[2024-01-24 12:15:18,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b167460-ae63-49c1-a732-eff777fc7717/dqc_reference
[2024-01-24 12:15:20,259] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,260] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c5b8a9e-6d15-4999-af74-c3f8797a074d/GCF_014779675.1_ASM1477967v1_genomic.fna.gz | prodigal -d GCF_014779675.1_ASM1477967v1_genomic.fna/cds.fna -a GCF_014779675.1_ASM1477967v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:33,995] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:33,996] [INFO] Task started: HMMsearch
[2024-01-24 12:15:33,996] [INFO] Running command: hmmsearch --tblout GCF_014779675.1_ASM1477967v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b167460-ae63-49c1-a732-eff777fc7717/dqc_reference/reference_markers.hmm GCF_014779675.1_ASM1477967v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:34,314] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:34,316] [INFO] Found 6/6 markers.
[2024-01-24 12:15:34,363] [INFO] Query marker FASTA was written to GCF_014779675.1_ASM1477967v1_genomic.fna/markers.fasta
[2024-01-24 12:15:34,364] [INFO] Task started: Blastn
[2024-01-24 12:15:34,364] [INFO] Running command: blastn -query GCF_014779675.1_ASM1477967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b167460-ae63-49c1-a732-eff777fc7717/dqc_reference/reference_markers.fasta -out GCF_014779675.1_ASM1477967v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:35,698] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:35,705] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:35,705] [INFO] Target genome list was writen to GCF_014779675.1_ASM1477967v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:35,717] [INFO] Task started: fastANI
[2024-01-24 12:15:35,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c5b8a9e-6d15-4999-af74-c3f8797a074d/GCF_014779675.1_ASM1477967v1_genomic.fna.gz --refList GCF_014779675.1_ASM1477967v1_genomic.fna/target_genomes.txt --output GCF_014779675.1_ASM1477967v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:51,077] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:51,078] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b167460-ae63-49c1-a732-eff777fc7717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:51,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b167460-ae63-49c1-a732-eff777fc7717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:51,125] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:15:51,126] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:51,126] [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 cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	100.0	1612	1612	95	conclusive
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	99.9997	1611	1612	95	conclusive
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	86.6793	1079	1612	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	86.3804	1089	1612	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	86.1499	1020	1612	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	85.8042	1023	1612	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	85.7489	963	1612	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.661	1080	1612	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	85.6136	1066	1612	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	85.5555	1066	1612	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	85.5121	1070	1612	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	85.4736	1039	1612	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.3507	1053	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:51,128] [INFO] DFAST Taxonomy check result was written to GCF_014779675.1_ASM1477967v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:51,129] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:51,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:51,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b167460-ae63-49c1-a732-eff777fc7717/dqc_reference/checkm_data
[2024-01-24 12:15:51,131] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:51,179] [INFO] Task started: CheckM
[2024-01-24 12:15:51,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014779675.1_ASM1477967v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014779675.1_ASM1477967v1_genomic.fna/checkm_input GCF_014779675.1_ASM1477967v1_genomic.fna/checkm_result
[2024-01-24 12:17:04,759] [INFO] Task succeeded: CheckM
[2024-01-24 12:17:04,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:17:04,785] [INFO] ===== Completeness check finished =====
[2024-01-24 12:17:04,785] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:17:04,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014779675.1_ASM1477967v1_genomic.fna/markers.fasta)
[2024-01-24 12:17:04,786] [INFO] Task started: Blastn
[2024-01-24 12:17:04,786] [INFO] Running command: blastn -query GCF_014779675.1_ASM1477967v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b167460-ae63-49c1-a732-eff777fc7717/dqc_reference/reference_markers_gtdb.fasta -out GCF_014779675.1_ASM1477967v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:17:06,861] [INFO] Task succeeded: Blastn
[2024-01-24 12:17:06,865] [INFO] Selected 16 target genomes.
[2024-01-24 12:17:06,866] [INFO] Target genome list was writen to GCF_014779675.1_ASM1477967v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:17:06,878] [INFO] Task started: fastANI
[2024-01-24 12:17:06,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c5b8a9e-6d15-4999-af74-c3f8797a074d/GCF_014779675.1_ASM1477967v1_genomic.fna.gz --refList GCF_014779675.1_ASM1477967v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014779675.1_ASM1477967v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:17:24,574] [INFO] Task succeeded: fastANI
[2024-01-24 12:17:24,590] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:17:24,591] [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_016907475.1	s__Nocardioides cavernae	99.9997	1611	1612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_013155335.1	s__Nocardioides sp013155335	89.1534	1229	1612	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	87.021	1055	1612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014779655.1	s__Nocardioides ganghwensis	86.6982	1077	1612	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	86.4358	1083	1612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653115.1	s__Nocardioides flavus	86.1275	1022	1612	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	85.9734	995	1612	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	85.9194	1072	1612	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	85.8872	992	1612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_013155375.1	s__Nocardioides sp013155375	85.8814	1084	1612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	85.6901	1077	1612	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	85.6157	1066	1612	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	85.58	1064	1612	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003633575.1	s__Nocardioides sp003633575	85.5027	1014	1612	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	85.3814	1033	1612	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	85.3484	1055	1612	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 12:17:24,592] [INFO] GTDB search result was written to GCF_014779675.1_ASM1477967v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:17:24,593] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:17:24,597] [INFO] DFAST_QC result json was written to GCF_014779675.1_ASM1477967v1_genomic.fna/dqc_result.json
[2024-01-24 12:17:24,597] [INFO] DFAST_QC completed!
[2024-01-24 12:17:24,597] [INFO] Total running time: 0h2m6s