[2024-01-25 19:03:50,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:50,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:50,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd426a5e-44ea-4bcf-b6ab-8cb3a4217561/dqc_reference
[2024-01-25 19:03:51,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:51,756] [INFO] Task started: Prodigal
[2024-01-25 19:03:51,756] [INFO] Running command: gunzip -c /var/lib/cwl/stga4014a35-80f7-4f3a-9607-4ebff988f76a/GCF_023554635.1_ASM2355463v1_genomic.fna.gz | prodigal -d GCF_023554635.1_ASM2355463v1_genomic.fna/cds.fna -a GCF_023554635.1_ASM2355463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:02,368] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:02,368] [INFO] Task started: HMMsearch
[2024-01-25 19:04:02,368] [INFO] Running command: hmmsearch --tblout GCF_023554635.1_ASM2355463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd426a5e-44ea-4bcf-b6ab-8cb3a4217561/dqc_reference/reference_markers.hmm GCF_023554635.1_ASM2355463v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:02,607] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:02,609] [INFO] Found 6/6 markers.
[2024-01-25 19:04:02,647] [INFO] Query marker FASTA was written to GCF_023554635.1_ASM2355463v1_genomic.fna/markers.fasta
[2024-01-25 19:04:02,647] [INFO] Task started: Blastn
[2024-01-25 19:04:02,647] [INFO] Running command: blastn -query GCF_023554635.1_ASM2355463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd426a5e-44ea-4bcf-b6ab-8cb3a4217561/dqc_reference/reference_markers.fasta -out GCF_023554635.1_ASM2355463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:03,879] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:03,881] [INFO] Selected 25 target genomes.
[2024-01-25 19:04:03,882] [INFO] Target genome list was writen to GCF_023554635.1_ASM2355463v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:03,894] [INFO] Task started: fastANI
[2024-01-25 19:04:03,895] [INFO] Running command: fastANI --query /var/lib/cwl/stga4014a35-80f7-4f3a-9607-4ebff988f76a/GCF_023554635.1_ASM2355463v1_genomic.fna.gz --refList GCF_023554635.1_ASM2355463v1_genomic.fna/target_genomes.txt --output GCF_023554635.1_ASM2355463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:27,837] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:27,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd426a5e-44ea-4bcf-b6ab-8cb3a4217561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:27,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd426a5e-44ea-4bcf-b6ab-8cb3a4217561/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:27,852] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:04:27,852] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:04:27,852] [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 salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	81.3327	785	1435	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	81.3091	785	1435	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	81.2765	780	1435	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.2672	789	1435	95	below_threshold
Nocardioides marinus	strain=DSM 18248	GCA_013408145.1	374514	374514	type	True	81.2667	759	1435	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.1066	803	1435	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.7195	766	1435	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.585	688	1435	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.5699	682	1435	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.4652	675	1435	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.1656	667	1435	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.03	669	1435	95	below_threshold
Nocardioides litoris	strain=DSM 103718	GCA_006346315.1	1926648	1926648	type	True	80.0192	720	1435	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	79.9886	738	1435	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	79.9859	712	1435	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.8443	632	1435	95	below_threshold
Nocardioides sediminis	strain=KCTC 19271	GCA_003047295.1	433648	433648	type	True	79.7878	634	1435	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	79.7826	678	1435	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	79.7124	615	1435	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	79.6325	728	1435	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.4879	616	1435	95	below_threshold
Pimelobacter simplex	strain=ATCC 6946	GCA_900114845.1	2045	2045	type	True	79.4643	700	1435	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.439	576	1435	95	below_threshold
Marmoricola aurantiacus	strain=DSM 12652	GCA_003752505.1	86796	86796	type	True	79.3929	619	1435	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.128	667	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:27,853] [INFO] DFAST Taxonomy check result was written to GCF_023554635.1_ASM2355463v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:27,854] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:27,854] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:27,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd426a5e-44ea-4bcf-b6ab-8cb3a4217561/dqc_reference/checkm_data
[2024-01-25 19:04:27,855] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:27,894] [INFO] Task started: CheckM
[2024-01-25 19:04:27,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023554635.1_ASM2355463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023554635.1_ASM2355463v1_genomic.fna/checkm_input GCF_023554635.1_ASM2355463v1_genomic.fna/checkm_result
[2024-01-25 19:05:34,361] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:34,362] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:34,383] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:34,383] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:34,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023554635.1_ASM2355463v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:34,384] [INFO] Task started: Blastn
[2024-01-25 19:05:34,384] [INFO] Running command: blastn -query GCF_023554635.1_ASM2355463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd426a5e-44ea-4bcf-b6ab-8cb3a4217561/dqc_reference/reference_markers_gtdb.fasta -out GCF_023554635.1_ASM2355463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:36,441] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:36,445] [INFO] Selected 19 target genomes.
[2024-01-25 19:05:36,445] [INFO] Target genome list was writen to GCF_023554635.1_ASM2355463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:36,469] [INFO] Task started: fastANI
[2024-01-25 19:05:36,469] [INFO] Running command: fastANI --query /var/lib/cwl/stga4014a35-80f7-4f3a-9607-4ebff988f76a/GCF_023554635.1_ASM2355463v1_genomic.fna.gz --refList GCF_023554635.1_ASM2355463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023554635.1_ASM2355463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:55,106] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:55,118] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:05:55,118] [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_004919085.1	s__Nocardioides sp004919085	84.8583	1051	1435	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	81.3873	664	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_016907435.1	s__Nocardioides salarius	81.3301	773	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	3	-
GCF_013408145.1	s__Nocardioides marinus	81.2963	756	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.85	95.82	0.82	0.73	3	-
GCA_009701885.1	s__Nocardioides sp009701885	80.8959	723	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070375.1	s__Nocardioides kribbensis	80.683	770	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCA_002729525.1	s__Nocardioides sp002729525	80.6699	744	1435	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	80.6501	681	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013155365.1	s__Nocardioides sp013155365	80.5541	686	1435	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	80.5358	678	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	80.3907	706	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.1401	671	1435	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	80.1166	669	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_006346315.1	s__Nocardioides litoris	80.076	713	1435	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	80.0367	700	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013466985.1	s__Nocardioides ungokensis	80.0059	672	1435	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	79.8957	669	1435	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	79.6188	731	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018831735.1	s__Nocardioides sp018831735	79.5027	698	1435	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:55,120] [INFO] GTDB search result was written to GCF_023554635.1_ASM2355463v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:55,121] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:55,124] [INFO] DFAST_QC result json was written to GCF_023554635.1_ASM2355463v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:55,124] [INFO] DFAST_QC completed!
[2024-01-25 19:05:55,125] [INFO] Total running time: 0h2m4s