[2023-06-08 05:13:48,889] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:13:48,891] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:13:48,891] [INFO] DQC Reference Directory: /var/lib/cwl/stga0faadd4-d822-4d83-a743-5688983bf88b/dqc_reference
[2023-06-08 05:13:50,279] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:13:50,283] [INFO] Task started: Prodigal
[2023-06-08 05:13:50,284] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c46fc2c-f85c-41e4-a094-a9bb526359f4/GCA_945897815.1_MoE-23oct19-15_genomic.fna.gz | prodigal -d GCA_945897815.1_MoE-23oct19-15_genomic.fna/cds.fna -a GCA_945897815.1_MoE-23oct19-15_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:14:02,099] [INFO] Task succeeded: Prodigal
[2023-06-08 05:14:02,099] [INFO] Task started: HMMsearch
[2023-06-08 05:14:02,100] [INFO] Running command: hmmsearch --tblout GCA_945897815.1_MoE-23oct19-15_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0faadd4-d822-4d83-a743-5688983bf88b/dqc_reference/reference_markers.hmm GCA_945897815.1_MoE-23oct19-15_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:14:02,416] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:14:02,417] [INFO] Found 6/6 markers.
[2023-06-08 05:14:02,451] [INFO] Query marker FASTA was written to GCA_945897815.1_MoE-23oct19-15_genomic.fna/markers.fasta
[2023-06-08 05:14:02,451] [INFO] Task started: Blastn
[2023-06-08 05:14:02,452] [INFO] Running command: blastn -query GCA_945897815.1_MoE-23oct19-15_genomic.fna/markers.fasta -db /var/lib/cwl/stga0faadd4-d822-4d83-a743-5688983bf88b/dqc_reference/reference_markers.fasta -out GCA_945897815.1_MoE-23oct19-15_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:14:03,271] [INFO] Task succeeded: Blastn
[2023-06-08 05:14:03,275] [INFO] Selected 35 target genomes.
[2023-06-08 05:14:03,276] [INFO] Target genome list was writen to GCA_945897815.1_MoE-23oct19-15_genomic.fna/target_genomes.txt
[2023-06-08 05:14:03,314] [INFO] Task started: fastANI
[2023-06-08 05:14:03,314] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c46fc2c-f85c-41e4-a094-a9bb526359f4/GCA_945897815.1_MoE-23oct19-15_genomic.fna.gz --refList GCA_945897815.1_MoE-23oct19-15_genomic.fna/target_genomes.txt --output GCA_945897815.1_MoE-23oct19-15_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:14:28,147] [INFO] Task succeeded: fastANI
[2023-06-08 05:14:28,148] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0faadd4-d822-4d83-a743-5688983bf88b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:14:28,148] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0faadd4-d822-4d83-a743-5688983bf88b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:14:28,160] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:14:28,160] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:14:28,161] [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 songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	76.2796	53	1117	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	76.0112	59	1117	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.9277	58	1117	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=NBRC 13583	GCA_002091815.1	1218129	301	type	True	75.8451	64	1117	95	below_threshold
Pseudomonas oleovorans	strain=NCTC10692	GCA_900455615.1	301	301	type	True	75.8227	65	1117	95	below_threshold
Pseudomonas japonica	strain=DSM 22348	GCA_900188455.1	256466	256466	type	True	75.8027	56	1117	95	below_threshold
Pseudomonas oleovorans subsp. oleovorans	strain=DSM 1045	GCA_002197815.1	1218129	301	type	True	75.8005	66	1117	95	below_threshold
Pseudomonas fakonensis	strain=COW40	GCA_019139895.1	2842355	2842355	type	True	75.7501	70	1117	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.7447	62	1117	95	below_threshold
Pseudomonas xanthosomae	strain=COR54	GCA_019139835.1	2842356	2842356	type	True	75.7373	70	1117	95	below_threshold
Pseudomonas bharatica	strain=CSV86	GCA_000319305.2	2692112	2692112	type	True	75.7302	69	1117	95	below_threshold
Marinobacter bohaiensis	strain=T17	GCA_003258515.1	2201898	2201898	type	True	75.7253	53	1117	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_021602465.1	2740517	2740517	suspected-type	True	75.6787	60	1117	95	below_threshold
