[2024-01-24 13:22:11,417] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:11,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:11,429] [INFO] DQC Reference Directory: /var/lib/cwl/stg876b9cd7-5848-4d09-a3b2-8dc2a740bb19/dqc_reference
[2024-01-24 13:22:13,357] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:13,360] [INFO] Task started: Prodigal
[2024-01-24 13:22:13,360] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f6f195a-9b2b-4fc8-994a-ce17a023ffea/GCF_009720255.1_ASM972025v2_genomic.fna.gz | prodigal -d GCF_009720255.1_ASM972025v2_genomic.fna/cds.fna -a GCF_009720255.1_ASM972025v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:23,265] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:23,265] [INFO] Task started: HMMsearch
[2024-01-24 13:22:23,265] [INFO] Running command: hmmsearch --tblout GCF_009720255.1_ASM972025v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg876b9cd7-5848-4d09-a3b2-8dc2a740bb19/dqc_reference/reference_markers.hmm GCF_009720255.1_ASM972025v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:23,609] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:23,610] [INFO] Found 6/6 markers.
[2024-01-24 13:22:23,649] [INFO] Query marker FASTA was written to GCF_009720255.1_ASM972025v2_genomic.fna/markers.fasta
[2024-01-24 13:22:23,650] [INFO] Task started: Blastn
[2024-01-24 13:22:23,650] [INFO] Running command: blastn -query GCF_009720255.1_ASM972025v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg876b9cd7-5848-4d09-a3b2-8dc2a740bb19/dqc_reference/reference_markers.fasta -out GCF_009720255.1_ASM972025v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:24,882] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:24,885] [INFO] Selected 19 target genomes.
[2024-01-24 13:22:24,885] [INFO] Target genome list was writen to GCF_009720255.1_ASM972025v2_genomic.fna/target_genomes.txt
[2024-01-24 13:22:24,890] [INFO] Task started: fastANI
[2024-01-24 13:22:24,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6f195a-9b2b-4fc8-994a-ce17a023ffea/GCF_009720255.1_ASM972025v2_genomic.fna.gz --refList GCF_009720255.1_ASM972025v2_genomic.fna/target_genomes.txt --output GCF_009720255.1_ASM972025v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:39,913] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:39,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg876b9cd7-5848-4d09-a3b2-8dc2a740bb19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:39,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg876b9cd7-5848-4d09-a3b2-8dc2a740bb19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:39,926] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:39,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:39,926] [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 humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	100.0	1060	1081	95	conclusive
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	86.1622	691	1081	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	85.3517	663	1081	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	84.1788	542	1081	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	83.9172	610	1081	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	83.6444	524	1081	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	83.4575	617	1081	95	below_threshold
Agromyces albus	strain=DSM 15934	GCA_004134825.1	205332	205332	type	True	83.426	580	1081	95	below_threshold
Agromyces terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	83.3587	572	1081	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.3295	580	1081	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	83.3127	545	1081	95	below_threshold
Agromyces aureus	strain=AR33	GCA_001660485.1	453304	453304	type	True	83.2971	625	1081	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.2337	607	1081	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.8408	588	1081	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	82.7266	575	1081	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	82.0798	488	1081	95	below_threshold
Agromyces intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	82.0321	541	1081	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.8904	454	1081	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	78.7048	319	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:39,928] [INFO] DFAST Taxonomy check result was written to GCF_009720255.1_ASM972025v2_genomic.fna/tc_result.tsv
[2024-01-24 13:22:39,928] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:39,928] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:39,929] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg876b9cd7-5848-4d09-a3b2-8dc2a740bb19/dqc_reference/checkm_data
[2024-01-24 13:22:39,929] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:39,973] [INFO] Task started: CheckM
[2024-01-24 13:22:39,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720255.1_ASM972025v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720255.1_ASM972025v2_genomic.fna/checkm_input GCF_009720255.1_ASM972025v2_genomic.fna/checkm_result
[2024-01-24 13:23:15,594] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:15,595] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:15,704] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:15,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:15,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720255.1_ASM972025v2_genomic.fna/markers.fasta)
[2024-01-24 13:23:15,705] [INFO] Task started: Blastn
[2024-01-24 13:23:15,705] [INFO] Running command: blastn -query GCF_009720255.1_ASM972025v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg876b9cd7-5848-4d09-a3b2-8dc2a740bb19/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720255.1_ASM972025v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:17,892] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:17,894] [INFO] Selected 17 target genomes.
[2024-01-24 13:23:17,894] [INFO] Target genome list was writen to GCF_009720255.1_ASM972025v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:17,902] [INFO] Task started: fastANI
[2024-01-24 13:23:17,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f6f195a-9b2b-4fc8-994a-ce17a023ffea/GCF_009720255.1_ASM972025v2_genomic.fna.gz --refList GCF_009720255.1_ASM972025v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009720255.1_ASM972025v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:31,814] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:31,824] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:31,825] [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_009720255.1	s__Agromyces humi	100.0	1060	1081	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_004216665.1	s__Agromyces ramosus	86.1964	689	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	85.3034	666	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428255.1	s__Agromyces sp001428255	85.1123	639	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	84.1286	584	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715355.1	s__Agromyces sp006715355	84.1077	652	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710805.1	s__Agromyces tardus	83.8278	617	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410355.1	s__Agromyces hippuratus	83.8065	579	1081	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	83.6714	522	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_016907835.1	s__Agromyces cerinus_A	83.6265	578	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429165.1	s__Agromyces sp001429165	83.562	553	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749385.1	s__Agromyces allii	83.4455	619	1081	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	83.3768	597	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135055.1	s__Agromyces binzhouensis	83.0643	427	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009647605.1	s__Agromyces sp009647605	82.8595	587	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648575.1	s__Agromyces mediolanus	82.4413	510	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634985.1	s__Agromyces sp003634985	82.1745	552	1081	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:31,826] [INFO] GTDB search result was written to GCF_009720255.1_ASM972025v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:31,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:31,830] [INFO] DFAST_QC result json was written to GCF_009720255.1_ASM972025v2_genomic.fna/dqc_result.json
[2024-01-24 13:23:31,830] [INFO] DFAST_QC completed!
[2024-01-24 13:23:31,831] [INFO] Total running time: 0h1m20s