[2024-01-24 14:47:08,155] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:08,170] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:08,170] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6c7d162-a18e-45dd-958d-2f6c2c8f0f0c/dqc_reference
[2024-01-24 14:47:09,569] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:09,570] [INFO] Task started: Prodigal
[2024-01-24 14:47:09,570] [INFO] Running command: gunzip -c /var/lib/cwl/stg3cfb5d8c-c770-44f4-9099-30128bd26ee2/GCF_013177455.1_ASM1317745v1_genomic.fna.gz | prodigal -d GCF_013177455.1_ASM1317745v1_genomic.fna/cds.fna -a GCF_013177455.1_ASM1317745v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:21,502] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:21,503] [INFO] Task started: HMMsearch
[2024-01-24 14:47:21,503] [INFO] Running command: hmmsearch --tblout GCF_013177455.1_ASM1317745v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6c7d162-a18e-45dd-958d-2f6c2c8f0f0c/dqc_reference/reference_markers.hmm GCF_013177455.1_ASM1317745v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:21,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:21,868] [INFO] Found 6/6 markers.
[2024-01-24 14:47:21,914] [INFO] Query marker FASTA was written to GCF_013177455.1_ASM1317745v1_genomic.fna/markers.fasta
[2024-01-24 14:47:21,915] [INFO] Task started: Blastn
[2024-01-24 14:47:21,915] [INFO] Running command: blastn -query GCF_013177455.1_ASM1317745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c7d162-a18e-45dd-958d-2f6c2c8f0f0c/dqc_reference/reference_markers.fasta -out GCF_013177455.1_ASM1317745v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:23,363] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:23,367] [INFO] Selected 21 target genomes.
[2024-01-24 14:47:23,367] [INFO] Target genome list was writen to GCF_013177455.1_ASM1317745v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:23,373] [INFO] Task started: fastANI
[2024-01-24 14:47:23,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cfb5d8c-c770-44f4-9099-30128bd26ee2/GCF_013177455.1_ASM1317745v1_genomic.fna.gz --refList GCF_013177455.1_ASM1317745v1_genomic.fna/target_genomes.txt --output GCF_013177455.1_ASM1317745v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:46,357] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:46,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6c7d162-a18e-45dd-958d-2f6c2c8f0f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:46,358] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6c7d162-a18e-45dd-958d-2f6c2c8f0f0c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:46,374] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:47:46,374] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:47:46,375] [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=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	88.2815	1085	1463	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	88.229	1083	1463	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	83.5356	937	1463	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.6448	825	1463	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	82.471	855	1463	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015070765.1	374513	374513	type	True	82.4299	863	1463	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	82.4262	838	1463	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_015339545.1	374513	374513	type	True	82.3976	864	1463	95	below_threshold
Nocardioides salarius	strain=DSM 18239	GCA_016907435.1	374513	374513	type	True	82.3502	887	1463	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	82.3434	835	1463	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	82.2887	855	1463	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.1997	786	1463	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.9308	809	1463	95	below_threshold
Nocardioides flavescens	strain=YIM 123512	GCA_009823805.1	2691959	2691959	type	True	81.5829	819	1463	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	81.3599	757	1463	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.9236	767	1463	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.827	723	1463	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.6201	681	1463	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	80.5037	782	1463	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	80.3409	722	1463	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	80.08	705	1463	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:46,376] [INFO] DFAST Taxonomy check result was written to GCF_013177455.1_ASM1317745v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:46,377] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:46,377] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:46,377] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6c7d162-a18e-45dd-958d-2f6c2c8f0f0c/dqc_reference/checkm_data
[2024-01-24 14:47:46,378] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:46,422] [INFO] Task started: CheckM
[2024-01-24 14:47:46,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013177455.1_ASM1317745v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013177455.1_ASM1317745v1_genomic.fna/checkm_input GCF_013177455.1_ASM1317745v1_genomic.fna/checkm_result
[2024-01-24 14:48:55,832] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:55,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:55,853] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:55,853] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:55,854] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013177455.1_ASM1317745v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:55,854] [INFO] Task started: Blastn
[2024-01-24 14:48:55,855] [INFO] Running command: blastn -query GCF_013177455.1_ASM1317745v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6c7d162-a18e-45dd-958d-2f6c2c8f0f0c/dqc_reference/reference_markers_gtdb.fasta -out GCF_013177455.1_ASM1317745v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:58,250] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:58,253] [INFO] Selected 16 target genomes.
[2024-01-24 14:48:58,253] [INFO] Target genome list was writen to GCF_013177455.1_ASM1317745v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:58,262] [INFO] Task started: fastANI
[2024-01-24 14:48:58,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg3cfb5d8c-c770-44f4-9099-30128bd26ee2/GCF_013177455.1_ASM1317745v1_genomic.fna.gz --refList GCF_013177455.1_ASM1317745v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013177455.1_ASM1317745v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:17,590] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:17,611] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:17,611] [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	100.0	1463	1463	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	88.4573	1063	1463	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	88.2354	1083	1463	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	83.596	930	1463	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	82.9168	874	1463	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	82.3836	841	1463	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	82.3478	834	1463	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	82.1292	793	1463	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	82.1171	822	1463	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	81.9585	803	1463	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	81.8669	844	1463	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	81.7641	887	1463	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	81.6375	812	1463	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	81.1831	775	1463	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	80.8372	721	1463	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	80.7767	729	1463	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 14:49:17,613] [INFO] GTDB search result was written to GCF_013177455.1_ASM1317745v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:17,614] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:17,618] [INFO] DFAST_QC result json was written to GCF_013177455.1_ASM1317745v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:17,619] [INFO] DFAST_QC completed!
[2024-01-24 14:49:17,619] [INFO] Total running time: 0h2m9s