[2023-06-19 02:45:59,456] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:45:59,459] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:45:59,459] [INFO] DQC Reference Directory: /var/lib/cwl/stgc5f305bf-6609-48a3-a493-6ceab4a5e349/dqc_reference
[2023-06-19 02:46:00,659] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:46:00,660] [INFO] Task started: Prodigal
[2023-06-19 02:46:00,660] [INFO] Running command: gunzip -c /var/lib/cwl/stgc7d14092-63bd-45a3-9d71-48fc01040081/GCA_018607415.1_ASM1860741v1_genomic.fna.gz | prodigal -d GCA_018607415.1_ASM1860741v1_genomic.fna/cds.fna -a GCA_018607415.1_ASM1860741v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:46:05,810] [INFO] Task succeeded: Prodigal
[2023-06-19 02:46:05,811] [INFO] Task started: HMMsearch
[2023-06-19 02:46:05,811] [INFO] Running command: hmmsearch --tblout GCA_018607415.1_ASM1860741v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc5f305bf-6609-48a3-a493-6ceab4a5e349/dqc_reference/reference_markers.hmm GCA_018607415.1_ASM1860741v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:46:06,062] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:46:06,063] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc7d14092-63bd-45a3-9d71-48fc01040081/GCA_018607415.1_ASM1860741v1_genomic.fna.gz]
[2023-06-19 02:46:06,104] [INFO] Query marker FASTA was written to GCA_018607415.1_ASM1860741v1_genomic.fna/markers.fasta
[2023-06-19 02:46:06,105] [INFO] Task started: Blastn
[2023-06-19 02:46:06,105] [INFO] Running command: blastn -query GCA_018607415.1_ASM1860741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f305bf-6609-48a3-a493-6ceab4a5e349/dqc_reference/reference_markers.fasta -out GCA_018607415.1_ASM1860741v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:46:06,747] [INFO] Task succeeded: Blastn
[2023-06-19 02:46:06,752] [INFO] Selected 18 target genomes.
[2023-06-19 02:46:06,752] [INFO] Target genome list was writen to GCA_018607415.1_ASM1860741v1_genomic.fna/target_genomes.txt
[2023-06-19 02:46:06,755] [INFO] Task started: fastANI
[2023-06-19 02:46:06,755] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7d14092-63bd-45a3-9d71-48fc01040081/GCA_018607415.1_ASM1860741v1_genomic.fna.gz --refList GCA_018607415.1_ASM1860741v1_genomic.fna/target_genomes.txt --output GCA_018607415.1_ASM1860741v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:46:16,627] [INFO] Task succeeded: fastANI
[2023-06-19 02:46:16,628] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc5f305bf-6609-48a3-a493-6ceab4a5e349/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:46:16,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc5f305bf-6609-48a3-a493-6ceab4a5e349/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:46:16,630] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:46:16,630] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 02:46:16,630] [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 02:46:16,632] [INFO] DFAST Taxonomy check result was written to GCA_018607415.1_ASM1860741v1_genomic.fna/tc_result.tsv
[2023-06-19 02:46:16,632] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:46:16,632] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:46:16,632] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc5f305bf-6609-48a3-a493-6ceab4a5e349/dqc_reference/checkm_data
[2023-06-19 02:46:16,635] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:46:16,662] [INFO] Task started: CheckM
[2023-06-19 02:46:16,662] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018607415.1_ASM1860741v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018607415.1_ASM1860741v1_genomic.fna/checkm_input GCA_018607415.1_ASM1860741v1_genomic.fna/checkm_result
[2023-06-19 02:46:40,511] [INFO] Task succeeded: CheckM
[2023-06-19 02:46:40,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:46:40,534] [INFO] ===== Completeness check finished =====
[2023-06-19 02:46:40,535] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:46:40,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018607415.1_ASM1860741v1_genomic.fna/markers.fasta)
[2023-06-19 02:46:40,535] [INFO] Task started: Blastn
[2023-06-19 02:46:40,535] [INFO] Running command: blastn -query GCA_018607415.1_ASM1860741v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc5f305bf-6609-48a3-a493-6ceab4a5e349/dqc_reference/reference_markers_gtdb.fasta -out GCA_018607415.1_ASM1860741v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:46:41,520] [INFO] Task succeeded: Blastn
[2023-06-19 02:46:41,527] [INFO] Selected 26 target genomes.
[2023-06-19 02:46:41,527] [INFO] Target genome list was writen to GCA_018607415.1_ASM1860741v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:46:41,560] [INFO] Task started: fastANI
[2023-06-19 02:46:41,561] [INFO] Running command: fastANI --query /var/lib/cwl/stgc7d14092-63bd-45a3-9d71-48fc01040081/GCA_018607415.1_ASM1860741v1_genomic.fna.gz --refList GCA_018607415.1_ASM1860741v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018607415.1_ASM1860741v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:46:53,123] [INFO] Task succeeded: fastANI
[2023-06-19 02:46:53,138] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:46:53,138] [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_003491845.1	s__HTCC2207 sp003491845	99.0046	531	746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	98.96	98.96	0.71	0.71	2	conclusive
GCA_002313335.1	s__HTCC2207 sp002313335	77.8852	59	746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685195.1	s__HTCC2207 sp002685195	77.3978	59	746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	97.12	96.72	0.71	0.66	10	-
GCA_905182275.1	s__HTCC2207 sp905182275	77.296	84	746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381985.1	s__HTCC2207 sp014381985	77.2499	61	746	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Porticoccaceae;g__HTCC2207	95.0	96.01	96.01	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-19 02:46:53,140] [INFO] GTDB search result was written to GCA_018607415.1_ASM1860741v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:46:53,141] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:46:53,144] [INFO] DFAST_QC result json was written to GCA_018607415.1_ASM1860741v1_genomic.fna/dqc_result.json
[2023-06-19 02:46:53,144] [INFO] DFAST_QC completed!
[2023-06-19 02:46:53,144] [INFO] Total running time: 0h0m54s