[2024-01-25 19:32:35,993] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:32:35,995] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:32:35,995] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f407377-5753-47b0-8bdc-e3c666f22177/dqc_reference
[2024-01-25 19:32:37,152] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:32:37,153] [INFO] Task started: Prodigal
[2024-01-25 19:32:37,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg43e5fda0-cafe-47a7-92ee-feb3d6463ca1/GCF_024346955.1_ASM2434695v1_genomic.fna.gz | prodigal -d GCF_024346955.1_ASM2434695v1_genomic.fna/cds.fna -a GCF_024346955.1_ASM2434695v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:32:49,100] [INFO] Task succeeded: Prodigal
[2024-01-25 19:32:49,100] [INFO] Task started: HMMsearch
[2024-01-25 19:32:49,100] [INFO] Running command: hmmsearch --tblout GCF_024346955.1_ASM2434695v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f407377-5753-47b0-8bdc-e3c666f22177/dqc_reference/reference_markers.hmm GCF_024346955.1_ASM2434695v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:32:49,382] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:32:49,384] [INFO] Found 6/6 markers.
[2024-01-25 19:32:49,424] [INFO] Query marker FASTA was written to GCF_024346955.1_ASM2434695v1_genomic.fna/markers.fasta
[2024-01-25 19:32:49,424] [INFO] Task started: Blastn
[2024-01-25 19:32:49,424] [INFO] Running command: blastn -query GCF_024346955.1_ASM2434695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f407377-5753-47b0-8bdc-e3c666f22177/dqc_reference/reference_markers.fasta -out GCF_024346955.1_ASM2434695v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:32:50,157] [INFO] Task succeeded: Blastn
[2024-01-25 19:32:50,159] [INFO] Selected 10 target genomes.
[2024-01-25 19:32:50,160] [INFO] Target genome list was writen to GCF_024346955.1_ASM2434695v1_genomic.fna/target_genomes.txt
[2024-01-25 19:32:50,167] [INFO] Task started: fastANI
[2024-01-25 19:32:50,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e5fda0-cafe-47a7-92ee-feb3d6463ca1/GCF_024346955.1_ASM2434695v1_genomic.fna.gz --refList GCF_024346955.1_ASM2434695v1_genomic.fna/target_genomes.txt --output GCF_024346955.1_ASM2434695v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:33:00,218] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:00,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f407377-5753-47b0-8bdc-e3c666f22177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:33:00,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f407377-5753-47b0-8bdc-e3c666f22177/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:33:00,226] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:33:00,226] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:33:00,226] [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
Vibrio mangrovi	strain=CECT 7927	GCA_024346955.1	474394	474394	type	True	100.0	1665	1668	95	conclusive
Vibrio mangrovi	strain=CECT 7927	GCA_900184095.1	474394	474394	type	True	99.9889	1632	1668	95	conclusive
Vibrio ruber	strain=CECT 7878	GCA_900163965.1	184755	184755	type	True	81.7348	862	1668	95	below_threshold
Vibrio gazogenes	strain=PB1	GCA_023920225.1	687	687	type	True	81.6312	893	1668	95	below_threshold
Vibrio gazogenes	strain=ATCC 29988	GCA_024346915.1	687	687	type	True	81.5813	894	1668	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_024347135.1	1918945	1918945	type	True	81.4984	940	1668	95	below_threshold
Vibrio rhizosphaerae	strain=LMG 23790	GCA_024347095.1	398736	398736	type	True	81.4872	883	1668	95	below_threshold
Vibrio spartinae	strain=CECT 9026	GCA_900149295.1	1918945	1918945	type	True	81.4473	902	1668	95	below_threshold
Vibrio rhizosphaerae	strain=DSM 18581	GCA_000711805.1	398736	398736	type	True	81.2341	887	1668	95	below_threshold
Vibrio gazogenes	strain=type strain: CECT 5068	GCA_900163915.1	687	687	type	True	81.0458	706	1668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:33:00,228] [INFO] DFAST Taxonomy check result was written to GCF_024346955.1_ASM2434695v1_genomic.fna/tc_result.tsv
[2024-01-25 19:33:00,229] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:33:00,229] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:33:00,229] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f407377-5753-47b0-8bdc-e3c666f22177/dqc_reference/checkm_data
[2024-01-25 19:33:00,230] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:33:00,278] [INFO] Task started: CheckM
[2024-01-25 19:33:00,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024346955.1_ASM2434695v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024346955.1_ASM2434695v1_genomic.fna/checkm_input GCF_024346955.1_ASM2434695v1_genomic.fna/checkm_result
[2024-01-25 19:33:41,906] [INFO] Task succeeded: CheckM
[2024-01-25 19:33:41,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:33:41,928] [INFO] ===== Completeness check finished =====
[2024-01-25 19:33:41,928] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:33:41,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024346955.1_ASM2434695v1_genomic.fna/markers.fasta)
[2024-01-25 19:33:41,931] [INFO] Task started: Blastn
[2024-01-25 19:33:41,931] [INFO] Running command: blastn -query GCF_024346955.1_ASM2434695v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f407377-5753-47b0-8bdc-e3c666f22177/dqc_reference/reference_markers_gtdb.fasta -out GCF_024346955.1_ASM2434695v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:43,005] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:43,009] [INFO] Selected 7 target genomes.
[2024-01-25 19:33:43,009] [INFO] Target genome list was writen to GCF_024346955.1_ASM2434695v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:33:43,012] [INFO] Task started: fastANI
[2024-01-25 19:33:43,012] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e5fda0-cafe-47a7-92ee-feb3d6463ca1/GCF_024346955.1_ASM2434695v1_genomic.fna.gz --refList GCF_024346955.1_ASM2434695v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024346955.1_ASM2434695v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:33:50,529] [INFO] Task succeeded: fastANI
[2024-01-25 19:33:50,534] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:33:50,535] [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_900184095.1	s__Vibrio mangrovi	99.9889	1632	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001506075.1	s__Vibrio sp001506075	81.9065	908	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900163965.1	s__Vibrio ruber	81.696	868	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002196515.1	s__Vibrio gazogenes_A	81.5454	867	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900149295.1	s__Vibrio spartinae	81.4492	901	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.28	99.28	0.90	0.90	2	-
GCF_900129185.1	s__Vibrio gazogenes	81.4154	867	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.97	99.97	0.98	0.98	2	-
GCF_000711805.1	s__Vibrio rhizosphaerae	81.2333	887	1668	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:33:50,536] [INFO] GTDB search result was written to GCF_024346955.1_ASM2434695v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:33:50,539] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:33:50,541] [INFO] DFAST_QC result json was written to GCF_024346955.1_ASM2434695v1_genomic.fna/dqc_result.json
[2024-01-25 19:33:50,542] [INFO] DFAST_QC completed!
[2024-01-25 19:33:50,542] [INFO] Total running time: 0h1m15s