[2024-01-24 11:26:11,344] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:11,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:11,351] [INFO] DQC Reference Directory: /var/lib/cwl/stg4971ea6a-b934-40e5-bf83-4954e7f62fc3/dqc_reference
[2024-01-24 11:26:12,658] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:12,659] [INFO] Task started: Prodigal
[2024-01-24 11:26:12,660] [INFO] Running command: gunzip -c /var/lib/cwl/stg366f83d5-9d86-440c-8de9-4c31f8141aa7/GCF_004217415.1_ASM421741v1_genomic.fna.gz | prodigal -d GCF_004217415.1_ASM421741v1_genomic.fna/cds.fna -a GCF_004217415.1_ASM421741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:18,803] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:18,803] [INFO] Task started: HMMsearch
[2024-01-24 11:26:18,803] [INFO] Running command: hmmsearch --tblout GCF_004217415.1_ASM421741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4971ea6a-b934-40e5-bf83-4954e7f62fc3/dqc_reference/reference_markers.hmm GCF_004217415.1_ASM421741v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:19,102] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:19,103] [INFO] Found 6/6 markers.
[2024-01-24 11:26:19,124] [INFO] Query marker FASTA was written to GCF_004217415.1_ASM421741v1_genomic.fna/markers.fasta
[2024-01-24 11:26:19,125] [INFO] Task started: Blastn
[2024-01-24 11:26:19,125] [INFO] Running command: blastn -query GCF_004217415.1_ASM421741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4971ea6a-b934-40e5-bf83-4954e7f62fc3/dqc_reference/reference_markers.fasta -out GCF_004217415.1_ASM421741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:20,045] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:20,048] [INFO] Selected 11 target genomes.
[2024-01-24 11:26:20,048] [INFO] Target genome list was writen to GCF_004217415.1_ASM421741v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:20,061] [INFO] Task started: fastANI
[2024-01-24 11:26:20,061] [INFO] Running command: fastANI --query /var/lib/cwl/stg366f83d5-9d86-440c-8de9-4c31f8141aa7/GCF_004217415.1_ASM421741v1_genomic.fna.gz --refList GCF_004217415.1_ASM421741v1_genomic.fna/target_genomes.txt --output GCF_004217415.1_ASM421741v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:25,718] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:25,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4971ea6a-b934-40e5-bf83-4954e7f62fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:25,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4971ea6a-b934-40e5-bf83-4954e7f62fc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:25,729] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:25,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:25,729] [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
Spiribacter vilamensis	strain=DSM 21056	GCA_004217415.1	531306	531306	type	True	100.0	691	691	95	conclusive
Spiribacter vilamensis	strain=DSM 21056	GCA_007625165.1	531306	531306	type	True	99.9987	688	691	95	conclusive
Spiribacter curvatus	strain=UAH-SP71	GCA_000485905.1	1335757	1335757	type	True	83.4784	467	691	95	below_threshold
Spiribacter aquaticus	strain=SP30	GCA_007625215.1	1935996	1935996	type	True	81.3251	435	691	95	below_threshold
Spiribacter salinus	strain=M19-40	GCA_000319575.2	1335746	1335746	type	True	77.7378	185	691	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	77.5322	183	691	95	below_threshold
Aquisalimonas asiatica	strain=CGMCC 1.6291	GCA_900110585.1	406100	406100	type	True	77.1217	120	691	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.4068	72	691	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	76.1601	62	691	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	76.0343	59	691	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.0073	60	691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:25,731] [INFO] DFAST Taxonomy check result was written to GCF_004217415.1_ASM421741v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:25,731] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:25,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:25,732] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4971ea6a-b934-40e5-bf83-4954e7f62fc3/dqc_reference/checkm_data
[2024-01-24 11:26:25,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:25,773] [INFO] Task started: CheckM
[2024-01-24 11:26:25,773] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004217415.1_ASM421741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004217415.1_ASM421741v1_genomic.fna/checkm_input GCF_004217415.1_ASM421741v1_genomic.fna/checkm_result
[2024-01-24 11:26:50,245] [INFO] Task succeeded: CheckM
[2024-01-24 11:26:50,246] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:26:50,264] [INFO] ===== Completeness check finished =====
[2024-01-24 11:26:50,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:26:50,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004217415.1_ASM421741v1_genomic.fna/markers.fasta)
[2024-01-24 11:26:50,265] [INFO] Task started: Blastn
[2024-01-24 11:26:50,265] [INFO] Running command: blastn -query GCF_004217415.1_ASM421741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4971ea6a-b934-40e5-bf83-4954e7f62fc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004217415.1_ASM421741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:52,039] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:52,043] [INFO] Selected 11 target genomes.
[2024-01-24 11:26:52,043] [INFO] Target genome list was writen to GCF_004217415.1_ASM421741v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:26:52,073] [INFO] Task started: fastANI
[2024-01-24 11:26:52,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg366f83d5-9d86-440c-8de9-4c31f8141aa7/GCF_004217415.1_ASM421741v1_genomic.fna.gz --refList GCF_004217415.1_ASM421741v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004217415.1_ASM421741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:26:59,155] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:59,170] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:26:59,171] [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_004217415.1	s__Spiribacter vilamensis	100.0	691	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000485905.1	s__Spiribacter curvatus	83.4784	467	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813635.1	s__Spiribacter roseus	81.3594	424	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	98.20	97.75	0.92	0.91	7	-
GCF_003149435.1	s__E85 sp003149435	78.2867	257	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__E85	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009676705.1	s__Spiribacter sp009676705	78.2577	198	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Spiribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374645.1	s__Arhodomonas aquaeolei	77.5125	185	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Nitrococcaceae;g__Arhodomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002798175.1	s__Luteimonas sp002798175	77.2899	57	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003664325.1	s__Alkalilimnicola mobilis	77.2413	118	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Halorhodospiraceae;g__Alkalilimnicola	95.0	98.61	98.57	0.90	0.85	3	-
GCF_900110585.1	s__Aquisalimonas asiatica	77.0998	121	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__Aquisalimonadaceae;g__Aquisalimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009295635.1	s__S0819 sp009295635	76.6854	110	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nitrococcales;f__AK92;g__S0819	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014836665.1	s__Luteimonas sp014836665	76.4824	76	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:26:59,172] [INFO] GTDB search result was written to GCF_004217415.1_ASM421741v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:26:59,173] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:26:59,176] [INFO] DFAST_QC result json was written to GCF_004217415.1_ASM421741v1_genomic.fna/dqc_result.json
[2024-01-24 11:26:59,176] [INFO] DFAST_QC completed!
[2024-01-24 11:26:59,176] [INFO] Total running time: 0h0m48s