[2024-01-24 14:06:29,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:29,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:29,150] [INFO] DQC Reference Directory: /var/lib/cwl/stg98d455f2-99d5-4457-a035-a3f625b6d194/dqc_reference
[2024-01-24 14:06:30,415] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:30,416] [INFO] Task started: Prodigal
[2024-01-24 14:06:30,416] [INFO] Running command: gunzip -c /var/lib/cwl/stg26056fad-d1aa-4259-a496-4d97c09a5a9c/GCF_004341205.1_ASM434120v1_genomic.fna.gz | prodigal -d GCF_004341205.1_ASM434120v1_genomic.fna/cds.fna -a GCF_004341205.1_ASM434120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:37,461] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:37,461] [INFO] Task started: HMMsearch
[2024-01-24 14:06:37,462] [INFO] Running command: hmmsearch --tblout GCF_004341205.1_ASM434120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98d455f2-99d5-4457-a035-a3f625b6d194/dqc_reference/reference_markers.hmm GCF_004341205.1_ASM434120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:37,771] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:37,772] [INFO] Found 6/6 markers.
[2024-01-24 14:06:37,804] [INFO] Query marker FASTA was written to GCF_004341205.1_ASM434120v1_genomic.fna/markers.fasta
[2024-01-24 14:06:37,804] [INFO] Task started: Blastn
[2024-01-24 14:06:37,804] [INFO] Running command: blastn -query GCF_004341205.1_ASM434120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98d455f2-99d5-4457-a035-a3f625b6d194/dqc_reference/reference_markers.fasta -out GCF_004341205.1_ASM434120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:38,406] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:38,410] [INFO] Selected 28 target genomes.
[2024-01-24 14:06:38,410] [INFO] Target genome list was writen to GCF_004341205.1_ASM434120v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:38,423] [INFO] Task started: fastANI
[2024-01-24 14:06:38,423] [INFO] Running command: fastANI --query /var/lib/cwl/stg26056fad-d1aa-4259-a496-4d97c09a5a9c/GCF_004341205.1_ASM434120v1_genomic.fna.gz --refList GCF_004341205.1_ASM434120v1_genomic.fna/target_genomes.txt --output GCF_004341205.1_ASM434120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:53,591] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:53,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98d455f2-99d5-4457-a035-a3f625b6d194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:53,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98d455f2-99d5-4457-a035-a3f625b6d194/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:53,614] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:53,614] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:53,614] [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
Anoxybacillus calidus	strain=DSM 25220	GCA_013760845.1	575178	575178	type	True	79.9615	390	944	95	below_threshold
Anoxybacillus karvacharensis	strain=K1	GCA_001996285.1	1919277	1919277	type	True	79.7061	388	944	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_001187595.1	198467	198467	suspected-type	True	79.354	413	944	95	below_threshold
Anoxybacillus kamchatkensis	strain=DSM 14988	GCA_013761015.1	196180	196180	type	True	79.2878	386	944	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	79.2472	417	944	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	79.2374	367	944	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	79.2016	301	944	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	79.1923	302	944	95	below_threshold
Anoxybacillus mongoliensis	strain=DSM 19169	GCA_014201515.1	452565	452565	type	True	79.1536	372	944	95	below_threshold
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	79.1133	302	944	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	79.0796	389	944	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001418025.1	1325335	1325335	type	True	79.0214	390	944	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001517225.1	1325335	1325335	type	True	79.0214	390	944	95	below_threshold
Anoxybacillus tengchongensis	strain=DSM 23211	GCA_014201585.1	576944	576944	type	True	78.9346	406	944	95	below_threshold
Parageobacillus thermantarcticus	strain=M1	GCA_900111865.1	186116	186116	type	True	78.5189	273	944	95	below_threshold
Parageobacillus thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	78.4716	289	944	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	78.4704	288	944	95	below_threshold
Anoxybacillus voinovskiensis	strain=DSM 17075	GCA_014196205.1	230470	230470	type	True	77.8978	285	944	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	76.615	77	944	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	76.3076	63	944	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:53,616] [INFO] DFAST Taxonomy check result was written to GCF_004341205.1_ASM434120v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:53,616] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:53,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:53,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98d455f2-99d5-4457-a035-a3f625b6d194/dqc_reference/checkm_data
[2024-01-24 14:06:53,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:53,646] [INFO] Task started: CheckM
[2024-01-24 14:06:53,647] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341205.1_ASM434120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341205.1_ASM434120v1_genomic.fna/checkm_input GCF_004341205.1_ASM434120v1_genomic.fna/checkm_result
[2024-01-24 14:07:21,128] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:21,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:21,152] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:21,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:21,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341205.1_ASM434120v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:21,153] [INFO] Task started: Blastn
[2024-01-24 14:07:21,153] [INFO] Running command: blastn -query GCF_004341205.1_ASM434120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98d455f2-99d5-4457-a035-a3f625b6d194/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341205.1_ASM434120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:21,939] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:21,943] [INFO] Selected 21 target genomes.
[2024-01-24 14:07:21,943] [INFO] Target genome list was writen to GCF_004341205.1_ASM434120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:21,961] [INFO] Task started: fastANI
[2024-01-24 14:07:21,961] [INFO] Running command: fastANI --query /var/lib/cwl/stg26056fad-d1aa-4259-a496-4d97c09a5a9c/GCF_004341205.1_ASM434120v1_genomic.fna.gz --refList GCF_004341205.1_ASM434120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341205.1_ASM434120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:35,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:35,745] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:35,745] [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_004341205.1	s__Thermolongibacillus altinsuensis	100.0	943	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Thermolongibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_013760845.1	s__Anoxybacillus_B calidus	79.9536	391	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197485.1	s__Anoxybacillus flavithermus_G	79.6297	401	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.60	95.08	0.91	0.76	28	-
GCF_001187595.1	s__Anoxybacillus gonensis	79.3715	411	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	-
GCF_000836725.1	s__Anoxybacillus thermarum	79.2374	367	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000833605.1	s__Anoxybacillus ayderensis	79.2229	401	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	97.55	97.17	0.91	0.88	8	-
GCF_003688615.2	s__Parageobacillus toebii	79.2136	308	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCA_002243705.1	s__Anoxybacillus flavithermus	79.1907	406	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.37	95.30	0.87	0.86	4	-
GCF_014201515.1	s__Anoxybacillus mongoliensis	79.1536	372	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002742685.1	s__Anoxybacillus flavithermus_E	79.0571	387	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	99.92	99.92	0.93	0.93	2	-
GCF_014201585.1	s__Anoxybacillus tengchongensis	78.9219	406	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	-
GCF_000632715.1	s__Saccharococcus caldoxylosilyticus	78.9198	259	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	-
GCF_000632515.1	s__Saccharococcus sp000632515	78.8595	291	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001655645.1	s__Parageobacillus thermoglucosidasius_A	78.6301	307	944	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	78.4659	289	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
GCF_011761475.1	s__Saccharococcus thermophilus	78.4207	267	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018343535.1	s__Neobacillus sp018343535	76.3076	63	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCA_019219025.1	s__Neobacillus sp019219025	76.1179	67	944	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:35,747] [INFO] GTDB search result was written to GCF_004341205.1_ASM434120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:35,748] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:35,751] [INFO] DFAST_QC result json was written to GCF_004341205.1_ASM434120v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:35,752] [INFO] DFAST_QC completed!
[2024-01-24 14:07:35,752] [INFO] Total running time: 0h1m7s