[2024-01-24 12:52:51,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:51,117] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:51,117] [INFO] DQC Reference Directory: /var/lib/cwl/stgad6f557a-e50d-4e23-93f0-76355cd259bb/dqc_reference
[2024-01-24 12:52:53,749] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:53,751] [INFO] Task started: Prodigal
[2024-01-24 12:52:53,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg5881789a-1db6-4839-82b8-25901257b743/GCF_024172065.1_ASM2417206v1_genomic.fna.gz | prodigal -d GCF_024172065.1_ASM2417206v1_genomic.fna/cds.fna -a GCF_024172065.1_ASM2417206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:04,149] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:04,150] [INFO] Task started: HMMsearch
[2024-01-24 12:53:04,150] [INFO] Running command: hmmsearch --tblout GCF_024172065.1_ASM2417206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad6f557a-e50d-4e23-93f0-76355cd259bb/dqc_reference/reference_markers.hmm GCF_024172065.1_ASM2417206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:04,406] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:04,408] [INFO] Found 6/6 markers.
[2024-01-24 12:53:04,445] [INFO] Query marker FASTA was written to GCF_024172065.1_ASM2417206v1_genomic.fna/markers.fasta
[2024-01-24 12:53:04,446] [INFO] Task started: Blastn
[2024-01-24 12:53:04,446] [INFO] Running command: blastn -query GCF_024172065.1_ASM2417206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad6f557a-e50d-4e23-93f0-76355cd259bb/dqc_reference/reference_markers.fasta -out GCF_024172065.1_ASM2417206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:05,687] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:05,691] [INFO] Selected 15 target genomes.
[2024-01-24 12:53:05,692] [INFO] Target genome list was writen to GCF_024172065.1_ASM2417206v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:05,712] [INFO] Task started: fastANI
[2024-01-24 12:53:05,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg5881789a-1db6-4839-82b8-25901257b743/GCF_024172065.1_ASM2417206v1_genomic.fna.gz --refList GCF_024172065.1_ASM2417206v1_genomic.fna/target_genomes.txt --output GCF_024172065.1_ASM2417206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:20,611] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:20,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad6f557a-e50d-4e23-93f0-76355cd259bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:20,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad6f557a-e50d-4e23-93f0-76355cd259bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:20,628] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:20,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:20,628] [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
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	99.9833	1222	1237	95	conclusive
Agromyces aureus	strain=AR33	GCA_001660485.1	453304	453304	type	True	86.5026	970	1237	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	86.4902	972	1237	95	below_threshold
Agromyces salentinus	strain=JCM 14323	GCA_009749395.1	269421	269421	type	True	86.3439	981	1237	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	83.4976	811	1237	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	83.4741	802	1237	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	83.445	573	1237	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.295	816	1237	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	83.2539	717	1237	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	83.1606	848	1237	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.6901	815	1237	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	82.6869	771	1237	95	below_threshold
Agromyces albus	strain=DSM 15934	GCA_004134825.1	205332	205332	type	True	82.4835	729	1237	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	82.4413	782	1237	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.8662	638	1237	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:20,631] [INFO] DFAST Taxonomy check result was written to GCF_024172065.1_ASM2417206v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:20,631] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:20,632] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:20,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad6f557a-e50d-4e23-93f0-76355cd259bb/dqc_reference/checkm_data
[2024-01-24 12:53:20,634] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:20,675] [INFO] Task started: CheckM
[2024-01-24 12:53:20,675] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024172065.1_ASM2417206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024172065.1_ASM2417206v1_genomic.fna/checkm_input GCF_024172065.1_ASM2417206v1_genomic.fna/checkm_result
[2024-01-24 12:54:17,323] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:17,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:17,348] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:17,349] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:17,349] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024172065.1_ASM2417206v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:17,349] [INFO] Task started: Blastn
[2024-01-24 12:54:17,350] [INFO] Running command: blastn -query GCF_024172065.1_ASM2417206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad6f557a-e50d-4e23-93f0-76355cd259bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_024172065.1_ASM2417206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:19,391] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:19,397] [INFO] Selected 8 target genomes.
[2024-01-24 12:54:19,397] [INFO] Target genome list was writen to GCF_024172065.1_ASM2417206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:19,426] [INFO] Task started: fastANI
[2024-01-24 12:54:19,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg5881789a-1db6-4839-82b8-25901257b743/GCF_024172065.1_ASM2417206v1_genomic.fna.gz --refList GCF_024172065.1_ASM2417206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024172065.1_ASM2417206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:28,496] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:28,506] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:28,506] [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_009749465.1	s__Agromyces terreus	99.9833	1222	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001421565.1	s__Agromyces sp001421565	86.721	997	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	86.56	964	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660485.1	s__Agromyces aureus	86.5055	968	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009749385.1	s__Agromyces allii	86.4879	972	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749395.1	s__Agromyces salentinus	86.3802	978	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113185.1	s__Agromyces sp900113185	86.291	945	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003070885.1	s__Agromyces badenianii	83.2866	717	1237	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:28,508] [INFO] GTDB search result was written to GCF_024172065.1_ASM2417206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:28,508] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:28,513] [INFO] DFAST_QC result json was written to GCF_024172065.1_ASM2417206v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:28,513] [INFO] DFAST_QC completed!
[2024-01-24 12:54:28,513] [INFO] Total running time: 0h1m37s