[2024-01-25 20:16:20,677] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:16:20,678] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:16:20,679] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc32f47d-f860-4caa-842e-7bf0c211a2bd/dqc_reference
[2024-01-25 20:16:21,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:16:21,758] [INFO] Task started: Prodigal
[2024-01-25 20:16:21,759] [INFO] Running command: gunzip -c /var/lib/cwl/stgb22bd935-8d6d-497c-bbf1-ed5c49262a65/GCF_003268475.1_ASM326847v1_genomic.fna.gz | prodigal -d GCF_003268475.1_ASM326847v1_genomic.fna/cds.fna -a GCF_003268475.1_ASM326847v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:16:35,916] [INFO] Task succeeded: Prodigal
[2024-01-25 20:16:35,917] [INFO] Task started: HMMsearch
[2024-01-25 20:16:35,917] [INFO] Running command: hmmsearch --tblout GCF_003268475.1_ASM326847v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc32f47d-f860-4caa-842e-7bf0c211a2bd/dqc_reference/reference_markers.hmm GCF_003268475.1_ASM326847v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:16:36,280] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:16:36,281] [INFO] Found 6/6 markers.
[2024-01-25 20:16:36,357] [INFO] Query marker FASTA was written to GCF_003268475.1_ASM326847v1_genomic.fna/markers.fasta
[2024-01-25 20:16:36,358] [INFO] Task started: Blastn
[2024-01-25 20:16:36,358] [INFO] Running command: blastn -query GCF_003268475.1_ASM326847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc32f47d-f860-4caa-842e-7bf0c211a2bd/dqc_reference/reference_markers.fasta -out GCF_003268475.1_ASM326847v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:16:36,977] [INFO] Task succeeded: Blastn
[2024-01-25 20:16:36,980] [INFO] Selected 16 target genomes.
[2024-01-25 20:16:36,980] [INFO] Target genome list was writen to GCF_003268475.1_ASM326847v1_genomic.fna/target_genomes.txt
[2024-01-25 20:16:36,990] [INFO] Task started: fastANI
[2024-01-25 20:16:36,990] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22bd935-8d6d-497c-bbf1-ed5c49262a65/GCF_003268475.1_ASM326847v1_genomic.fna.gz --refList GCF_003268475.1_ASM326847v1_genomic.fna/target_genomes.txt --output GCF_003268475.1_ASM326847v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:16:53,292] [INFO] Task succeeded: fastANI
[2024-01-25 20:16:53,292] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc32f47d-f860-4caa-842e-7bf0c211a2bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:16:53,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc32f47d-f860-4caa-842e-7bf0c211a2bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:16:53,299] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:16:53,299] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:16:53,299] [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
Thermogemmatispora tikiterensis	strain=T81	GCA_003268475.1	1825093	1825093	type	True	99.9902	1970	1988	95	conclusive
Thermogemmatispora aurantia	strain=A1-2	GCA_008974285.1	2045279	2045279	type	True	94.3062	1745	1988	95	below_threshold
Thermogemmatispora carboxidivorans	strain=PM5	GCA_000702505.1	1382306	1382306	type	True	87.7782	1654	1988	95	below_threshold
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	75.7204	78	1988	95	below_threshold
Ktedonosporobacter rubrisoli	strain=SCAWS-G2	GCA_004208415.1	2509675	2509675	type	True	75.6724	93	1988	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	75.6632	102	1988	95	below_threshold
Dictyobacter arantiisoli	strain=Uno17	GCA_008326305.1	2014874	2014874	type	True	75.5166	67	1988	95	below_threshold
Dictyobacter vulcani	strain=W12	GCA_008974265.1	2607529	2607529	type	True	75.2751	51	1988	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:16:53,301] [INFO] DFAST Taxonomy check result was written to GCF_003268475.1_ASM326847v1_genomic.fna/tc_result.tsv
[2024-01-25 20:16:53,301] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:16:53,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:16:53,302] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc32f47d-f860-4caa-842e-7bf0c211a2bd/dqc_reference/checkm_data
[2024-01-25 20:16:53,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:16:53,359] [INFO] Task started: CheckM
[2024-01-25 20:16:53,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003268475.1_ASM326847v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003268475.1_ASM326847v1_genomic.fna/checkm_input GCF_003268475.1_ASM326847v1_genomic.fna/checkm_result
[2024-01-25 20:17:34,220] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:34,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:34,240] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:34,240] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:34,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003268475.1_ASM326847v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:34,241] [INFO] Task started: Blastn
[2024-01-25 20:17:34,241] [INFO] Running command: blastn -query GCF_003268475.1_ASM326847v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc32f47d-f860-4caa-842e-7bf0c211a2bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003268475.1_ASM326847v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:35,038] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:35,041] [INFO] Selected 8 target genomes.
[2024-01-25 20:17:35,041] [INFO] Target genome list was writen to GCF_003268475.1_ASM326847v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:35,058] [INFO] Task started: fastANI
[2024-01-25 20:17:35,058] [INFO] Running command: fastANI --query /var/lib/cwl/stgb22bd935-8d6d-497c-bbf1-ed5c49262a65/GCF_003268475.1_ASM326847v1_genomic.fna.gz --refList GCF_003268475.1_ASM326847v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003268475.1_ASM326847v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:45,703] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:45,709] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:45,709] [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_003268475.1	s__Thermogemmatispora tikiterensis	99.9902	1970	1988	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008974285.1	s__Thermogemmatispora aurantia	94.31	1745	1988	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	99.32	99.32	0.97	0.97	2	-
GCF_001748285.1	s__Thermogemmatispora onikobensis	87.965	1600	1988	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702505.1	s__Thermogemmatispora carboxidivorans	87.7859	1653	1988	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Thermogemmatispora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896635.1	s__Bu33 sp014896635	75.8436	100	1988	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Bu33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902810755.1	s__CADDYT01 sp902810755	75.8303	138	1988	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__CADDYT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	75.6606	102	1988	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:45,712] [INFO] GTDB search result was written to GCF_003268475.1_ASM326847v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:45,713] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:45,715] [INFO] DFAST_QC result json was written to GCF_003268475.1_ASM326847v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:45,716] [INFO] DFAST_QC completed!
[2024-01-25 20:17:45,716] [INFO] Total running time: 0h1m25s