[2024-01-24 15:18:19,632] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:19,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:19,634] [INFO] DQC Reference Directory: /var/lib/cwl/stge726de68-fbf8-41f5-b11a-9cffe3c8afc7/dqc_reference
[2024-01-24 15:18:20,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,884] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c455b67-f88e-4d1e-ab9c-2f9735c1ed66/GCF_009660035.1_ASM966003v1_genomic.fna.gz | prodigal -d GCF_009660035.1_ASM966003v1_genomic.fna/cds.fna -a GCF_009660035.1_ASM966003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:32,404] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:32,405] [INFO] Task started: HMMsearch
[2024-01-24 15:18:32,405] [INFO] Running command: hmmsearch --tblout GCF_009660035.1_ASM966003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge726de68-fbf8-41f5-b11a-9cffe3c8afc7/dqc_reference/reference_markers.hmm GCF_009660035.1_ASM966003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:32,663] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:32,664] [INFO] Found 6/6 markers.
[2024-01-24 15:18:32,700] [INFO] Query marker FASTA was written to GCF_009660035.1_ASM966003v1_genomic.fna/markers.fasta
[2024-01-24 15:18:32,700] [INFO] Task started: Blastn
[2024-01-24 15:18:32,700] [INFO] Running command: blastn -query GCF_009660035.1_ASM966003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge726de68-fbf8-41f5-b11a-9cffe3c8afc7/dqc_reference/reference_markers.fasta -out GCF_009660035.1_ASM966003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:33,506] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:33,509] [INFO] Selected 11 target genomes.
[2024-01-24 15:18:33,509] [INFO] Target genome list was writen to GCF_009660035.1_ASM966003v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:33,514] [INFO] Task started: fastANI
[2024-01-24 15:18:33,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c455b67-f88e-4d1e-ab9c-2f9735c1ed66/GCF_009660035.1_ASM966003v1_genomic.fna.gz --refList GCF_009660035.1_ASM966003v1_genomic.fna/target_genomes.txt --output GCF_009660035.1_ASM966003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:42,541] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:42,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge726de68-fbf8-41f5-b11a-9cffe3c8afc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:42,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge726de68-fbf8-41f5-b11a-9cffe3c8afc7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:42,555] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:42,555] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:42,555] [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
Halomonas piezotolerans	strain=NBT06E8	GCA_009660035.1	2609667	2609667	type	True	100.0	1285	1288	95	conclusive
Halomonas piezotolerans	strain=NBT06E8	GCA_012427705.1	2609667	2609667	type	True	99.9957	1279	1288	95	conclusive
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	87.5064	843	1288	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	87.4928	828	1288	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	87.4186	881	1288	95	below_threshold
Halomonas lutescens	strain=CGMCC 1.15122	GCA_014640815.1	1602943	1602943	type	True	84.544	956	1288	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	79.3593	444	1288	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	79.2896	448	1288	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.2787	346	1288	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	78.2594	306	1288	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.7808	287	1288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:42,557] [INFO] DFAST Taxonomy check result was written to GCF_009660035.1_ASM966003v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:42,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:42,557] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:42,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge726de68-fbf8-41f5-b11a-9cffe3c8afc7/dqc_reference/checkm_data
[2024-01-24 15:18:42,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:42,596] [INFO] Task started: CheckM
[2024-01-24 15:18:42,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009660035.1_ASM966003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009660035.1_ASM966003v1_genomic.fna/checkm_input GCF_009660035.1_ASM966003v1_genomic.fna/checkm_result
[2024-01-24 15:19:20,298] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:20,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:20,323] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:20,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:20,324] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009660035.1_ASM966003v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:20,324] [INFO] Task started: Blastn
[2024-01-24 15:19:20,324] [INFO] Running command: blastn -query GCF_009660035.1_ASM966003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge726de68-fbf8-41f5-b11a-9cffe3c8afc7/dqc_reference/reference_markers_gtdb.fasta -out GCF_009660035.1_ASM966003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:21,701] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:21,705] [INFO] Selected 8 target genomes.
[2024-01-24 15:19:21,706] [INFO] Target genome list was writen to GCF_009660035.1_ASM966003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:21,712] [INFO] Task started: fastANI
[2024-01-24 15:19:21,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c455b67-f88e-4d1e-ab9c-2f9735c1ed66/GCF_009660035.1_ASM966003v1_genomic.fna.gz --refList GCF_009660035.1_ASM966003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009660035.1_ASM966003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:28,499] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:28,511] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:28,511] [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
GCF_012427705.1	s__Halomonas piezotolerans	99.9957	1279	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	conclusive
GCF_009846525.1	s__Halomonas sp002696125	87.9907	1029	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_900110265.1	s__Halomonas aquamarina	87.4955	828	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_002087295.1	s__Halomonas lionensis	85.3016	850	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640815.1	s__Halomonas lutescens	84.5432	955	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651775.1	s__Halomonas hamiltonii	83.0445	801	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	98.09	97.51	0.90	0.88	5	-
GCF_000275725.1	s__Halomonas stevensii	82.885	769	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.843	97.33	97.21	0.85	0.83	5	-
GCF_003002925.1	s__Halomonas songnenensis	80.0945	588	1288	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:28,518] [INFO] GTDB search result was written to GCF_009660035.1_ASM966003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:28,520] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:28,524] [INFO] DFAST_QC result json was written to GCF_009660035.1_ASM966003v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:28,525] [INFO] DFAST_QC completed!
[2024-01-24 15:19:28,525] [INFO] Total running time: 0h1m9s