[2024-01-24 12:14:49,554] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:49,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:49,556] [INFO] DQC Reference Directory: /var/lib/cwl/stgdd69590b-37ea-433e-b979-e0b6591a7369/dqc_reference
[2024-01-24 12:14:51,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:51,022] [INFO] Task started: Prodigal
[2024-01-24 12:14:51,022] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc55675b-7c38-45f9-b5bd-7dda1f0affe8/GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/cds.fna -a GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:55,131] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:55,131] [INFO] Task started: HMMsearch
[2024-01-24 12:14:55,131] [INFO] Running command: hmmsearch --tblout GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdd69590b-37ea-433e-b979-e0b6591a7369/dqc_reference/reference_markers.hmm GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:55,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:55,384] [INFO] Found 6/6 markers.
[2024-01-24 12:14:55,409] [INFO] Query marker FASTA was written to GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:14:55,409] [INFO] Task started: Blastn
[2024-01-24 12:14:55,409] [INFO] Running command: blastn -query GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd69590b-37ea-433e-b979-e0b6591a7369/dqc_reference/reference_markers.fasta -out GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:56,006] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:56,011] [INFO] Selected 25 target genomes.
[2024-01-24 12:14:56,011] [INFO] Target genome list was writen to GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:14:56,021] [INFO] Task started: fastANI
[2024-01-24 12:14:56,021] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc55675b-7c38-45f9-b5bd-7dda1f0affe8/GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna.gz --refList GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:06,865] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:06,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdd69590b-37ea-433e-b979-e0b6591a7369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:06,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdd69590b-37ea-433e-b979-e0b6591a7369/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:06,877] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:06,877] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:06,877] [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
Alkalibacterium gilvum	strain=DSM 25751	GCA_900109085.1	1130080	1130080	type	True	99.9957	678	682	95	conclusive
Alkalibacterium kapii	strain=NBRC 103247	GCA_007988865.1	426704	426704	type	True	80.5688	344	682	95	below_threshold
Alkalibacterium putridalgicola	strain=NBRC 103243	GCA_007988845.1	426703	426703	type	True	79.4918	216	682	95	below_threshold
Alkalibacterium putridalgicola	strain=DSM 19182	GCA_900109825.1	426703	426703	type	True	79.4382	214	682	95	below_threshold
Alkalibacterium subtropicum	strain=DSM 23664	GCA_900112455.1	753702	753702	type	True	79.3565	195	682	95	below_threshold
Alkalibacterium olivapovliticus	strain=DSM 13175	GCA_003003275.1	99907	99907	type	True	78.6478	91	682	95	below_threshold
Alkalibacterium thalassium	strain=DSM 19181	GCA_900101165.1	426701	426701	type	True	78.3875	87	682	95	below_threshold
Marinilactibacillus psychrotolerans	strain=M13-2T	GCA_019650195.1	191770	191770	type	True	77.1548	67	682	95	below_threshold
Marinilactibacillus psychrotolerans	strain=DSM 19582	GCA_900101525.1	191770	191770	type	True	77.0173	68	682	95	below_threshold
Marinilactibacillus psychrotolerans	strain=NBRC 100002	GCA_007989385.1	191770	191770	type	True	76.8857	64	682	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:06,878] [INFO] DFAST Taxonomy check result was written to GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:15:06,879] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:06,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:06,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdd69590b-37ea-433e-b979-e0b6591a7369/dqc_reference/checkm_data
[2024-01-24 12:15:06,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:06,915] [INFO] Task started: CheckM
[2024-01-24 12:15:06,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/checkm_input GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:15:28,045] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:28,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:28,071] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:28,071] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:28,072] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:15:28,072] [INFO] Task started: Blastn
[2024-01-24 12:15:28,073] [INFO] Running command: blastn -query GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdd69590b-37ea-433e-b979-e0b6591a7369/dqc_reference/reference_markers_gtdb.fasta -out GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:28,862] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:28,865] [INFO] Selected 23 target genomes.
[2024-01-24 12:15:28,865] [INFO] Target genome list was writen to GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:28,882] [INFO] Task started: fastANI
[2024-01-24 12:15:28,882] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc55675b-7c38-45f9-b5bd-7dda1f0affe8/GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna.gz --refList GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:37,810] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:37,826] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:37,826] [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_900109085.1	s__Alkalibacterium gilvum	99.9957	678	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.35	99.35	0.91	0.91	2	conclusive
GCF_007988865.1	s__Alkalibacterium kapii	80.5688	344	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109825.1	s__Alkalibacterium putridalgicola	79.4382	214	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900112455.1	s__Alkalibacterium subtropicum	79.3999	197	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169305.1	s__Marinilactibacillus piezotolerans_A	78.7478	68	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Marinilactibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003275.1	s__Alkalibacterium olivapovliticus	78.6734	91	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101165.1	s__Alkalibacterium thalassium	78.3875	87	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001885615.1	s__Alkalibacterium sp001885615	78.1339	163	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692455.1	s__Alkalibacterium sp007692455	77.5488	81	682	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Carnobacteriaceae;g__Alkalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:37,827] [INFO] GTDB search result was written to GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:37,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:37,849] [INFO] DFAST_QC result json was written to GCF_900109085.1_IMG-taxon_2616644817_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:15:37,850] [INFO] DFAST_QC completed!
[2024-01-24 12:15:37,850] [INFO] Total running time: 0h0m48s