[2024-01-24 14:14:00,757] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:00,759] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:00,759] [INFO] DQC Reference Directory: /var/lib/cwl/stgc57950a8-d8e6-4e64-8fda-ba0a02950cfe/dqc_reference
[2024-01-24 14:14:02,070] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:02,071] [INFO] Task started: Prodigal
[2024-01-24 14:14:02,071] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fd66ad4-247c-43d8-807d-d7929b1b1b4e/GCF_004683965.1_ASM468396v1_genomic.fna.gz | prodigal -d GCF_004683965.1_ASM468396v1_genomic.fna/cds.fna -a GCF_004683965.1_ASM468396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:15,408] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:15,408] [INFO] Task started: HMMsearch
[2024-01-24 14:14:15,408] [INFO] Running command: hmmsearch --tblout GCF_004683965.1_ASM468396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc57950a8-d8e6-4e64-8fda-ba0a02950cfe/dqc_reference/reference_markers.hmm GCF_004683965.1_ASM468396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:15,867] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:15,869] [INFO] Found 6/6 markers.
[2024-01-24 14:14:15,942] [INFO] Query marker FASTA was written to GCF_004683965.1_ASM468396v1_genomic.fna/markers.fasta
[2024-01-24 14:14:15,943] [INFO] Task started: Blastn
[2024-01-24 14:14:15,943] [INFO] Running command: blastn -query GCF_004683965.1_ASM468396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc57950a8-d8e6-4e64-8fda-ba0a02950cfe/dqc_reference/reference_markers.fasta -out GCF_004683965.1_ASM468396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:17,850] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:17,853] [INFO] Selected 18 target genomes.
[2024-01-24 14:14:17,854] [INFO] Target genome list was writen to GCF_004683965.1_ASM468396v1_genomic.fna/target_genomes.txt
[2024-01-24 14:14:17,861] [INFO] Task started: fastANI
[2024-01-24 14:14:17,861] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd66ad4-247c-43d8-807d-d7929b1b1b4e/GCF_004683965.1_ASM468396v1_genomic.fna.gz --refList GCF_004683965.1_ASM468396v1_genomic.fna/target_genomes.txt --output GCF_004683965.1_ASM468396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:39,381] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:39,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc57950a8-d8e6-4e64-8fda-ba0a02950cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:39,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc57950a8-d8e6-4e64-8fda-ba0a02950cfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:39,396] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:14:39,396] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:39,397] [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 seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	100.0	1321	1324	95	conclusive
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	82.0813	789	1324	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	82.0585	776	1324	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	81.9805	773	1324	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	81.9527	801	1324	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	81.9526	792	1324	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	81.9522	796	1324	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	81.8967	800	1324	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	81.8579	763	1324	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	81.8409	773	1324	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	81.8139	778	1324	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	81.7512	780	1324	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	81.6839	791	1324	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	81.665	747	1324	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	81.6148	755	1324	95	below_threshold
Nocardioides allogilvus	strain=KCTC 49020	GCA_003047285.1	2072017	2072017	type	True	81.3425	724	1324	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	81.3189	746	1324	95	below_threshold
Nocardioides gansuensis	strain=WSJ-1	GCA_003076135.1	2138300	2138300	type	True	80.9466	687	1324	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:39,400] [INFO] DFAST Taxonomy check result was written to GCF_004683965.1_ASM468396v1_genomic.fna/tc_result.tsv
[2024-01-24 14:14:39,401] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:39,401] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:39,401] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc57950a8-d8e6-4e64-8fda-ba0a02950cfe/dqc_reference/checkm_data
[2024-01-24 14:14:39,403] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:39,447] [INFO] Task started: CheckM
[2024-01-24 14:14:39,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004683965.1_ASM468396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004683965.1_ASM468396v1_genomic.fna/checkm_input GCF_004683965.1_ASM468396v1_genomic.fna/checkm_result
[2024-01-24 14:15:46,801] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:46,802] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:46,823] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:46,823] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:46,823] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004683965.1_ASM468396v1_genomic.fna/markers.fasta)
[2024-01-24 14:15:46,824] [INFO] Task started: Blastn
[2024-01-24 14:15:46,824] [INFO] Running command: blastn -query GCF_004683965.1_ASM468396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc57950a8-d8e6-4e64-8fda-ba0a02950cfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_004683965.1_ASM468396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:48,941] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:48,945] [INFO] Selected 23 target genomes.
[2024-01-24 14:15:48,945] [INFO] Target genome list was writen to GCF_004683965.1_ASM468396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:48,963] [INFO] Task started: fastANI
[2024-01-24 14:15:48,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fd66ad4-247c-43d8-807d-d7929b1b1b4e/GCF_004683965.1_ASM468396v1_genomic.fna.gz --refList GCF_004683965.1_ASM468396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004683965.1_ASM468396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:10,406] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:10,430] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:10,431] [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_004683965.1	s__Nocardioides seonyuensis	100.0	1323	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001428125.1	s__Nocardioides sp001428125	82.1876	778	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009699265.1	s__Nocardioides sp009699265	82.0226	762	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	82.018	811	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633575.1	s__Nocardioides sp003633575	82.0094	778	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155335.1	s__Nocardioides sp013155335	82.0026	796	1324	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	81.9642	793	1324	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	81.9527	801	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004785795.1	s__Nocardioides eburneiflavus	81.9348	799	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	81.8594	772	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112035.1	s__Nocardioides alpinus	81.8197	777	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016735675.1	s__Nocardioides sp016735675	81.8127	776	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	81.7801	764	1324	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	81.7768	736	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_004137245.1	s__Nocardioides glacieisoli	81.7337	781	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872795.1	s__Nocardioides sp017872795	81.6879	783	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	81.6816	779	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779665.1	s__Nocardioides hwasunensis	81.6559	748	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410035.1	s__Nocardioides cavernae_A	81.631	777	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003047285.1	s__Nocardioides allogilvus	81.3489	723	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.72	98.72	0.92	0.92	2	-
GCA_902805885.1	s__Nocardioides sp902805885	81.3071	587	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076135.1	s__Nocardioides gansuensis	80.9645	685	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424755.1	s__Marmoricola sp001424755	79.8022	550	1324	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Marmoricola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:10,432] [INFO] GTDB search result was written to GCF_004683965.1_ASM468396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:10,433] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:10,439] [INFO] DFAST_QC result json was written to GCF_004683965.1_ASM468396v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:10,439] [INFO] DFAST_QC completed!
[2024-01-24 14:16:10,439] [INFO] Total running time: 0h2m10s