[2024-01-24 13:41:40,225] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,227] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,227] [INFO] DQC Reference Directory: /var/lib/cwl/stg5a0d2b5c-5832-4c60-95ca-d45b02267b38/dqc_reference
[2024-01-24 13:41:41,512] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:41,513] [INFO] Task started: Prodigal
[2024-01-24 13:41:41,513] [INFO] Running command: gunzip -c /var/lib/cwl/stg392686df-a5c1-418f-82d4-60b56d076de9/GCF_020102855.1_ASM2010285v1_genomic.fna.gz | prodigal -d GCF_020102855.1_ASM2010285v1_genomic.fna/cds.fna -a GCF_020102855.1_ASM2010285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:54,131] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:54,132] [INFO] Task started: HMMsearch
[2024-01-24 13:41:54,132] [INFO] Running command: hmmsearch --tblout GCF_020102855.1_ASM2010285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5a0d2b5c-5832-4c60-95ca-d45b02267b38/dqc_reference/reference_markers.hmm GCF_020102855.1_ASM2010285v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:54,419] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:54,421] [INFO] Found 6/6 markers.
[2024-01-24 13:41:54,465] [INFO] Query marker FASTA was written to GCF_020102855.1_ASM2010285v1_genomic.fna/markers.fasta
[2024-01-24 13:41:54,465] [INFO] Task started: Blastn
[2024-01-24 13:41:54,465] [INFO] Running command: blastn -query GCF_020102855.1_ASM2010285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a0d2b5c-5832-4c60-95ca-d45b02267b38/dqc_reference/reference_markers.fasta -out GCF_020102855.1_ASM2010285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:55,684] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:55,688] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:55,689] [INFO] Target genome list was writen to GCF_020102855.1_ASM2010285v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:55,709] [INFO] Task started: fastANI
[2024-01-24 13:41:55,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg392686df-a5c1-418f-82d4-60b56d076de9/GCF_020102855.1_ASM2010285v1_genomic.fna.gz --refList GCF_020102855.1_ASM2010285v1_genomic.fna/target_genomes.txt --output GCF_020102855.1_ASM2010285v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:10,343] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:10,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5a0d2b5c-5832-4c60-95ca-d45b02267b38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:10,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5a0d2b5c-5832-4c60-95ca-d45b02267b38/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:10,357] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:10,357] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:10,358] [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 lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	100.0	1473	1477	95	conclusive
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	93.1075	1082	1477	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	86.7304	1052	1477	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	86.5614	1029	1477	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	86.3608	1048	1477	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	86.3485	1088	1477	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	86.3088	1039	1477	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	86.0365	998	1477	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	86.0019	998	1477	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	85.9343	1014	1477	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	85.8806	1000	1477	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.7502	1029	1477	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	85.5373	961	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,360] [INFO] DFAST Taxonomy check result was written to GCF_020102855.1_ASM2010285v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:10,360] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:10,361] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:10,361] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5a0d2b5c-5832-4c60-95ca-d45b02267b38/dqc_reference/checkm_data
[2024-01-24 13:42:10,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:10,409] [INFO] Task started: CheckM
[2024-01-24 13:42:10,410] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020102855.1_ASM2010285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020102855.1_ASM2010285v1_genomic.fna/checkm_input GCF_020102855.1_ASM2010285v1_genomic.fna/checkm_result
[2024-01-24 13:43:13,253] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:13,254] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:13,274] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:13,275] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:13,275] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020102855.1_ASM2010285v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:13,275] [INFO] Task started: Blastn
[2024-01-24 13:43:13,276] [INFO] Running command: blastn -query GCF_020102855.1_ASM2010285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5a0d2b5c-5832-4c60-95ca-d45b02267b38/dqc_reference/reference_markers_gtdb.fasta -out GCF_020102855.1_ASM2010285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:15,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:15,255] [INFO] Selected 18 target genomes.
[2024-01-24 13:43:15,255] [INFO] Target genome list was writen to GCF_020102855.1_ASM2010285v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:15,385] [INFO] Task started: fastANI
[2024-01-24 13:43:15,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg392686df-a5c1-418f-82d4-60b56d076de9/GCF_020102855.1_ASM2010285v1_genomic.fna.gz --refList GCF_020102855.1_ASM2010285v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020102855.1_ASM2010285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:35,361] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:35,380] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:35,380] [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
GCA_009699265.1	s__Nocardioides sp009699265	96.4967	1155	1477	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_017310035.1	s__Nocardioides sp017310035	93.7929	1175	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428125.1	s__Nocardioides sp001428125	87.3758	1001	1477	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	86.6902	1056	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014653115.1	s__Nocardioides flavus	86.5631	1029	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785795.1	s__Nocardioides eburneiflavus	86.4162	1041	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137245.1	s__Nocardioides glacieisoli	86.3332	1090	1477	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	86.3195	1037	1477	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	86.0323	999	1477	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	85.9115	1024	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137345.1	s__Nocardioides sp004137345	85.8711	1001	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017086465.1	s__Nocardioides sp014265965	85.7969	946	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001425025.1	s__Nocardioides sp001425025	85.7596	1025	1477	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	85.6183	1007	1477	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	85.4974	965	1477	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	85.3767	916	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_017916425.1	s__Nocardioides sp017916425	85.0697	944	1477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213595.1	s__Fen-668 sp016213595	78.3154	183	1477	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 13:43:35,382] [INFO] GTDB search result was written to GCF_020102855.1_ASM2010285v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:35,382] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:35,386] [INFO] DFAST_QC result json was written to GCF_020102855.1_ASM2010285v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:35,386] [INFO] DFAST_QC completed!
[2024-01-24 13:43:35,386] [INFO] Total running time: 0h1m55s