[2024-01-24 14:20:14,434] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,436] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,437] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cfebcce-a38b-4af3-9b0a-7b4b49593330/dqc_reference
[2024-01-24 14:20:15,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,698] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,698] [INFO] Running command: gunzip -c /var/lib/cwl/stg07f158e8-f5be-4654-9fe6-eb03c70d7300/GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/cds.fna -a GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:28,441] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:28,442] [INFO] Task started: HMMsearch
[2024-01-24 14:20:28,442] [INFO] Running command: hmmsearch --tblout GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cfebcce-a38b-4af3-9b0a-7b4b49593330/dqc_reference/reference_markers.hmm GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:28,701] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:28,703] [INFO] Found 6/6 markers.
[2024-01-24 14:20:28,747] [INFO] Query marker FASTA was written to GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:20:28,748] [INFO] Task started: Blastn
[2024-01-24 14:20:28,748] [INFO] Running command: blastn -query GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cfebcce-a38b-4af3-9b0a-7b4b49593330/dqc_reference/reference_markers.fasta -out GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:29,999] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:30,002] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:30,003] [INFO] Target genome list was writen to GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:20:30,015] [INFO] Task started: fastANI
[2024-01-24 14:20:30,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f158e8-f5be-4654-9fe6-eb03c70d7300/GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna.gz --refList GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:43,365] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:43,365] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cfebcce-a38b-4af3-9b0a-7b4b49593330/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:43,366] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cfebcce-a38b-4af3-9b0a-7b4b49593330/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:43,376] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:43,376] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:43,376] [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 cerinus subsp. cerinus	strain=DSM 8595	GCA_900142065.1	232089	33878	type	True	100.0	1392	1392	95	conclusive
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	93.0081	1172	1392	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	90.2489	1102	1392	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	86.9002	840	1392	95	below_threshold
Agromyces laixinhei	strain=HY052	GCA_006337065.1	2585717	2585717	type	True	86.8348	843	1392	95	below_threshold
Agromyces subbeticus	strain=DSM 16689	GCA_000421565.1	293890	293890	type	True	85.8503	951	1392	95	below_threshold
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	84.517	937	1392	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.6079	890	1392	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	83.5568	862	1392	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.2788	834	1392	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	81.95	762	1392	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	81.1071	632	1392	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:43,378] [INFO] DFAST Taxonomy check result was written to GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:20:43,379] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:43,379] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:43,379] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cfebcce-a38b-4af3-9b0a-7b4b49593330/dqc_reference/checkm_data
[2024-01-24 14:20:43,380] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:43,442] [INFO] Task started: CheckM
[2024-01-24 14:20:43,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/checkm_input GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:21:28,653] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:28,655] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:28,675] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:28,675] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:28,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:21:28,676] [INFO] Task started: Blastn
[2024-01-24 14:21:28,676] [INFO] Running command: blastn -query GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cfebcce-a38b-4af3-9b0a-7b4b49593330/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:30,704] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:30,708] [INFO] Selected 5 target genomes.
[2024-01-24 14:21:30,708] [INFO] Target genome list was writen to GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:30,716] [INFO] Task started: fastANI
[2024-01-24 14:21:30,716] [INFO] Running command: fastANI --query /var/lib/cwl/stg07f158e8-f5be-4654-9fe6-eb03c70d7300/GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna.gz --refList GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:36,674] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:36,681] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:36,681] [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_900142065.1	s__Agromyces cerinus	100.0	1392	1392	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_016907835.1	s__Agromyces cerinus_A	93.2671	1184	1392	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	93.0081	1172	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004134865.1	s__Agromyces fucosus	90.2345	1103	1392	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.23	98.22	0.96	0.96	3	-
GCF_001429165.1	s__Agromyces sp001429165	90.1685	1084	1392	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 14:21:36,683] [INFO] GTDB search result was written to GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:36,683] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:36,687] [INFO] DFAST_QC result json was written to GCF_900142065.1_IMG-taxon_2698536811_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:21:36,687] [INFO] DFAST_QC completed!
[2024-01-24 14:21:36,687] [INFO] Total running time: 0h1m22s