[2023-06-18 20:56:23,460] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:23,464] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:23,464] [INFO] DQC Reference Directory: /var/lib/cwl/stgc295cb70-bf68-4fe4-a34c-7dde2febb7b9/dqc_reference
[2023-06-18 20:56:24,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:24,767] [INFO] Task started: Prodigal
[2023-06-18 20:56:24,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg29404912-86c6-45d8-808b-1ac3aadaa07a/GCA_018677335.1_ASM1867733v1_genomic.fna.gz | prodigal -d GCA_018677335.1_ASM1867733v1_genomic.fna/cds.fna -a GCA_018677335.1_ASM1867733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:32,421] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:32,422] [INFO] Task started: HMMsearch
[2023-06-18 20:56:32,422] [INFO] Running command: hmmsearch --tblout GCA_018677335.1_ASM1867733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc295cb70-bf68-4fe4-a34c-7dde2febb7b9/dqc_reference/reference_markers.hmm GCA_018677335.1_ASM1867733v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:32,672] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:32,674] [INFO] Found 6/6 markers.
[2023-06-18 20:56:32,704] [INFO] Query marker FASTA was written to GCA_018677335.1_ASM1867733v1_genomic.fna/markers.fasta
[2023-06-18 20:56:32,705] [INFO] Task started: Blastn
[2023-06-18 20:56:32,705] [INFO] Running command: blastn -query GCA_018677335.1_ASM1867733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc295cb70-bf68-4fe4-a34c-7dde2febb7b9/dqc_reference/reference_markers.fasta -out GCA_018677335.1_ASM1867733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:33,430] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:33,434] [INFO] Selected 30 target genomes.
[2023-06-18 20:56:33,435] [INFO] Target genome list was writen to GCA_018677335.1_ASM1867733v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:33,438] [INFO] Task started: fastANI
[2023-06-18 20:56:33,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg29404912-86c6-45d8-808b-1ac3aadaa07a/GCA_018677335.1_ASM1867733v1_genomic.fna.gz --refList GCA_018677335.1_ASM1867733v1_genomic.fna/target_genomes.txt --output GCA_018677335.1_ASM1867733v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:54,159] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:54,160] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc295cb70-bf68-4fe4-a34c-7dde2febb7b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:54,160] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc295cb70-bf68-4fe4-a34c-7dde2febb7b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:54,164] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 20:56:54,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 20:56:54,164] [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
Woeseia oceani	strain=XK5	GCA_001677435.1	1548547	1548547	type	True	76.8898	104	862	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:56:54,166] [INFO] DFAST Taxonomy check result was written to GCA_018677335.1_ASM1867733v1_genomic.fna/tc_result.tsv
[2023-06-18 20:56:54,167] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:54,167] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:54,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc295cb70-bf68-4fe4-a34c-7dde2febb7b9/dqc_reference/checkm_data
[2023-06-18 20:56:54,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:54,203] [INFO] Task started: CheckM
[2023-06-18 20:56:54,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018677335.1_ASM1867733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018677335.1_ASM1867733v1_genomic.fna/checkm_input GCA_018677335.1_ASM1867733v1_genomic.fna/checkm_result
[2023-06-18 20:57:22,710] [INFO] Task succeeded: CheckM
[2023-06-18 20:57:22,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 2.04%
Strain heterogeneity: 80.00%
--------------------------------------------------------------------------------
[2023-06-18 20:57:22,738] [INFO] ===== Completeness check finished =====
[2023-06-18 20:57:22,738] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:57:22,738] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018677335.1_ASM1867733v1_genomic.fna/markers.fasta)
[2023-06-18 20:57:22,739] [INFO] Task started: Blastn
[2023-06-18 20:57:22,739] [INFO] Running command: blastn -query GCA_018677335.1_ASM1867733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc295cb70-bf68-4fe4-a34c-7dde2febb7b9/dqc_reference/reference_markers_gtdb.fasta -out GCA_018677335.1_ASM1867733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:57:23,977] [INFO] Task succeeded: Blastn
[2023-06-18 20:57:23,983] [INFO] Selected 22 target genomes.
[2023-06-18 20:57:23,983] [INFO] Target genome list was writen to GCA_018677335.1_ASM1867733v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:57:23,992] [INFO] Task started: fastANI
[2023-06-18 20:57:23,993] [INFO] Running command: fastANI --query /var/lib/cwl/stg29404912-86c6-45d8-808b-1ac3aadaa07a/GCA_018677335.1_ASM1867733v1_genomic.fna.gz --refList GCA_018677335.1_ASM1867733v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018677335.1_ASM1867733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:57:36,074] [INFO] Task succeeded: fastANI
[2023-06-18 20:57:36,086] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:57:36,086] [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_013003155.1	s__Woeseia sp013003155	99.4173	682	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	99.53	99.50	0.81	0.79	4	conclusive
GCF_001677435.1	s__Woeseia oceani	76.8898	104	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__Woeseia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002338615.1	s__UBA1844 sp002338615	76.1585	52	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1844	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004282875.1	s__UBA1847 sp004282875	75.9777	60	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__UBA1847	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018677555.1	s__IDS-8 sp018677555	75.9757	69	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__IDS-8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937525.1	s__JAACFE01 sp009937525	75.6298	56	862	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Woeseiales;f__Woeseiaceae;g__JAACFE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:57:36,088] [INFO] GTDB search result was written to GCA_018677335.1_ASM1867733v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:57:36,089] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:57:36,098] [INFO] DFAST_QC result json was written to GCA_018677335.1_ASM1867733v1_genomic.fna/dqc_result.json
[2023-06-18 20:57:36,098] [INFO] DFAST_QC completed!
[2023-06-18 20:57:36,098] [INFO] Total running time: 0h1m13s