[2024-01-24 14:22:31,397] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:31,399] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:31,400] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f6decc3-1f9a-4337-9d3d-56dec4228d70/dqc_reference
[2024-01-24 14:22:32,692] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:32,693] [INFO] Task started: Prodigal
[2024-01-24 14:22:32,693] [INFO] Running command: gunzip -c /var/lib/cwl/stga5a0a8fe-27e9-4eb4-8ea0-39d1482b310f/GCF_004137235.1_ASM413723v1_genomic.fna.gz | prodigal -d GCF_004137235.1_ASM413723v1_genomic.fna/cds.fna -a GCF_004137235.1_ASM413723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:45,071] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:45,072] [INFO] Task started: HMMsearch
[2024-01-24 14:22:45,072] [INFO] Running command: hmmsearch --tblout GCF_004137235.1_ASM413723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f6decc3-1f9a-4337-9d3d-56dec4228d70/dqc_reference/reference_markers.hmm GCF_004137235.1_ASM413723v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:45,377] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:45,378] [INFO] Found 6/6 markers.
[2024-01-24 14:22:45,469] [INFO] Query marker FASTA was written to GCF_004137235.1_ASM413723v1_genomic.fna/markers.fasta
[2024-01-24 14:22:45,470] [INFO] Task started: Blastn
[2024-01-24 14:22:45,470] [INFO] Running command: blastn -query GCF_004137235.1_ASM413723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f6decc3-1f9a-4337-9d3d-56dec4228d70/dqc_reference/reference_markers.fasta -out GCF_004137235.1_ASM413723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:46,780] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:46,795] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:46,796] [INFO] Target genome list was writen to GCF_004137235.1_ASM413723v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:46,802] [INFO] Task started: fastANI
[2024-01-24 14:22:46,802] [INFO] Running command: fastANI --query /var/lib/cwl/stga5a0a8fe-27e9-4eb4-8ea0-39d1482b310f/GCF_004137235.1_ASM413723v1_genomic.fna.gz --refList GCF_004137235.1_ASM413723v1_genomic.fna/target_genomes.txt --output GCF_004137235.1_ASM413723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:00,557] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:00,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f6decc3-1f9a-4337-9d3d-56dec4228d70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:00,559] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f6decc3-1f9a-4337-9d3d-56dec4228d70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:00,572] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:00,573] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:00,573] [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	99.9992	1474	1474	95	conclusive
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	91.3623	1213	1474	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	89.0855	1116	1474	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	86.7573	1087	1474	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	86.7172	1052	1474	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	86.6632	1094	1474	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	86.5828	1015	1474	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.8167	1036	1474	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	85.798	1037	1474	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	85.7202	1020	1474	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	85.5804	1050	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:00,576] [INFO] DFAST Taxonomy check result was written to GCF_004137235.1_ASM413723v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:00,577] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:00,577] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:00,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f6decc3-1f9a-4337-9d3d-56dec4228d70/dqc_reference/checkm_data
[2024-01-24 14:23:00,579] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:00,626] [INFO] Task started: CheckM
[2024-01-24 14:23:00,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004137235.1_ASM413723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004137235.1_ASM413723v1_genomic.fna/checkm_input GCF_004137235.1_ASM413723v1_genomic.fna/checkm_result
[2024-01-24 14:24:11,008] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:11,010] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:11,033] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:11,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:11,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004137235.1_ASM413723v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:11,035] [INFO] Task started: Blastn
[2024-01-24 14:24:11,035] [INFO] Running command: blastn -query GCF_004137235.1_ASM413723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f6decc3-1f9a-4337-9d3d-56dec4228d70/dqc_reference/reference_markers_gtdb.fasta -out GCF_004137235.1_ASM413723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:13,281] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:13,286] [INFO] Selected 17 target genomes.
[2024-01-24 14:24:13,286] [INFO] Target genome list was writen to GCF_004137235.1_ASM413723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:13,323] [INFO] Task started: fastANI
[2024-01-24 14:24:13,323] [INFO] Running command: fastANI --query /var/lib/cwl/stga5a0a8fe-27e9-4eb4-8ea0-39d1482b310f/GCF_004137235.1_ASM413723v1_genomic.fna.gz --refList GCF_004137235.1_ASM413723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004137235.1_ASM413723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:35,291] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:35,311] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:35,312] [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	99.9992	1474	1474	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	91.3606	1212	1474	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	89.0965	1116	1474	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	87.0307	1114	1474	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	86.8267	1045	1474	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	86.6901	1091	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013410035.1	s__Nocardioides cavernae_A	86.3007	1027	1474	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	86.2962	1016	1474	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	86.259	991	1474	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013155375.1	s__Nocardioides sp013155375	85.9193	1025	1474	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	85.8021	1037	1474	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	85.7314	1019	1474	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	85.7036	1009	1474	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	85.7002	1062	1474	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	85.6123	1019	1474	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	85.5551	1052	1474	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	85.4672	1028	1474	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 14:24:35,313] [INFO] GTDB search result was written to GCF_004137235.1_ASM413723v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:35,314] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:35,317] [INFO] DFAST_QC result json was written to GCF_004137235.1_ASM413723v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:35,317] [INFO] DFAST_QC completed!
[2024-01-24 14:24:35,318] [INFO] Total running time: 0h2m4s