[2024-01-24 13:41:40,149] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,150] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f8035c1-7d6c-4aa6-a0bc-8228df4d1665/dqc_reference
[2024-01-24 13:41:41,373] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,374] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,374] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fc3d6b2-e225-4a10-ab67-b2a142c84cb7/GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna.gz | prodigal -d GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/cds.fna -a GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:50,655] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:50,656] [INFO] Task started: HMMsearch
[2024-01-24 13:41:50,656] [INFO] Running command: hmmsearch --tblout GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f8035c1-7d6c-4aa6-a0bc-8228df4d1665/dqc_reference/reference_markers.hmm GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:50,872] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:50,873] [INFO] Found 6/6 markers.
[2024-01-24 13:41:50,911] [INFO] Query marker FASTA was written to GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/markers.fasta
[2024-01-24 13:41:50,912] [INFO] Task started: Blastn
[2024-01-24 13:41:50,912] [INFO] Running command: blastn -query GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f8035c1-7d6c-4aa6-a0bc-8228df4d1665/dqc_reference/reference_markers.fasta -out GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:52,035] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:52,039] [INFO] Selected 25 target genomes.
[2024-01-24 13:41:52,039] [INFO] Target genome list was writen to GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/target_genomes.txt
[2024-01-24 13:41:52,047] [INFO] Task started: fastANI
[2024-01-24 13:41:52,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc3d6b2-e225-4a10-ab67-b2a142c84cb7/GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna.gz --refList GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/target_genomes.txt --output GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:11,022] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:11,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f8035c1-7d6c-4aa6-a0bc-8228df4d1665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:11,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f8035c1-7d6c-4aa6-a0bc-8228df4d1665/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:11,042] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:11,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:11,042] [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 massiliensis	strain=GD13	GCA_900067705.2	1325935	1325935	type	True	100.0	912	931	95	conclusive
Nocardioides dongkuii	strain=S-713	GCA_014127485.1	2760089	2760089	type	True	80.5004	461	931	95	below_threshold
Nocardioides ferulae	strain=SZ4R5S7	GCA_003660455.1	2340821	2340821	type	True	80.4093	487	931	95	below_threshold
Nocardioides iriomotensis	strain=NBRC 105384	GCA_004168035.1	715784	715784	type	True	80.3994	442	931	95	below_threshold
Nocardioides ginsengisegetis	strain=DSM 21349	GCA_014138045.1	661491	661491	type	True	80.3504	459	931	95	below_threshold
Nocardioides deserti	strain=CGMCC 4.7183	GCA_014646035.1	1588644	1588644	type	True	80.2145	485	931	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	80.2051	411	931	95	below_threshold
Nocardioides deserti	strain=SC8A-24	GCA_014266025.1	1588644	1588644	type	True	80.2017	488	931	95	below_threshold
Nocardioides dokdonensis	strain=FR1436	GCA_001653335.1	450734	450734	type	True	80.1716	461	931	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	80.1171	423	931	95	below_threshold
Nocardioides kribbensis	strain=DSM 16314	GCA_015070375.1	305517	305517	type	True	80.0696	451	931	95	below_threshold
Nocardioides guangzhouensis	strain=130	GCA_004519545.1	2497878	2497878	type	True	80.0121	408	931	95	below_threshold
Nocardioides luti	strain=KIGAM211	GCA_014212315.1	2761101	2761101	type	True	80.0045	463	931	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	80.0	435	931	95	below_threshold
Nocardioides donggukensis	strain=MJB4	GCA_014842875.1	2774019	2774019	type	True	79.9994	388	931	95	below_threshold
Nocardioides panacis	strain=G188	GCA_019039255.1	2849501	2849501	type	True	79.9864	432	931	95	below_threshold
Nocardioides lianchengensis	strain=CGMCC 4.6858	GCA_900101465.1	1045774	1045774	type	True	79.9543	470	931	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.8512	485	931	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	79.8124	397	931	95	below_threshold
Nocardioides szechwanensis	strain=NBRC 108562	GCA_007992395.1	1005944	1005944	type	True	79.7877	445	931	95	below_threshold
Nocardioides szechwanensis	strain=CGMCC 1.11147	GCA_900103935.1	1005944	1005944	type	True	79.7717	442	931	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	79.6574	418	931	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	79.6182	417	931	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	79.6064	423	931	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	79.5771	387	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,044] [INFO] DFAST Taxonomy check result was written to GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/tc_result.tsv
