[2023-06-19 08:45:32,073] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:45:32,078] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:45:32,078] [INFO] DQC Reference Directory: /var/lib/cwl/stg33fa08a1-ad41-49af-9c65-f177abb48d1a/dqc_reference
[2023-06-19 08:45:36,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:45:36,564] [INFO] Task started: Prodigal
[2023-06-19 08:45:36,564] [INFO] Running command: gunzip -c /var/lib/cwl/stgebc65b47-09e4-4a66-8bb4-09c4d2b3d5a4/GCA_018674015.1_ASM1867401v1_genomic.fna.gz | prodigal -d GCA_018674015.1_ASM1867401v1_genomic.fna/cds.fna -a GCA_018674015.1_ASM1867401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:45:48,284] [INFO] Task succeeded: Prodigal
[2023-06-19 08:45:48,285] [INFO] Task started: HMMsearch
[2023-06-19 08:45:48,285] [INFO] Running command: hmmsearch --tblout GCA_018674015.1_ASM1867401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33fa08a1-ad41-49af-9c65-f177abb48d1a/dqc_reference/reference_markers.hmm GCA_018674015.1_ASM1867401v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:45:48,604] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:45:48,606] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgebc65b47-09e4-4a66-8bb4-09c4d2b3d5a4/GCA_018674015.1_ASM1867401v1_genomic.fna.gz]
[2023-06-19 08:45:48,658] [INFO] Query marker FASTA was written to GCA_018674015.1_ASM1867401v1_genomic.fna/markers.fasta
[2023-06-19 08:45:48,659] [INFO] Task started: Blastn
[2023-06-19 08:45:48,659] [INFO] Running command: blastn -query GCA_018674015.1_ASM1867401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33fa08a1-ad41-49af-9c65-f177abb48d1a/dqc_reference/reference_markers.fasta -out GCA_018674015.1_ASM1867401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:45:49,289] [INFO] Task succeeded: Blastn
[2023-06-19 08:45:49,295] [INFO] Selected 24 target genomes.
[2023-06-19 08:45:49,295] [INFO] Target genome list was writen to GCA_018674015.1_ASM1867401v1_genomic.fna/target_genomes.txt
[2023-06-19 08:45:49,301] [INFO] Task started: fastANI
[2023-06-19 08:45:49,301] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc65b47-09e4-4a66-8bb4-09c4d2b3d5a4/GCA_018674015.1_ASM1867401v1_genomic.fna.gz --refList GCA_018674015.1_ASM1867401v1_genomic.fna/target_genomes.txt --output GCA_018674015.1_ASM1867401v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:46:03,512] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:03,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33fa08a1-ad41-49af-9c65-f177abb48d1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:46:03,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33fa08a1-ad41-49af-9c65-f177abb48d1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:46:03,515] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:46:03,515] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 08:46:03,515] [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
--------------------------------------------------------------------------------
[2023-06-19 08:46:03,519] [INFO] DFAST Taxonomy check result was written to GCA_018674015.1_ASM1867401v1_genomic.fna/tc_result.tsv
[2023-06-19 08:46:03,519] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:46:03,519] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:46:03,520] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33fa08a1-ad41-49af-9c65-f177abb48d1a/dqc_reference/checkm_data
[2023-06-19 08:46:03,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:46:03,570] [INFO] Task started: CheckM
[2023-06-19 08:46:03,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018674015.1_ASM1867401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018674015.1_ASM1867401v1_genomic.fna/checkm_input GCA_018674015.1_ASM1867401v1_genomic.fna/checkm_result
[2023-06-19 08:46:42,361] [INFO] Task succeeded: CheckM
[2023-06-19 08:46:42,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:46:42,392] [INFO] ===== Completeness check finished =====
[2023-06-19 08:46:42,393] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:46:42,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018674015.1_ASM1867401v1_genomic.fna/markers.fasta)
[2023-06-19 08:46:42,394] [INFO] Task started: Blastn
[2023-06-19 08:46:42,394] [INFO] Running command: blastn -query GCA_018674015.1_ASM1867401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33fa08a1-ad41-49af-9c65-f177abb48d1a/dqc_reference/reference_markers_gtdb.fasta -out GCA_018674015.1_ASM1867401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:46:43,286] [INFO] Task succeeded: Blastn
[2023-06-19 08:46:43,293] [INFO] Selected 12 target genomes.
[2023-06-19 08:46:43,293] [INFO] Target genome list was writen to GCA_018674015.1_ASM1867401v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:46:43,298] [INFO] Task started: fastANI
[2023-06-19 08:46:43,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgebc65b47-09e4-4a66-8bb4-09c4d2b3d5a4/GCA_018674015.1_ASM1867401v1_genomic.fna.gz --refList GCA_018674015.1_ASM1867401v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018674015.1_ASM1867401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:46:52,265] [INFO] Task succeeded: fastANI
[2023-06-19 08:46:52,275] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:46:52,276] [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
GCA_018665025.1	s__UBA9659 sp018665025	99.6169	1166	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.67	99.61	0.89	0.86	14	conclusive
GCA_012961165.1	s__UBA9659 sp012961165	94.6105	1108	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.55	99.55	0.89	0.89	2	-
GCA_018645845.1	s__UBA9659 sp018645845	89.1795	774	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	98.73	98.60	0.77	0.73	4	-
GCA_018667205.1	s__UBA9659 sp018667205	83.3537	553	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018607685.1	s__UBA9659 sp018607685	81.6557	601	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642855.1	s__UBA9659 sp017642855	75.9875	88	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	99.28	99.09	0.95	0.93	7	-
GCA_016779585.1	s__UBA9659 sp016779585	75.9543	81	1436	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__HTCC2089;g__UBA9659	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:46:52,280] [INFO] GTDB search result was written to GCA_018674015.1_ASM1867401v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:46:52,280] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:46:52,288] [INFO] DFAST_QC result json was written to GCA_018674015.1_ASM1867401v1_genomic.fna/dqc_result.json
[2023-06-19 08:46:52,288] [INFO] DFAST_QC completed!
[2023-06-19 08:46:52,289] [INFO] Total running time: 0h1m20s