[2024-01-24 14:21:50,035] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:21:50,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:21:50,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg54bb3f7a-9d20-4c4f-a317-5eb9115a8262/dqc_reference
[2024-01-24 14:21:51,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:21:51,398] [INFO] Task started: Prodigal
[2024-01-24 14:21:51,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg7690be89-eb78-4af4-b660-b0b3ba2247a1/GCF_014191495.1_ASM1419149v1_genomic.fna.gz | prodigal -d GCF_014191495.1_ASM1419149v1_genomic.fna/cds.fna -a GCF_014191495.1_ASM1419149v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:07,665] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:07,665] [INFO] Task started: HMMsearch
[2024-01-24 14:22:07,665] [INFO] Running command: hmmsearch --tblout GCF_014191495.1_ASM1419149v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg54bb3f7a-9d20-4c4f-a317-5eb9115a8262/dqc_reference/reference_markers.hmm GCF_014191495.1_ASM1419149v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:07,984] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:07,985] [INFO] Found 6/6 markers.
[2024-01-24 14:22:08,033] [INFO] Query marker FASTA was written to GCF_014191495.1_ASM1419149v1_genomic.fna/markers.fasta
[2024-01-24 14:22:08,034] [INFO] Task started: Blastn
[2024-01-24 14:22:08,034] [INFO] Running command: blastn -query GCF_014191495.1_ASM1419149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54bb3f7a-9d20-4c4f-a317-5eb9115a8262/dqc_reference/reference_markers.fasta -out GCF_014191495.1_ASM1419149v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:09,309] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:09,312] [INFO] Selected 26 target genomes.
[2024-01-24 14:22:09,313] [INFO] Target genome list was writen to GCF_014191495.1_ASM1419149v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:09,326] [INFO] Task started: fastANI
[2024-01-24 14:22:09,326] [INFO] Running command: fastANI --query /var/lib/cwl/stg7690be89-eb78-4af4-b660-b0b3ba2247a1/GCF_014191495.1_ASM1419149v1_genomic.fna.gz --refList GCF_014191495.1_ASM1419149v1_genomic.fna/target_genomes.txt --output GCF_014191495.1_ASM1419149v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:39,309] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:39,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg54bb3f7a-9d20-4c4f-a317-5eb9115a8262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:39,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg54bb3f7a-9d20-4c4f-a317-5eb9115a8262/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:39,328] [INFO] Found 26 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:39,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:39,329] [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 soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	100.0	1921	1925	95	conclusive
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	82.3273	855	1925	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	82.2832	856	1925	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	82.0291	818	1925	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	81.9829	948	1925	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	81.9178	846	1925	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_013409225.1	1045774	1045774	type	True	81.8915	961	1925	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	81.8226	863	1925	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	81.7447	871	1925	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	81.6406	811	1925	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	81.5798	807	1925	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013409965.1	419476	419476	type	True	81.5488	807	1925	95	below_threshold
Nocardioides marinisabuli	strain=DSM 18965	GCA_013466785.1	419476	419476	type	True	81.4026	809	1925	95	below_threshold
Nocardioides halotolerans	strain=DSM 19273	GCA_000422805.1	433660	433660	type	True	81.2966	876	1925	95	below_threshold
Nocardioides terrigena	strain=KCTC 19217	GCA_003047265.1	424797	424797	type	True	80.8943	766	1925	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.7891	831	1925	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.5584	797	1925	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	80.5563	664	1925	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	80.5469	778	1925	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	80.5449	683	1925	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	80.537	719	1925	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	80.5132	739	1925	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	80.4607	746	1925	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	80.4163	742	1925	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.911	732	1925	95	below_threshold
Nocardioides cavernaquae	strain=K1W22B-1	GCA_003600895.1	2321396	2321396	type	True	79.6937	538	1925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:39,330] [INFO] DFAST Taxonomy check result was written to GCF_014191495.1_ASM1419149v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:39,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:39,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:39,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg54bb3f7a-9d20-4c4f-a317-5eb9115a8262/dqc_reference/checkm_data
[2024-01-24 14:22:39,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:39,384] [INFO] Task started: CheckM
[2024-01-24 14:22:39,385] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191495.1_ASM1419149v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191495.1_ASM1419149v1_genomic.fna/checkm_input GCF_014191495.1_ASM1419149v1_genomic.fna/checkm_result
[2024-01-24 14:23:58,371] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:58,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:58,394] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:58,394] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:58,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191495.1_ASM1419149v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:58,395] [INFO] Task started: Blastn
[2024-01-24 14:23:58,395] [INFO] Running command: blastn -query GCF_014191495.1_ASM1419149v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg54bb3f7a-9d20-4c4f-a317-5eb9115a8262/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191495.1_ASM1419149v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:00,573] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:00,576] [INFO] Selected 17 target genomes.
[2024-01-24 14:24:00,576] [INFO] Target genome list was writen to GCF_014191495.1_ASM1419149v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:00,588] [INFO] Task started: fastANI
[2024-01-24 14:24:00,588] [INFO] Running command: fastANI --query /var/lib/cwl/stg7690be89-eb78-4af4-b660-b0b3ba2247a1/GCF_014191495.1_ASM1419149v1_genomic.fna.gz --refList GCF_014191495.1_ASM1419149v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191495.1_ASM1419149v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:21,081] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:21,106] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:21,106] [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_014191495.1	s__Nocardioides soli	100.0	1918	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.71	98.71	0.90	0.90	2	conclusive
GCF_013778305.1	s__Nocardioides sp013778305	84.536	1051	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425175.1	s__Nocardioides sp001425175	84.2989	1112	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000620705.1	s__Nocardioides sp000620705	83.6485	1019	1925	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	83.488	968	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000620645.1	s__Nocardioides sp000620645	83.3147	956	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015265.1	s__Nocardioides sp000015265	83.2627	999	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011250565.1	s__Nocardioides sp011250565	82.1009	869	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409645.1	s__Nocardioides panaciterrulae	82.038	819	1925	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	81.9988	836	1925	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	81.8161	864	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013466785.1	s__Nocardioides marinisabuli	81.4191	801	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004519545.1	s__Nocardioides guangzhouensis	80.7746	833	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779655.1	s__Nocardioides ganghwensis	80.5608	733	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017916425.1	s__Nocardioides sp017916425	80.2581	686	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009780515.1	s__Nocardioides sp009780515	80.189	637	1925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.88	99.88	0.93	0.93	2	-
GCA_016213595.1	s__Fen-668 sp016213595	77.2834	194	1925	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 14:24:21,108] [INFO] GTDB search result was written to GCF_014191495.1_ASM1419149v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:21,108] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:21,113] [INFO] DFAST_QC result json was written to GCF_014191495.1_ASM1419149v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:21,113] [INFO] DFAST_QC completed!
[2024-01-24 14:24:21,113] [INFO] Total running time: 0h2m31s