[2023-06-13 15:45:08,150] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:45:08,152] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:45:08,152] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c28a73a-897b-470b-bb75-82beb517c0fa/dqc_reference
[2023-06-13 15:45:09,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:45:09,464] [INFO] Task started: Prodigal
[2023-06-13 15:45:09,464] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4f27d0a-6c1f-464c-94b9-58a216f98317/GCA_947459565.1_RE-16jun15-110_genomic.fna.gz | prodigal -d GCA_947459565.1_RE-16jun15-110_genomic.fna/cds.fna -a GCA_947459565.1_RE-16jun15-110_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:18,456] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:18,457] [INFO] Task started: HMMsearch
[2023-06-13 15:45:18,457] [INFO] Running command: hmmsearch --tblout GCA_947459565.1_RE-16jun15-110_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c28a73a-897b-470b-bb75-82beb517c0fa/dqc_reference/reference_markers.hmm GCA_947459565.1_RE-16jun15-110_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:18,734] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:18,736] [INFO] Found 6/6 markers.
[2023-06-13 15:45:18,778] [INFO] Query marker FASTA was written to GCA_947459565.1_RE-16jun15-110_genomic.fna/markers.fasta
[2023-06-13 15:45:18,779] [INFO] Task started: Blastn
[2023-06-13 15:45:18,779] [INFO] Running command: blastn -query GCA_947459565.1_RE-16jun15-110_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c28a73a-897b-470b-bb75-82beb517c0fa/dqc_reference/reference_markers.fasta -out GCA_947459565.1_RE-16jun15-110_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:19,468] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:19,472] [INFO] Selected 35 target genomes.
[2023-06-13 15:45:19,472] [INFO] Target genome list was writen to GCA_947459565.1_RE-16jun15-110_genomic.fna/target_genomes.txt
[2023-06-13 15:45:19,473] [INFO] Task started: fastANI
[2023-06-13 15:45:19,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f27d0a-6c1f-464c-94b9-58a216f98317/GCA_947459565.1_RE-16jun15-110_genomic.fna.gz --refList GCA_947459565.1_RE-16jun15-110_genomic.fna/target_genomes.txt --output GCA_947459565.1_RE-16jun15-110_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:43,045] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:43,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c28a73a-897b-470b-bb75-82beb517c0fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:43,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c28a73a-897b-470b-bb75-82beb517c0fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:43,063] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:43,063] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 15:45:43,064] [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
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	76.0618	52	869	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	76.038	51	869	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	76.0264	51	869	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.013	55	869	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	75.8939	58	869	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	75.8245	52	869	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	75.8245	52	869	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	75.7666	54	869	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 15:45:43,071] [INFO] DFAST Taxonomy check result was written to GCA_947459565.1_RE-16jun15-110_genomic.fna/tc_result.tsv
[2023-06-13 15:45:43,072] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:43,072] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:43,072] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c28a73a-897b-470b-bb75-82beb517c0fa/dqc_reference/checkm_data
[2023-06-13 15:45:43,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:43,113] [INFO] Task started: CheckM
[2023-06-13 15:45:43,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947459565.1_RE-16jun15-110_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947459565.1_RE-16jun15-110_genomic.fna/checkm_input GCA_947459565.1_RE-16jun15-110_genomic.fna/checkm_result
[2023-06-13 15:46:14,203] [INFO] Task succeeded: CheckM
[2023-06-13 15:46:14,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.55%
Contamintation: 8.33%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-13 15:46:14,229] [INFO] ===== Completeness check finished =====
[2023-06-13 15:46:14,229] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:46:14,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947459565.1_RE-16jun15-110_genomic.fna/markers.fasta)
[2023-06-13 15:46:14,230] [INFO] Task started: Blastn
[2023-06-13 15:46:14,230] [INFO] Running command: blastn -query GCA_947459565.1_RE-16jun15-110_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c28a73a-897b-470b-bb75-82beb517c0fa/dqc_reference/reference_markers_gtdb.fasta -out GCA_947459565.1_RE-16jun15-110_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:46:15,429] [INFO] Task succeeded: Blastn
[2023-06-13 15:46:15,436] [INFO] Selected 22 target genomes.
[2023-06-13 15:46:15,436] [INFO] Target genome list was writen to GCA_947459565.1_RE-16jun15-110_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:46:15,439] [INFO] Task started: fastANI
[2023-06-13 15:46:15,439] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4f27d0a-6c1f-464c-94b9-58a216f98317/GCA_947459565.1_RE-16jun15-110_genomic.fna.gz --refList GCA_947459565.1_RE-16jun15-110_genomic.fna/target_genomes_gtdb.txt --output GCA_947459565.1_RE-16jun15-110_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:29,206] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:29,218] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 15:46:29,219] [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_903887045.1	s__CAILUG01 sp903887045	98.5236	750	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903853385.1	s__CAILUG01 sp903853385	77.8504	263	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	99.57	99.54	0.93	0.91	5	-
GCA_903837345.1	s__CAILUG01 sp903837345	77.8395	295	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	99.98	99.96	1.00	0.99	3	-
GCA_903926285.1	s__CAILUG01 sp903926285	76.0996	70	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000319305.2	s__Pseudomonas_E putida_C	76.0618	52	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	97.35	0.88	0.88	2	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	75.8706	51	869	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:29,221] [INFO] GTDB search result was written to GCA_947459565.1_RE-16jun15-110_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:29,221] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:29,224] [INFO] DFAST_QC result json was written to GCA_947459565.1_RE-16jun15-110_genomic.fna/dqc_result.json
[2023-06-13 15:46:29,224] [INFO] DFAST_QC completed!
[2023-06-13 15:46:29,224] [INFO] Total running time: 0h1m21s