[2024-01-24 11:05:24,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:24,700] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:24,700] [INFO] DQC Reference Directory: /var/lib/cwl/stg35f52e1c-35d8-4ec8-b701-2f2524c0ca8d/dqc_reference
[2024-01-24 11:05:26,372] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:26,373] [INFO] Task started: Prodigal
[2024-01-24 11:05:26,374] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb44e5c2-ea74-41f9-977e-ada7b7923c98/GCF_008365295.1_ASM836529v1_genomic.fna.gz | prodigal -d GCF_008365295.1_ASM836529v1_genomic.fna/cds.fna -a GCF_008365295.1_ASM836529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:37,346] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:37,346] [INFO] Task started: HMMsearch
[2024-01-24 11:05:37,347] [INFO] Running command: hmmsearch --tblout GCF_008365295.1_ASM836529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35f52e1c-35d8-4ec8-b701-2f2524c0ca8d/dqc_reference/reference_markers.hmm GCF_008365295.1_ASM836529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:37,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:37,623] [INFO] Found 6/6 markers.
[2024-01-24 11:05:37,659] [INFO] Query marker FASTA was written to GCF_008365295.1_ASM836529v1_genomic.fna/markers.fasta
[2024-01-24 11:05:37,659] [INFO] Task started: Blastn
[2024-01-24 11:05:37,660] [INFO] Running command: blastn -query GCF_008365295.1_ASM836529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35f52e1c-35d8-4ec8-b701-2f2524c0ca8d/dqc_reference/reference_markers.fasta -out GCF_008365295.1_ASM836529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:38,871] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:38,877] [INFO] Selected 17 target genomes.
[2024-01-24 11:05:38,877] [INFO] Target genome list was writen to GCF_008365295.1_ASM836529v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:38,886] [INFO] Task started: fastANI
[2024-01-24 11:05:38,886] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb44e5c2-ea74-41f9-977e-ada7b7923c98/GCF_008365295.1_ASM836529v1_genomic.fna.gz --refList GCF_008365295.1_ASM836529v1_genomic.fna/target_genomes.txt --output GCF_008365295.1_ASM836529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:54,239] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:54,239] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35f52e1c-35d8-4ec8-b701-2f2524c0ca8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:54,240] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35f52e1c-35d8-4ec8-b701-2f2524c0ca8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:54,257] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:05:54,257] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:54,257] [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 intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	100.0	1266	1266	95	conclusive
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	83.0498	827	1266	95	below_threshold
Agromyces protaetiae	strain=FW100M-8	GCA_004135405.1	2509455	2509455	type	True	82.5756	779	1266	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	82.513	771	1266	95	below_threshold
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	82.2469	524	1266	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	82.1009	709	1266	95	below_threshold
Agromyces aurantiacus	strain=DSM 14598	GCA_016907355.1	165814	165814	type	True	82.008	744	1266	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	81.9833	727	1266	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	81.9701	735	1266	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	81.8839	714	1266	95	below_threshold
Agromyces bracchium	strain=JCM 11433	GCA_009709675.1	88376	88376	type	True	81.8439	750	1266	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_900104685.1	589382	589382	type	True	81.7607	716	1266	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	81.7453	651	1266	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	81.6958	716	1266	95	below_threshold
Agromyces flavus	strain=CCM 7623	GCA_014635805.1	589382	589382	type	True	81.6869	721	1266	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	81.6639	647	1266	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.7785	626	1266	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:54,260] [INFO] DFAST Taxonomy check result was written to GCF_008365295.1_ASM836529v1_genomic.fna/tc_result.tsv
[2024-01-24 11:05:54,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:54,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:54,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35f52e1c-35d8-4ec8-b701-2f2524c0ca8d/dqc_reference/checkm_data
[2024-01-24 11:05:54,262] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:54,306] [INFO] Task started: CheckM
[2024-01-24 11:05:54,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008365295.1_ASM836529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008365295.1_ASM836529v1_genomic.fna/checkm_input GCF_008365295.1_ASM836529v1_genomic.fna/checkm_result
[2024-01-24 11:06:44,211] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:44,213] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:44,236] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:44,236] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:44,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008365295.1_ASM836529v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:44,237] [INFO] Task started: Blastn
[2024-01-24 11:06:44,238] [INFO] Running command: blastn -query GCF_008365295.1_ASM836529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35f52e1c-35d8-4ec8-b701-2f2524c0ca8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008365295.1_ASM836529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:46,226] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:46,230] [INFO] Selected 16 target genomes.
[2024-01-24 11:06:46,230] [INFO] Target genome list was writen to GCF_008365295.1_ASM836529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:46,242] [INFO] Task started: fastANI
[2024-01-24 11:06:46,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb44e5c2-ea74-41f9-977e-ada7b7923c98/GCF_008365295.1_ASM836529v1_genomic.fna.gz --refList GCF_008365295.1_ASM836529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008365295.1_ASM836529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:01,333] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:01,349] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:01,349] [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_008365295.1	s__Agromyces intestinalis	100.0	1266	1266	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_009647605.1	s__Agromyces sp009647605	83.0014	832	1266	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	82.9709	823	1266	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	82.6035	780	1266	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	82.4355	828	1266	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	82.2726	522	1266	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	82.16	704	1266	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	82.113	812	1266	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	82.0351	741	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216665.1	s__Agromyces ramosus	81.9306	739	1266	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	81.929	709	1266	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	81.8899	745	1266	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	81.8729	754	1266	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	81.7233	720	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014645655.1	s__Agromyces bauzanensis	81.6752	646	1266	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009674665.1	s__Agromyces kandeliae	81.6392	693	1266	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 11:07:01,351] [INFO] GTDB search result was written to GCF_008365295.1_ASM836529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:01,352] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:01,359] [INFO] DFAST_QC result json was written to GCF_008365295.1_ASM836529v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:01,359] [INFO] DFAST_QC completed!
[2024-01-24 11:07:01,359] [INFO] Total running time: 0h1m37s