[2024-01-24 11:03:47,735] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:03:47,738] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:03:47,738] [INFO] DQC Reference Directory: /var/lib/cwl/stga4f33c32-924b-4347-ad99-86c98f477dc0/dqc_reference
[2024-01-24 11:03:48,921] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:03:48,922] [INFO] Task started: Prodigal
[2024-01-24 11:03:48,923] [INFO] Running command: gunzip -c /var/lib/cwl/stg54b810e5-40ea-4b14-969f-b8f505f1e875/GCF_014779655.1_ASM1477965v1_genomic.fna.gz | prodigal -d GCF_014779655.1_ASM1477965v1_genomic.fna/cds.fna -a GCF_014779655.1_ASM1477965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:04:01,259] [INFO] Task succeeded: Prodigal
[2024-01-24 11:04:01,260] [INFO] Task started: HMMsearch
[2024-01-24 11:04:01,260] [INFO] Running command: hmmsearch --tblout GCF_014779655.1_ASM1477965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4f33c32-924b-4347-ad99-86c98f477dc0/dqc_reference/reference_markers.hmm GCF_014779655.1_ASM1477965v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:04:01,568] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:04:01,570] [INFO] Found 6/6 markers.
[2024-01-24 11:04:01,613] [INFO] Query marker FASTA was written to GCF_014779655.1_ASM1477965v1_genomic.fna/markers.fasta
[2024-01-24 11:04:01,613] [INFO] Task started: Blastn
[2024-01-24 11:04:01,614] [INFO] Running command: blastn -query GCF_014779655.1_ASM1477965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4f33c32-924b-4347-ad99-86c98f477dc0/dqc_reference/reference_markers.fasta -out GCF_014779655.1_ASM1477965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:04:02,881] [INFO] Task succeeded: Blastn
[2024-01-24 11:04:02,885] [INFO] Selected 11 target genomes.
[2024-01-24 11:04:02,886] [INFO] Target genome list was writen to GCF_014779655.1_ASM1477965v1_genomic.fna/target_genomes.txt
[2024-01-24 11:04:02,896] [INFO] Task started: fastANI
[2024-01-24 11:04:02,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg54b810e5-40ea-4b14-969f-b8f505f1e875/GCF_014779655.1_ASM1477965v1_genomic.fna.gz --refList GCF_014779655.1_ASM1477965v1_genomic.fna/target_genomes.txt --output GCF_014779655.1_ASM1477965v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:04:16,468] [INFO] Task succeeded: fastANI
[2024-01-24 11:04:16,469] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4f33c32-924b-4347-ad99-86c98f477dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:04:16,469] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4f33c32-924b-4347-ad99-86c98f477dc0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:04:16,483] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:04:16,483] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:04:16,483] [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 ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	100.0	1481	1481	95	conclusive
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	91.2962	1234	1481	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	89.0935	1112	1481	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	86.7736	1079	1481	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	86.7147	1084	1481	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	86.664	1059	1481	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	86.6112	1012	1481	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.8137	1022	1481	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	85.7533	1051	1481	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.6025	1055	1481	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	85.6022	1036	1481	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:04:16,485] [INFO] DFAST Taxonomy check result was written to GCF_014779655.1_ASM1477965v1_genomic.fna/tc_result.tsv
[2024-01-24 11:04:16,485] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:04:16,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:04:16,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4f33c32-924b-4347-ad99-86c98f477dc0/dqc_reference/checkm_data
[2024-01-24 11:04:16,486] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:04:16,528] [INFO] Task started: CheckM
[2024-01-24 11:04:16,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014779655.1_ASM1477965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014779655.1_ASM1477965v1_genomic.fna/checkm_input GCF_014779655.1_ASM1477965v1_genomic.fna/checkm_result
[2024-01-24 11:05:19,400] [INFO] Task succeeded: CheckM
[2024-01-24 11:05:19,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:05:19,427] [INFO] ===== Completeness check finished =====
[2024-01-24 11:05:19,428] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:05:19,428] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014779655.1_ASM1477965v1_genomic.fna/markers.fasta)
[2024-01-24 11:05:19,429] [INFO] Task started: Blastn
[2024-01-24 11:05:19,429] [INFO] Running command: blastn -query GCF_014779655.1_ASM1477965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4f33c32-924b-4347-ad99-86c98f477dc0/dqc_reference/reference_markers_gtdb.fasta -out GCF_014779655.1_ASM1477965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:21,494] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:21,498] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:21,498] [INFO] Target genome list was writen to GCF_014779655.1_ASM1477965v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:05:21,553] [INFO] Task started: fastANI
[2024-01-24 11:05:21,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg54b810e5-40ea-4b14-969f-b8f505f1e875/GCF_014779655.1_ASM1477965v1_genomic.fna.gz --refList GCF_014779655.1_ASM1477965v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014779655.1_ASM1477965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:05:41,090] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:41,107] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:05:41,107] [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_014779655.1	s__Nocardioides ganghwensis	100.0	1481	1481	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_004785795.1	s__Nocardioides eburneiflavus	91.2713	1237	1481	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	89.0808	1113	1481	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	86.8838	1125	1481	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	86.8018	1036	1481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907475.1	s__Nocardioides cavernae	86.7262	1083	1481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017086465.1	s__Nocardioides sp014265965	86.2626	991	1481	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001428125.1	s__Nocardioides sp001428125	86.221	1019	1481	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	86.1757	1042	1481	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	85.8833	1030	1481	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	85.7688	1054	1481	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	85.7146	1039	1481	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	85.6056	1036	1481	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	85.6021	1017	1481	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	85.5998	1055	1481	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	85.5481	1010	1481	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	85.4155	1029	1481	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 11:05:41,109] [INFO] GTDB search result was written to GCF_014779655.1_ASM1477965v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:05:41,109] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:05:41,113] [INFO] DFAST_QC result json was written to GCF_014779655.1_ASM1477965v1_genomic.fna/dqc_result.json
[2024-01-24 11:05:41,113] [INFO] DFAST_QC completed!
[2024-01-24 11:05:41,113] [INFO] Total running time: 0h1m53s