[2024-01-24 12:30:52,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:52,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:52,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg97876971-fc76-4b94-90e5-fe011247ec8f/dqc_reference
[2024-01-24 12:30:54,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:54,008] [INFO] Task started: Prodigal
[2024-01-24 12:30:54,008] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb0dceb6-ad30-43e9-b3fe-056f4cdb4c0d/GCF_004208415.1_ASM420841v1_genomic.fna.gz | prodigal -d GCF_004208415.1_ASM420841v1_genomic.fna/cds.fna -a GCF_004208415.1_ASM420841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:24,366] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:24,367] [INFO] Task started: HMMsearch
[2024-01-24 12:31:24,367] [INFO] Running command: hmmsearch --tblout GCF_004208415.1_ASM420841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97876971-fc76-4b94-90e5-fe011247ec8f/dqc_reference/reference_markers.hmm GCF_004208415.1_ASM420841v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:24,844] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:24,845] [INFO] Found 6/6 markers.
[2024-01-24 12:31:24,923] [INFO] Query marker FASTA was written to GCF_004208415.1_ASM420841v1_genomic.fna/markers.fasta
[2024-01-24 12:31:24,923] [INFO] Task started: Blastn
[2024-01-24 12:31:24,923] [INFO] Running command: blastn -query GCF_004208415.1_ASM420841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97876971-fc76-4b94-90e5-fe011247ec8f/dqc_reference/reference_markers.fasta -out GCF_004208415.1_ASM420841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:25,504] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:25,508] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:25,508] [INFO] Target genome list was writen to GCF_004208415.1_ASM420841v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:25,514] [INFO] Task started: fastANI
[2024-01-24 12:31:25,514] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb0dceb6-ad30-43e9-b3fe-056f4cdb4c0d/GCF_004208415.1_ASM420841v1_genomic.fna.gz --refList GCF_004208415.1_ASM420841v1_genomic.fna/target_genomes.txt --output GCF_004208415.1_ASM420841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:43,521] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:43,521] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97876971-fc76-4b94-90e5-fe011247ec8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:43,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97876971-fc76-4b94-90e5-fe011247ec8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:43,529] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:43,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:43,529] [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
Ktedonosporobacter rubrisoli	strain=SCAWS-G2	GCA_004208415.1	2509675	2509675	type	True	100.0	3780	3780	95	conclusive
Reticulibacter mediterranei	strain=150040	GCA_016587455.1	2778369	2778369	type	True	77.9735	347	3780	95	below_threshold
Tengunoibacter tsumagoiensis	strain=Uno3	GCA_003967535.1	2014871	2014871	type	True	77.5122	144	3780	95	below_threshold
Ktedonobacter racemifer	strain=SOSP1-21	GCA_000178855.1	363277	363277	type	True	77.5034	283	3780	95	below_threshold
Dictyobacter formicarum	strain=SOSP1-9	GCA_016587435.1	2778368	2778368	type	True	77.3264	196	3780	95	below_threshold
Dictyobacter aurantiacus	strain=S-27	GCA_003967515.1	1936993	1936993	type	True	76.9058	182	3780	95	below_threshold
Dictyobacter kobayashii	strain=Uno11	GCA_003967555.1	2014872	2014872	type	True	76.6793	163	3780	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:43,531] [INFO] DFAST Taxonomy check result was written to GCF_004208415.1_ASM420841v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:43,531] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:43,532] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:43,532] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97876971-fc76-4b94-90e5-fe011247ec8f/dqc_reference/checkm_data
[2024-01-24 12:31:43,533] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:43,651] [INFO] Task started: CheckM
[2024-01-24 12:31:43,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004208415.1_ASM420841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004208415.1_ASM420841v1_genomic.fna/checkm_input GCF_004208415.1_ASM420841v1_genomic.fna/checkm_result
[2024-01-24 12:33:08,182] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:08,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:08,214] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:08,214] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:08,214] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004208415.1_ASM420841v1_genomic.fna/markers.fasta)
[2024-01-24 12:33:08,215] [INFO] Task started: Blastn
[2024-01-24 12:33:08,215] [INFO] Running command: blastn -query GCF_004208415.1_ASM420841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97876971-fc76-4b94-90e5-fe011247ec8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_004208415.1_ASM420841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:08,931] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:08,936] [INFO] Selected 22 target genomes.
[2024-01-24 12:33:08,937] [INFO] Target genome list was writen to GCF_004208415.1_ASM420841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:08,954] [INFO] Task started: fastANI
[2024-01-24 12:33:08,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb0dceb6-ad30-43e9-b3fe-056f4cdb4c0d/GCF_004208415.1_ASM420841v1_genomic.fna.gz --refList GCF_004208415.1_ASM420841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004208415.1_ASM420841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:31,589] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:31,604] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:31,605] [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_004208415.1	s__Ktedonosporobacter rubrisoli	100.0	3780	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonosporobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003967535.1	s__Tengunoibacter tsumagoiensis	77.5992	146	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Tengunoibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178855.1	s__Ktedonobacter racemifer	77.4596	286	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587415.1	s__Ktedonobacter sp016587415	77.3636	262	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Ktedonobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587435.1	s__Dictyobacter sp016587435	77.2319	195	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967515.1	s__Dictyobacter aurantiacus	76.8575	184	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967555.1	s__Dictyobacter kobayashii	76.7335	164	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008974265.1	s__Dictyobacter vulcani	76.6852	148	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Dictyobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005881295.1	s__UBA11361 sp005881295	76.2463	72	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	97.35	96.80	0.70	0.62	6	-
GCA_005881495.1	s__UBA11361 sp005881495	76.2002	108	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011389075.1	s__DTNP01 sp011389075	76.1931	87	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__DTNP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014896635.1	s__Bu33 sp014896635	76.1057	121	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__Bu33	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001919995.1	s__UBA11361 sp001919995	76.0923	54	3780	d__Bacteria;p__Chloroflexota;c__Ktedonobacteria;o__Ktedonobacterales;f__Ktedonobacteraceae;g__UBA11361	95.0	98.21	97.62	0.55	0.54	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:31,608] [INFO] GTDB search result was written to GCF_004208415.1_ASM420841v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:31,608] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:31,613] [INFO] DFAST_QC result json was written to GCF_004208415.1_ASM420841v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:31,614] [INFO] DFAST_QC completed!
[2024-01-24 12:33:31,614] [INFO] Total running time: 0h2m39s