[2024-01-25 17:53:50,606] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:53:50,608] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:53:50,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg44878c0b-a64c-4488-b3c0-a8f15334001c/dqc_reference
[2024-01-25 17:53:51,974] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:53:51,975] [INFO] Task started: Prodigal
[2024-01-25 17:53:51,975] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a2bd182-7d4a-445e-be98-c195af548fb8/GCF_025574485.1_ASM2557448v1_genomic.fna.gz | prodigal -d GCF_025574485.1_ASM2557448v1_genomic.fna/cds.fna -a GCF_025574485.1_ASM2557448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:01,268] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:01,269] [INFO] Task started: HMMsearch
[2024-01-25 17:54:01,269] [INFO] Running command: hmmsearch --tblout GCF_025574485.1_ASM2557448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44878c0b-a64c-4488-b3c0-a8f15334001c/dqc_reference/reference_markers.hmm GCF_025574485.1_ASM2557448v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:01,511] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:01,512] [INFO] Found 6/6 markers.
[2024-01-25 17:54:01,541] [INFO] Query marker FASTA was written to GCF_025574485.1_ASM2557448v1_genomic.fna/markers.fasta
[2024-01-25 17:54:01,541] [INFO] Task started: Blastn
[2024-01-25 17:54:01,542] [INFO] Running command: blastn -query GCF_025574485.1_ASM2557448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44878c0b-a64c-4488-b3c0-a8f15334001c/dqc_reference/reference_markers.fasta -out GCF_025574485.1_ASM2557448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:02,136] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:02,139] [INFO] Selected 25 target genomes.
[2024-01-25 17:54:02,140] [INFO] Target genome list was writen to GCF_025574485.1_ASM2557448v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:02,147] [INFO] Task started: fastANI
[2024-01-25 17:54:02,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a2bd182-7d4a-445e-be98-c195af548fb8/GCF_025574485.1_ASM2557448v1_genomic.fna.gz --refList GCF_025574485.1_ASM2557448v1_genomic.fna/target_genomes.txt --output GCF_025574485.1_ASM2557448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:54:15,403] [INFO] Task succeeded: fastANI
[2024-01-25 17:54:15,403] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44878c0b-a64c-4488-b3c0-a8f15334001c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:54:15,404] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44878c0b-a64c-4488-b3c0-a8f15334001c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:54:15,409] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:54:15,409] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:54:15,409] [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
Kordiimonas lacus	strain=S3-22	GCA_001550055.1	637679	637679	type	True	78.2329	61	1257	95	below_threshold
Kordiimonas lipolytica	strain=M41	GCA_001550065.1	1662421	1662421	type	True	77.7073	53	1257	95	below_threshold
Kordiimonas pumila	strain=N18	GCA_015240255.1	2161677	2161677	type	True	77.6905	75	1257	95	below_threshold
Kordiimonas lacus	strain=CGMCC 1.9109	GCA_900101935.1	637679	637679	type	True	77.3419	55	1257	95	below_threshold
Kordiimonas laminariae	strain=5E331	GCA_023008165.1	2917717	2917717	type	True	76.9471	83	1257	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:54:15,410] [INFO] DFAST Taxonomy check result was written to GCF_025574485.1_ASM2557448v1_genomic.fna/tc_result.tsv
[2024-01-25 17:54:15,411] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:54:15,411] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:54:15,411] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44878c0b-a64c-4488-b3c0-a8f15334001c/dqc_reference/checkm_data
[2024-01-25 17:54:15,412] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:54:15,449] [INFO] Task started: CheckM
[2024-01-25 17:54:15,450] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025574485.1_ASM2557448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025574485.1_ASM2557448v1_genomic.fna/checkm_input GCF_025574485.1_ASM2557448v1_genomic.fna/checkm_result
[2024-01-25 17:54:45,712] [INFO] Task succeeded: CheckM
[2024-01-25 17:54:45,713] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:54:45,734] [INFO] ===== Completeness check finished =====
[2024-01-25 17:54:45,734] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:54:45,734] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025574485.1_ASM2557448v1_genomic.fna/markers.fasta)
[2024-01-25 17:54:45,734] [INFO] Task started: Blastn
[2024-01-25 17:54:45,734] [INFO] Running command: blastn -query GCF_025574485.1_ASM2557448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44878c0b-a64c-4488-b3c0-a8f15334001c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025574485.1_ASM2557448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:46,742] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:46,746] [INFO] Selected 27 target genomes.
[2024-01-25 17:54:46,746] [INFO] Target genome list was writen to GCF_025574485.1_ASM2557448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:54:46,771] [INFO] Task started: fastANI
[2024-01-25 17:54:46,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a2bd182-7d4a-445e-be98-c195af548fb8/GCF_025574485.1_ASM2557448v1_genomic.fna.gz --refList GCF_025574485.1_ASM2557448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025574485.1_ASM2557448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:55:00,110] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:00,115] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:55:00,115] [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_001550055.1	s__Kordiimonas lacus	78.5748	63	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	98.68	97.35	0.95	0.90	3	-
GCF_001550065.1	s__Kordiimonas lipolytica	78.007	54	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015240255.1	s__Kordiimonas pumila	77.6905	75	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011088215.1	s__Kordiimonas sp011088215	76.8828	105	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640725.1	s__Kordiimonas sp017640725	76.7501	113	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	100.00	100.00	0.99	0.98	3	-
GCA_015485385.1	s__Kordiimonas sp015485385	76.4679	65	1257	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Kordiimonadaceae;g__Kordiimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:55:00,117] [INFO] GTDB search result was written to GCF_025574485.1_ASM2557448v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:55:00,117] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:55:00,119] [INFO] DFAST_QC result json was written to GCF_025574485.1_ASM2557448v1_genomic.fna/dqc_result.json
[2024-01-25 17:55:00,119] [INFO] DFAST_QC completed!
[2024-01-25 17:55:00,119] [INFO] Total running time: 0h1m10s