[2024-01-24 11:26:20,962] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:20,964] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:20,964] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ecaa6c3-e04b-4f74-b47c-9d7abe2c12e3/dqc_reference
[2024-01-24 11:26:22,193] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:22,194] [INFO] Task started: Prodigal
[2024-01-24 11:26:22,194] [INFO] Running command: gunzip -c /var/lib/cwl/stg65ceec8a-45d7-4d76-826e-83565d49d24c/GCF_011761475.1_ASM1176147v1_genomic.fna.gz | prodigal -d GCF_011761475.1_ASM1176147v1_genomic.fna/cds.fna -a GCF_011761475.1_ASM1176147v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:30,673] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:30,673] [INFO] Task started: HMMsearch
[2024-01-24 11:26:30,674] [INFO] Running command: hmmsearch --tblout GCF_011761475.1_ASM1176147v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ecaa6c3-e04b-4f74-b47c-9d7abe2c12e3/dqc_reference/reference_markers.hmm GCF_011761475.1_ASM1176147v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:31,004] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:31,006] [INFO] Found 6/6 markers.
[2024-01-24 11:26:31,036] [INFO] Query marker FASTA was written to GCF_011761475.1_ASM1176147v1_genomic.fna/markers.fasta
[2024-01-24 11:26:31,036] [INFO] Task started: Blastn
[2024-01-24 11:26:31,036] [INFO] Running command: blastn -query GCF_011761475.1_ASM1176147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ecaa6c3-e04b-4f74-b47c-9d7abe2c12e3/dqc_reference/reference_markers.fasta -out GCF_011761475.1_ASM1176147v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:31,625] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:31,629] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:31,630] [INFO] Target genome list was writen to GCF_011761475.1_ASM1176147v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:31,644] [INFO] Task started: fastANI
[2024-01-24 11:26:31,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg65ceec8a-45d7-4d76-826e-83565d49d24c/GCF_011761475.1_ASM1176147v1_genomic.fna.gz --refList GCF_011761475.1_ASM1176147v1_genomic.fna/target_genomes.txt --output GCF_011761475.1_ASM1176147v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:43,832] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:43,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ecaa6c3-e04b-4f74-b47c-9d7abe2c12e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:43,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ecaa6c3-e04b-4f74-b47c-9d7abe2c12e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:43,848] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:43,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:43,848] [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	90.1934	805	1047	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	90.1366	792	1047	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	85.3255	765	1047	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	85.0681	740	1047	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	84.9704	748	1047	95	below_threshold
Parageobacillus thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	83.342	721	1047	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	83.2366	710	1047	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_000966225.1	1426	1426	type	True	82.991	695	1047	95	below_threshold
Parageobacillus thermantarcticus	strain=M1	GCA_900111865.1	186116	186116	type	True	82.9293	668	1047	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	80.1883	55	1047	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	79.3457	54	1047	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	77.9004	184	1047	95	below_threshold
Anoxybacillus kamchatkensis	strain=DSM 14988	GCA_013761015.1	196180	196180	type	True	77.4438	186	1047	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	76.4799	50	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:43,850] [INFO] DFAST Taxonomy check result was written to GCF_011761475.1_ASM1176147v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:43,851] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:43,851] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:43,851] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ecaa6c3-e04b-4f74-b47c-9d7abe2c12e3/dqc_reference/checkm_data
[2024-01-24 11:26:43,852] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:43,882] [INFO] Task started: CheckM
[2024-01-24 11:26:43,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011761475.1_ASM1176147v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011761475.1_ASM1176147v1_genomic.fna/checkm_input GCF_011761475.1_ASM1176147v1_genomic.fna/checkm_result
[2024-01-24 11:27:14,674] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:14,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:14,693] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:14,694] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:14,694] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011761475.1_ASM1176147v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:14,695] [INFO] Task started: Blastn
[2024-01-24 11:27:14,695] [INFO] Running command: blastn -query GCF_011761475.1_ASM1176147v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ecaa6c3-e04b-4f74-b47c-9d7abe2c12e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_011761475.1_ASM1176147v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:15,490] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:15,493] [INFO] Selected 8 target genomes.
[2024-01-24 11:27:15,494] [INFO] Target genome list was writen to GCF_011761475.1_ASM1176147v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:15,523] [INFO] Task started: fastANI
[2024-01-24 11:27:15,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg65ceec8a-45d7-4d76-826e-83565d49d24c/GCF_011761475.1_ASM1176147v1_genomic.fna.gz --refList GCF_011761475.1_ASM1176147v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011761475.1_ASM1176147v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:24,287] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:24,300] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:24,301] [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_011761475.1	s__Saccharococcus thermophilus	100.0	1046	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000632515.1	s__Saccharococcus sp000632515	90.3824	843	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632715.1	s__Saccharococcus caldoxylosilyticus	90.1366	792	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	-
GCF_003688615.2	s__Parageobacillus toebii	85.3342	768	1047	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	83.225	692	1047	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	83.2075	709	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
GCF_900111865.1	s__Parageobacillus thermantarcticus	82.9169	671	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:24,303] [INFO] GTDB search result was written to GCF_011761475.1_ASM1176147v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:24,304] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:24,309] [INFO] DFAST_QC result json was written to GCF_011761475.1_ASM1176147v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:24,309] [INFO] DFAST_QC completed!
[2024-01-24 11:27:24,309] [INFO] Total running time: 0h1m3s