[2024-01-24 13:42:11,044] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:11,045] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:11,045] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f8035c1-7d6c-4aa6-a0bc-8228df4d1665/dqc_reference/checkm_data
[2024-01-24 13:42:11,046] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:11,089] [INFO] Task started: CheckM
[2024-01-24 13:42:11,090] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/checkm_input GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/checkm_result
[2024-01-24 13:42:41,522] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:41,523] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:41,900] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:41,900] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:41,901] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/markers.fasta)
[2024-01-24 13:42:41,901] [INFO] Task started: Blastn
[2024-01-24 13:42:41,901] [INFO] Running command: blastn -query GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f8035c1-7d6c-4aa6-a0bc-8228df4d1665/dqc_reference/reference_markers_gtdb.fasta -out GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:43,688] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:43,691] [INFO] Selected 24 target genomes.
[2024-01-24 13:42:43,691] [INFO] Target genome list was writen to GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:43,725] [INFO] Task started: fastANI
[2024-01-24 13:42:43,726] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc3d6b2-e225-4a10-ab67-b2a142c84cb7/GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna.gz --refList GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/target_genomes_gtdb.txt --output GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:01,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:01,559] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:01,559] [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_900067705.2	s__Nocardioides_A massiliensis	100.0	912	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011250565.1	s__Nocardioides sp011250565	80.5298	478	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168035.1	s__Nocardioides_B iriomotensis	80.513	434	931	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_009557055.1	s__Nocardioides sp009557055	80.3982	458	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014138045.1	s__Nocardioides ginsengisegetis	80.3502	459	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	96.18	96.18	0.84	0.84	2	-
GCF_011420305.2	s__Nocardioides sp011420305	80.3455	471	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.38	99.38	0.96	0.96	2	-
GCF_003710085.1	s__Nocardioides sp003710085	80.3314	421	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.05	99.05	0.97	0.97	2	-
GCF_014266025.1	s__Nocardioides deserti	80.2955	480	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013466985.1	s__Nocardioides ungokensis	80.2747	406	931	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	80.2081	458	931	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	80.1182	447	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	97.79	97.79	0.94	0.92	3	-
GCF_002117935.1	s__Nocardioides sp002117935	80.0432	438	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001425175.1	s__Nocardioides sp001425175	80.0222	436	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014395785.1	s__Nocardioides_B mesophilus	80.0087	418	931	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_013409645.1	s__Nocardioides panaciterrulae	79.9869	436	931	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	79.9263	470	931	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	79.9128	464	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003057875.1	s__Nocardioides currus	79.8121	397	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620645.1	s__Nocardioides sp000620645	79.8091	416	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916455.1	s__Nocardioides sp017916455	79.8005	399	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_900103935.1	s__Nocardioides szechwanensis	79.7269	447	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016907475.1	s__Nocardioides cavernae	79.6426	420	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902805845.1	s__Marmoricola_A sp902805845	78.9167	309	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805865.1	s__Marmoricola_A sp902805865	78.888	318	931	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:01,561] [INFO] GTDB search result was written to GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:01,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:01,567] [INFO] DFAST_QC result json was written to GCF_900067705.2_Nocardioides_massiliensis_str._GD13_genomic.fna/dqc_result.json
[2024-01-24 13:43:01,567] [INFO] DFAST_QC completed!
[2024-01-24 13:43:01,568] [INFO] Total running time: 0h1m21s