755.1_ASM1068675v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:02,590] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:02,591] [INFO] Found 6/6 markers.
[2024-01-24 12:15:02,639] [INFO] Query marker FASTA was written to GCF_010686755.1_ASM1068675v1_genomic.fna/markers.fasta
[2024-01-24 12:15:02,639] [INFO] Task started: Blastn
[2024-01-24 12:15:02,639] [INFO] Running command: blastn -query GCF_010686755.1_ASM1068675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3119c75-44f1-4fd9-82b6-e36e0b353818/dqc_reference/reference_markers.fasta -out GCF_010686755.1_ASM1068675v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:03,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:03,934] [INFO] Selected 28 target genomes.
[2024-01-24 12:15:03,934] [INFO] Target genome list was writen to GCF_010686755.1_ASM1068675v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:03,946] [INFO] Task started: fastANI
[2024-01-24 12:15:03,946] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3cf95e5-9f6b-493d-8cce-7edf714b8d4f/GCF_010686755.1_ASM1068675v1_genomic.fna.gz --refList GCF_010686755.1_ASM1068675v1_genomic.fna/target_genomes.txt --output GCF_010686755.1_ASM1068675v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:29,777] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:29,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3119c75-44f1-4fd9-82b6-e36e0b353818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:29,779] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3119c75-44f1-4fd9-82b6-e36e0b353818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:29,804] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:29,805] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:29,805] [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 alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	82.5329	940	1451	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	79.9906	687	1451	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	79.8853	696	1451	95	below_threshold
Nocardioides lijunqiniae	strain=S-531	GCA_015024225.1	2760832	2760832	type	True	79.8091	654	1451	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	79.7297	695	1451	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	79.7235	627	1451	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	79.6556	730	1451	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.6461	733	1451	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.6268	640	1451	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	79.531	623	1451	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	79.5255	593	1451	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.4974	664	1451	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	79.4825	634	1451	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.4626	635	1451	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	79.4584	600	1451	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.4568	594	1451	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.4071	689	1451	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	79.4043	644	1451	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	79.3944	633	1451	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	79.3827	619	1451	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	79.3784	634	1451	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.3784	595	1451	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.3595	628	1451	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	79.3202	651	1451	95	below_threshold
Pimelobacter simplex	strain=NBRC 12069	GCA_006538965.1	2045	2045	type	True	79.1441	731	1451	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.0921	546	1451	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	79.0781	728	1451	95	below_threshold
Nocardioides yefusunii	strain=HY056	GCA_004014875.1	2500546	2500546	type	True	78.5228	428	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:29,807] [INFO] DFAST Taxonomy check result was written to GCF_010686755.1_ASM1068675v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:29,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:29,808] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:29,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3119c75-44f1-4fd9-82b6-e36e0b353818/dqc_reference/checkm_data
[2024-01-24 12:15:29,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:29,855] [INFO] Task started: CheckM
[2024-01-24 12:15:29,856] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010686755.1_ASM1068675v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010686755.1_ASM1068675v1_genomic.fna/checkm_input GCF_010686755.1_ASM1068675v1_genomic.fna/checkm_result
[2024-01-24 12:16:34,191] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:34,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:34,217] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:34,217] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:34,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010686755.1_ASM1068675v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:34,218] [INFO] Task started: Blastn
[2024-01-24 12:16:34,218] [INFO] Running command: blastn -query GCF_010686755.1_ASM1068675v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3119c75-44f1-4fd9-82b6-e36e0b353818/dqc_reference/reference_markers_gtdb.fasta -out GCF_010686755.1_ASM1068675v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:36,157] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:36,161] [INFO] Selected 24 target genomes.
[2024-01-24 12:16:36,161] [INFO] Target genome list was writen to GCF_010686755.1_ASM1068675v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:36,176] [INFO] Task started: fastANI
[2024-01-24 12:16:36,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3cf95e5-9f6b-493d-8cce-7edf714b8d4f/GCF_010686755.1_ASM1068675v1_genomic.fna.gz --refList GCF_010686755.1_ASM1068675v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010686755.1_ASM1068675v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:58,946] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:58,971] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:58,972] [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_010686755.1	s__Nocardioides zeae	100.0	1449	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000426525.1	s__Nocardioides alkalitolerans	82.5354	940	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011250565.1	s__Nocardioides sp011250565	80.0229	690	1451	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	79.6741	674	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002117935.1	s__Nocardioides sp002117935	79.5862	643	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900101465.1	s__Nocardioides lianchengensis	79.5837	742	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003076135.1	s__Nocardioides gansuensis	79.5759	588	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425175.1	s__Nocardioides sp001425175	79.5576	686	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_009699265.1	s__Nocardioides sp009699265	79.5532	623	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013466985.1	s__Nocardioides ungokensis	79.5504	620	1451	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	79.5285	607	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_013410035.1	s__Nocardioides cavernae_A	79.5157	639	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017310035.1	s__Nocardioides sp017310035	79.4811	625	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752505.1	s__Marmoricola aurantiacus	79.4261	589	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191495.1	s__Nocardioides soli	79.4241	686	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	-
GCF_001425025.1	s__Nocardioides sp001425025	79.4068	639	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346315.1	s__Nocardioides litoris	79.3962	727	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729525.1	s__Nocardioides sp002729525	79.376	688	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653335.1	s__Nocardioides dokdonensis	79.3541	623	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907475.1	s__Nocardioides cavernae	79.3414	639	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003660455.1	s__Nocardioides ferulae	79.3279	650	1451	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	79.2265	635	1451	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	79.1017	587	1451	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.04	99.04	0.95	0.95	2	-
GCA_016213595.1	s__Fen-668 sp016213595	76.7599	198	1451	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 12:16:58,974] [INFO] GTDB search result was written to GCF_010686755.1_ASM1068675v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:58,974] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:58,979] [INFO] DFAST_QC result json was written to GCF_010686755.1_ASM1068675v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:58,979] [INFO] DFAST_QC completed!
[2024-01-24 12:16:58,979] [INFO] Total running time: 0h2m10s