[2024-01-24 14:38:45,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:45,609] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:45,609] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2e4a264-a361-4593-a753-0c726ce9de14/dqc_reference
[2024-01-24 14:38:47,232] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:47,233] [INFO] Task started: Prodigal
[2024-01-24 14:38:47,234] [INFO] Running command: gunzip -c /var/lib/cwl/stg23ddcc1c-cd48-4f7b-9a14-834256e686ca/GCF_014648575.1_ASM1464857v1_genomic.fna.gz | prodigal -d GCF_014648575.1_ASM1464857v1_genomic.fna/cds.fna -a GCF_014648575.1_ASM1464857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:38:57,855] [INFO] Task succeeded: Prodigal
[2024-01-24 14:38:57,855] [INFO] Task started: HMMsearch
[2024-01-24 14:38:57,855] [INFO] Running command: hmmsearch --tblout GCF_014648575.1_ASM1464857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2e4a264-a361-4593-a753-0c726ce9de14/dqc_reference/reference_markers.hmm GCF_014648575.1_ASM1464857v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:38:58,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:38:58,152] [INFO] Found 6/6 markers.
[2024-01-24 14:38:58,193] [INFO] Query marker FASTA was written to GCF_014648575.1_ASM1464857v1_genomic.fna/markers.fasta
[2024-01-24 14:38:58,193] [INFO] Task started: Blastn
[2024-01-24 14:38:58,194] [INFO] Running command: blastn -query GCF_014648575.1_ASM1464857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2e4a264-a361-4593-a753-0c726ce9de14/dqc_reference/reference_markers.fasta -out GCF_014648575.1_ASM1464857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:59,638] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:59,641] [INFO] Selected 17 target genomes.
[2024-01-24 14:38:59,642] [INFO] Target genome list was writen to GCF_014648575.1_ASM1464857v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:59,648] [INFO] Task started: fastANI
[2024-01-24 14:38:59,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg23ddcc1c-cd48-4f7b-9a14-834256e686ca/GCF_014648575.1_ASM1464857v1_genomic.fna.gz --refList GCF_014648575.1_ASM1464857v1_genomic.fna/target_genomes.txt --output GCF_014648575.1_ASM1464857v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:15,837] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:15,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2e4a264-a361-4593-a753-0c726ce9de14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:15,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2e4a264-a361-4593-a753-0c726ce9de14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:15,857] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:15,857] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:15,857] [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 mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	100.0	1281	1282	95	conclusive
Agromyces lapidis	strain=JCM 14321	GCA_009749405.1	279574	279574	type	True	83.3947	802	1282	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	83.1554	762	1282	95	below_threshold
Agromyces italicus	strain=DSM 16388	GCA_000421545.1	279572	279572	type	True	83.1551	757	1282	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	82.7975	745	1282	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	82.6217	509	1282	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	82.5499	768	1282	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.3956	744	1282	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	82.2777	733	1282	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	82.2267	729	1282	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	82.1743	731	1282	95	below_threshold
Agromyces protaetiae	strain=FW100M-8	GCA_004135405.1	2509455	2509455	type	True	82.064	692	1282	95	below_threshold
Agromyces intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	82.0261	709	1282	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	81.9935	668	1282	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	81.8359	685	1282	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	81.7859	689	1282	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	81.3211	637	1282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:15,859] [INFO] DFAST Taxonomy check result was written to GCF_014648575.1_ASM1464857v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:15,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:15,860] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:15,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2e4a264-a361-4593-a753-0c726ce9de14/dqc_reference/checkm_data
[2024-01-24 14:39:15,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:15,898] [INFO] Task started: CheckM
[2024-01-24 14:39:15,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014648575.1_ASM1464857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014648575.1_ASM1464857v1_genomic.fna/checkm_input GCF_014648575.1_ASM1464857v1_genomic.fna/checkm_result
[2024-01-24 14:40:02,234] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:02,236] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:02,254] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:02,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:02,255] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014648575.1_ASM1464857v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:02,255] [INFO] Task started: Blastn
[2024-01-24 14:40:02,255] [INFO] Running command: blastn -query GCF_014648575.1_ASM1464857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2e4a264-a361-4593-a753-0c726ce9de14/dqc_reference/reference_markers_gtdb.fasta -out GCF_014648575.1_ASM1464857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:04,927] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:04,931] [INFO] Selected 18 target genomes.
[2024-01-24 14:40:04,931] [INFO] Target genome list was writen to GCF_014648575.1_ASM1464857v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:04,944] [INFO] Task started: fastANI
[2024-01-24 14:40:04,944] [INFO] Running command: fastANI --query /var/lib/cwl/stg23ddcc1c-cd48-4f7b-9a14-834256e686ca/GCF_014648575.1_ASM1464857v1_genomic.fna.gz --refList GCF_014648575.1_ASM1464857v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014648575.1_ASM1464857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:24,805] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:24,824] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:24,824] [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_014648575.1	s__Agromyces mediolanus	100.0	1281	1282	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_009749405.1	s__Agromyces lapidis	83.4079	801	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000421545.1	s__Agromyces italicus	83.1417	758	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008122505.1	s__Agromyces sp008122505	82.7725	747	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720255.1	s__Agromyces humi	82.6017	510	1282	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	82.5129	751	1282	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	82.3493	750	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907355.1	s__Agromyces aurantiacus	82.2959	733	1282	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	82.2512	725	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009709675.1	s__Agromyces bracchium	82.247	736	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421565.1	s__Agromyces sp001421565	82.2398	784	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620055.1	s__Agromyces sp001620055	82.1574	649	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729855.1	s__Agromyces luteolus	82.132	737	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135405.1	s__Agromyces protaetiae	82.0798	691	1282	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	81.9591	698	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004006235.1	s__Agromyces sp004006235	81.9491	770	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104685.1	s__Agromyces flavus	81.8739	689	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003634985.1	s__Agromyces sp003634985	81.8428	710	1282	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 14:40:24,826] [INFO] GTDB search result was written to GCF_014648575.1_ASM1464857v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:24,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:24,832] [INFO] DFAST_QC result json was written to GCF_014648575.1_ASM1464857v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:24,833] [INFO] DFAST_QC completed!
[2024-01-24 14:40:24,833] [INFO] Total running time: 0h1m39s