[2024-01-24 11:26:20,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,937] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,938] [INFO] DQC Reference Directory: /var/lib/cwl/stg16c95c7c-56be-4ab4-bdfa-36c8e153d679/dqc_reference
[2024-01-24 11:26:22,142] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,143] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,143] [INFO] Running command: gunzip -c /var/lib/cwl/stga3fb23ba-7d1d-4a35-857d-29e72bd1f4cd/GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/cds.fna -a GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:34,861] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:34,861] [INFO] Task started: HMMsearch
[2024-01-24 11:26:34,861] [INFO] Running command: hmmsearch --tblout GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16c95c7c-56be-4ab4-bdfa-36c8e153d679/dqc_reference/reference_markers.hmm GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:35,215] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:35,217] [INFO] Found 6/6 markers.
[2024-01-24 11:26:35,267] [INFO] Query marker FASTA was written to GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:26:35,267] [INFO] Task started: Blastn
[2024-01-24 11:26:35,267] [INFO] Running command: blastn -query GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c95c7c-56be-4ab4-bdfa-36c8e153d679/dqc_reference/reference_markers.fasta -out GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:36,547] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:36,551] [INFO] Selected 13 target genomes.
[2024-01-24 11:26:36,551] [INFO] Target genome list was writen to GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:26:36,558] [INFO] Task started: fastANI
[2024-01-24 11:26:36,558] [INFO] Running command: fastANI --query /var/lib/cwl/stga3fb23ba-7d1d-4a35-857d-29e72bd1f4cd/GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna.gz --refList GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:51,718] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:51,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16c95c7c-56be-4ab4-bdfa-36c8e153d679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:51,720] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16c95c7c-56be-4ab4-bdfa-36c8e153d679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:51,736] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:51,736] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:51,736] [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 exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	100.0	1529	1533	95	conclusive
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	87.2655	1151	1533	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	86.0165	1069	1533	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	85.7893	1040	1533	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	85.7485	1062	1533	95	below_threshold
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	85.7409	1070	1533	95	below_threshold
Nocardioides zhouii	strain=HLT2-9	GCA_004137345.1	1168729	1168729	type	True	85.6589	1024	1533	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	85.6565	1021	1533	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	85.6277	1007	1533	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	85.6232	1062	1533	95	below_threshold
Nocardioides eburneiflavus	strain=MMS17-SY213	GCA_004785795.1	2518372	2518372	type	True	85.491	1054	1533	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	85.4189	966	1533	95	below_threshold
Nocardioides flavus Wang et al. 2016	strain=CGMCC 1.12791	GCA_014653115.1	2058780	2058780	type	True	85.3195	961	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:51,738] [INFO] DFAST Taxonomy check result was written to GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:26:51,738] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:51,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:51,739] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16c95c7c-56be-4ab4-bdfa-36c8e153d679/dqc_reference/checkm_data
[2024-01-24 11:26:51,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:51,781] [INFO] Task started: CheckM
[2024-01-24 11:26:51,781] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/checkm_input GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:28:11,490] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:11,491] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:11,514] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:11,514] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:11,514] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:28:11,515] [INFO] Task started: Blastn
[2024-01-24 11:28:11,515] [INFO] Running command: blastn -query GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c95c7c-56be-4ab4-bdfa-36c8e153d679/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:13,614] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:13,618] [INFO] Selected 14 target genomes.
[2024-01-24 11:28:13,618] [INFO] Target genome list was writen to GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:13,631] [INFO] Task started: fastANI
[2024-01-24 11:28:13,631] [INFO] Running command: fastANI --query /var/lib/cwl/stga3fb23ba-7d1d-4a35-857d-29e72bd1f4cd/GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna.gz --refList GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:29,831] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:29,847] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:29,848] [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_900105585.1	s__Nocardioides exalbidus	100.0	1530	1533	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_004137255.1	s__Nocardioides oleivorans	91.1813	1321	1533	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	87.2481	1153	1533	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	86.0671	1065	1533	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	85.8215	1103	1533	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	85.7832	952	1533	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	85.7783	1041	1533	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	85.6675	1086	1533	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	85.6512	1022	1533	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	85.5746	1057	1533	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	85.5615	990	1533	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	85.481	1053	1533	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	85.4622	1034	1533	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	85.2977	963	1533	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 11:28:29,849] [INFO] GTDB search result was written to GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:29,850] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:29,853] [INFO] DFAST_QC result json was written to GCF_900105585.1_IMG-taxon_2639762616_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:28:29,853] [INFO] DFAST_QC completed!
[2024-01-24 11:28:29,854] [INFO] Total running time: 0h2m9s