[2024-01-25 19:45:21,034] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:21,036] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:21,036] [INFO] DQC Reference Directory: /var/lib/cwl/stgc82b4327-a322-47a7-98e5-7f3059e9c3c3/dqc_reference
[2024-01-25 19:45:22,214] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:22,215] [INFO] Task started: Prodigal
[2024-01-25 19:45:22,215] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e996bcb-28a1-41d2-b30a-b2591a8fb8ea/GCF_014196025.1_ASM1419602v1_genomic.fna.gz | prodigal -d GCF_014196025.1_ASM1419602v1_genomic.fna/cds.fna -a GCF_014196025.1_ASM1419602v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:30,681] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:30,682] [INFO] Task started: HMMsearch
[2024-01-25 19:45:30,682] [INFO] Running command: hmmsearch --tblout GCF_014196025.1_ASM1419602v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc82b4327-a322-47a7-98e5-7f3059e9c3c3/dqc_reference/reference_markers.hmm GCF_014196025.1_ASM1419602v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:30,910] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:30,911] [INFO] Found 6/6 markers.
[2024-01-25 19:45:30,942] [INFO] Query marker FASTA was written to GCF_014196025.1_ASM1419602v1_genomic.fna/markers.fasta
[2024-01-25 19:45:30,942] [INFO] Task started: Blastn
[2024-01-25 19:45:30,942] [INFO] Running command: blastn -query GCF_014196025.1_ASM1419602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc82b4327-a322-47a7-98e5-7f3059e9c3c3/dqc_reference/reference_markers.fasta -out GCF_014196025.1_ASM1419602v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:31,497] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:31,499] [INFO] Selected 16 target genomes.
[2024-01-25 19:45:31,499] [INFO] Target genome list was writen to GCF_014196025.1_ASM1419602v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:31,509] [INFO] Task started: fastANI
[2024-01-25 19:45:31,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e996bcb-28a1-41d2-b30a-b2591a8fb8ea/GCF_014196025.1_ASM1419602v1_genomic.fna.gz --refList GCF_014196025.1_ASM1419602v1_genomic.fna/target_genomes.txt --output GCF_014196025.1_ASM1419602v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:43,733] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:43,734] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc82b4327-a322-47a7-98e5-7f3059e9c3c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:43,734] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc82b4327-a322-47a7-98e5-7f3059e9c3c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:43,742] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:45:43,742] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:45:43,742] [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
Parageobacillus caldoxylosilyticus	strain=DSM 12041	GCA_014196025.1	81408	81408	type	True	100.0	1223	1225	95	conclusive
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	99.9594	1163	1225	95	conclusive
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	84.8429	821	1225	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	84.8175	813	1225	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	84.7781	818	1225	95	below_threshold
Parageobacillus thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	83.436	821	1225	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_000966225.1	1426	1426	type	True	83.4081	808	1225	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	83.3151	807	1225	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	76.6019	57	1225	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.253	61	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:43,743] [INFO] DFAST Taxonomy check result was written to GCF_014196025.1_ASM1419602v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:43,744] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:43,744] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:43,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc82b4327-a322-47a7-98e5-7f3059e9c3c3/dqc_reference/checkm_data
[2024-01-25 19:45:43,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:43,783] [INFO] Task started: CheckM
[2024-01-25 19:45:43,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196025.1_ASM1419602v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196025.1_ASM1419602v1_genomic.fna/checkm_input GCF_014196025.1_ASM1419602v1_genomic.fna/checkm_result
[2024-01-25 19:46:12,082] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:12,083] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:12,099] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:12,100] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:12,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196025.1_ASM1419602v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:12,101] [INFO] Task started: Blastn
[2024-01-25 19:46:12,101] [INFO] Running command: blastn -query GCF_014196025.1_ASM1419602v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc82b4327-a322-47a7-98e5-7f3059e9c3c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196025.1_ASM1419602v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:12,891] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:12,894] [INFO] Selected 9 target genomes.
[2024-01-25 19:46:12,894] [INFO] Target genome list was writen to GCF_014196025.1_ASM1419602v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:12,901] [INFO] Task started: fastANI
[2024-01-25 19:46:12,901] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e996bcb-28a1-41d2-b30a-b2591a8fb8ea/GCF_014196025.1_ASM1419602v1_genomic.fna.gz --refList GCF_014196025.1_ASM1419602v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196025.1_ASM1419602v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:20,677] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:20,682] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:20,683] [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_000632715.1	s__Saccharococcus caldoxylosilyticus	99.9594	1163	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	conclusive
GCF_000632515.1	s__Saccharococcus sp000632515	91.8897	927	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761475.1	s__Saccharococcus thermophilus	89.9988	810	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688615.2	s__Parageobacillus toebii	84.8231	823	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_001655645.1	s__Parageobacillus thermoglucosidasius_A	84.2467	861	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111865.1	s__Parageobacillus thermantarcticus	83.3187	768	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295365.1	s__Parageobacillus thermoglucosidasius	83.3133	808	1225	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:20,684] [INFO] GTDB search result was written to GCF_014196025.1_ASM1419602v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:20,684] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:20,687] [INFO] DFAST_QC result json was written to GCF_014196025.1_ASM1419602v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:20,687] [INFO] DFAST_QC completed!
[2024-01-25 19:46:20,687] [INFO] Total running time: 0h0m60s