[2024-01-24 12:34:20,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,488] [INFO] DQC Reference Directory: /var/lib/cwl/stg66e173e5-d139-4c6e-b61b-3c6a5bc7c487/dqc_reference
[2024-01-24 12:34:21,707] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,708] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,708] [INFO] Running command: gunzip -c /var/lib/cwl/stgde8caf27-af29-498e-841c-00735818ca07/GCF_019039255.1_ASM1903925v1_genomic.fna.gz | prodigal -d GCF_019039255.1_ASM1903925v1_genomic.fna/cds.fna -a GCF_019039255.1_ASM1903925v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:35,288] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:35,289] [INFO] Task started: HMMsearch
[2024-01-24 12:34:35,289] [INFO] Running command: hmmsearch --tblout GCF_019039255.1_ASM1903925v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66e173e5-d139-4c6e-b61b-3c6a5bc7c487/dqc_reference/reference_markers.hmm GCF_019039255.1_ASM1903925v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:35,572] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:35,573] [INFO] Found 6/6 markers.
[2024-01-24 12:34:35,615] [INFO] Query marker FASTA was written to GCF_019039255.1_ASM1903925v1_genomic.fna/markers.fasta
[2024-01-24 12:34:35,616] [INFO] Task started: Blastn
[2024-01-24 12:34:35,616] [INFO] Running command: blastn -query GCF_019039255.1_ASM1903925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66e173e5-d139-4c6e-b61b-3c6a5bc7c487/dqc_reference/reference_markers.fasta -out GCF_019039255.1_ASM1903925v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:36,915] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:36,919] [INFO] Selected 20 target genomes.
[2024-01-24 12:34:36,919] [INFO] Target genome list was writen to GCF_019039255.1_ASM1903925v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:36,928] [INFO] Task started: fastANI
[2024-01-24 12:34:36,928] [INFO] Running command: fastANI --query /var/lib/cwl/stgde8caf27-af29-498e-841c-00735818ca07/GCF_019039255.1_ASM1903925v1_genomic.fna.gz --refList GCF_019039255.1_ASM1903925v1_genomic.fna/target_genomes.txt --output GCF_019039255.1_ASM1903925v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:56,902] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:56,902] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66e173e5-d139-4c6e-b61b-3c6a5bc7c487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:56,903] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66e173e5-d139-4c6e-b61b-3c6a5bc7c487/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:56,922] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:34:56,923] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:56,923] [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 panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	100.0	1630	1633	95	conclusive
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	81.8999	906	1633	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.604	730	1633	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.5224	756	1633	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.5157	750	1633	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.4493	662	1633	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.3677	765	1633	95	below_threshold
Marmoricola scoriae	strain=DSM 22127	GCA_900104965.1	642780	642780	type	True	80.2731	745	1633	95	below_threshold
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	80.1937	719	1633	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.1824	696	1633	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	80.0882	703	1633	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.9752	719	1633	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.9742	654	1633	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.9142	671	1633	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.8971	731	1633	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	79.6252	692	1633	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	79.5613	661	1633	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	79.5372	629	1633	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.5184	685	1633	95	below_threshold
Nocardioides alkalitolerans	strain=DSM 16699	GCA_000426525.1	281714	281714	type	True	79.0251	635	1633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:56,925] [INFO] DFAST Taxonomy check result was written to GCF_019039255.1_ASM1903925v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:56,925] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:56,925] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:56,926] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66e173e5-d139-4c6e-b61b-3c6a5bc7c487/dqc_reference/checkm_data
[2024-01-24 12:34:56,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:56,975] [INFO] Task started: CheckM
[2024-01-24 12:34:56,975] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019039255.1_ASM1903925v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019039255.1_ASM1903925v1_genomic.fna/checkm_input GCF_019039255.1_ASM1903925v1_genomic.fna/checkm_result
[2024-01-24 12:36:15,497] [INFO] Task succeeded: CheckM
[2024-01-24 12:36:15,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:36:15,517] [INFO] ===== Completeness check finished =====
[2024-01-24 12:36:15,517] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:36:15,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019039255.1_ASM1903925v1_genomic.fna/markers.fasta)
[2024-01-24 12:36:15,518] [INFO] Task started: Blastn
[2024-01-24 12:36:15,518] [INFO] Running command: blastn -query GCF_019039255.1_ASM1903925v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66e173e5-d139-4c6e-b61b-3c6a5bc7c487/dqc_reference/reference_markers_gtdb.fasta -out GCF_019039255.1_ASM1903925v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:17,598] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:17,602] [INFO] Selected 19 target genomes.
[2024-01-24 12:36:17,603] [INFO] Target genome list was writen to GCF_019039255.1_ASM1903925v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:36:17,617] [INFO] Task started: fastANI
[2024-01-24 12:36:17,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgde8caf27-af29-498e-841c-00735818ca07/GCF_019039255.1_ASM1903925v1_genomic.fna.gz --refList GCF_019039255.1_ASM1903925v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019039255.1_ASM1903925v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:36:35,523] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:35,543] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:36:35,543] [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_019039255.1	s__JABFXA01 sp019039255	100.0	1632	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013361955.1	s__JABFXA01 sp013361955	83.3011	853	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__JABFXA01	95.0	99.75	99.75	0.92	0.92	2	-
GCF_014395785.1	s__Nocardioides_B mesophilus	82.3054	864	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	81.9238	904	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002384855.1	s__UBA4001 sp002384855	81.0062	657	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__UBA4001	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.5806	729	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_013409645.1	s__Nocardioides panaciterrulae	80.5075	758	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014842875.1	s__Nocardioides sp014842875	80.5049	656	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014212315.1	s__Nocardioides luti	80.3989	760	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003660455.1	s__Nocardioides ferulae	80.2248	690	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104965.1	s__Marmoricola scoriae	80.2225	752	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013177455.1	s__Nocardioides sp013177455	80.2021	699	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.28	98.92	0.97	0.95	4	-
GCF_014127485.1	s__Nocardioides sp014127485	80.1973	718	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.37	99.37	0.97	0.97	2	-
GCF_011250565.1	s__Nocardioides sp011250565	80.1677	668	1633	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	80.1278	687	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900103935.1	s__Nocardioides szechwanensis	80.0101	650	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_013778305.1	s__Nocardioides sp013778305	80.0053	734	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001627335.1	s__Nocardioides sp001627335	79.9017	544	1633	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	96.50	0.91	0.88	12	-
GCF_018275325.1	s__Nocardioides sp018275325	79.7477	711	1633	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 12:36:35,545] [INFO] GTDB search result was written to GCF_019039255.1_ASM1903925v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:36:35,545] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:36:35,549] [INFO] DFAST_QC result json was written to GCF_019039255.1_ASM1903925v1_genomic.fna/dqc_result.json
[2024-01-24 12:36:35,549] [INFO] DFAST_QC completed!
[2024-01-24 12:36:35,549] [INFO] Total running time: 0h2m15s