Pseudomonas urethralis	strain=BML-PP042	GCA_013373915.1	2740517	2740517	suspected-type	True	75.6671	57	1117	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:14:28,163] [INFO] DFAST Taxonomy check result was written to GCA_945897815.1_MoE-23oct19-15_genomic.fna/tc_result.tsv
[2023-06-08 05:14:28,164] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:14:28,164] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:14:28,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0faadd4-d822-4d83-a743-5688983bf88b/dqc_reference/checkm_data
[2023-06-08 05:14:28,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:14:28,206] [INFO] Task started: CheckM
[2023-06-08 05:14:28,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945897815.1_MoE-23oct19-15_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945897815.1_MoE-23oct19-15_genomic.fna/checkm_input GCA_945897815.1_MoE-23oct19-15_genomic.fna/checkm_result
[2023-06-08 05:15:05,759] [INFO] Task succeeded: CheckM
[2023-06-08 05:15:05,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:15:05,780] [INFO] ===== Completeness check finished =====
[2023-06-08 05:15:05,780] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:15:05,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945897815.1_MoE-23oct19-15_genomic.fna/markers.fasta)
[2023-06-08 05:15:05,781] [INFO] Task started: Blastn
[2023-06-08 05:15:05,781] [INFO] Running command: blastn -query GCA_945897815.1_MoE-23oct19-15_genomic.fna/markers.fasta -db /var/lib/cwl/stga0faadd4-d822-4d83-a743-5688983bf88b/dqc_reference/reference_markers_gtdb.fasta -out GCA_945897815.1_MoE-23oct19-15_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:15:06,913] [INFO] Task succeeded: Blastn
[2023-06-08 05:15:06,918] [INFO] Selected 20 target genomes.
[2023-06-08 05:15:06,918] [INFO] Target genome list was writen to GCA_945897815.1_MoE-23oct19-15_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:15:06,969] [INFO] Task started: fastANI
[2023-06-08 05:15:06,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c46fc2c-f85c-41e4-a094-a9bb526359f4/GCA_945897815.1_MoE-23oct19-15_genomic.fna.gz --refList GCA_945897815.1_MoE-23oct19-15_genomic.fna/target_genomes_gtdb.txt --output GCA_945897815.1_MoE-23oct19-15_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:15:19,680] [INFO] Task succeeded: fastANI
[2023-06-08 05:15:19,693] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:15:19,693] [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	98.0561	880	1117	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_903837345.1	s__CAILUG01 sp903837345	78.1178	339	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	99.98	99.96	1.00	0.99	3	-
GCA_903853385.1	s__CAILUG01 sp903853385	77.7998	311	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	99.57	99.54	0.93	0.91	5	-
GCA_903926285.1	s__CAILUG01 sp903926285	76.3904	80	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudohongiellaceae;g__CAILUG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004801855.1	s__Pseudomonas_K sp004801855	76.2091	59	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	98.38	98.38	0.89	0.89	2	-
GCF_009189165.1	s__Pseudomonas sp009189165	76.0177	60	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	75.8855	62	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_013179515.1	s__Pseudomonas_E sp013179515	75.7592	55	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.93	98.93	0.82	0.82	2	-
GCF_000319305.2	s__Pseudomonas_E putida_C	75.7113	70	1117	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.35	97.35	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-08 05:15:19,695] [INFO] GTDB search result was written to GCA_945897815.1_MoE-23oct19-15_genomic.fna/result_gtdb.tsv
[2023-06-08 05:15:19,695] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:15:19,699] [INFO] DFAST_QC result json was written to GCA_945897815.1_MoE-23oct19-15_genomic.fna/dqc_result.json
[2023-06-08 05:15:19,699] [INFO] DFAST_QC completed!
[2023-06-08 05:15:19,699] [INFO] Total running time: 0h1m31s