[2024-01-24 11:51:06,811] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,816] [INFO] DQC Reference Directory: /var/lib/cwl/stga57e31be-b49e-4bdd-a639-047206ea89f5/dqc_reference
[2024-01-24 11:51:08,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:08,005] [INFO] Task started: Prodigal
[2024-01-24 11:51:08,005] [INFO] Running command: gunzip -c /var/lib/cwl/stgfef6303e-fde0-4ebd-8d0e-c7a8e0bebacd/GCF_014646615.1_ASM1464661v1_genomic.fna.gz | prodigal -d GCF_014646615.1_ASM1464661v1_genomic.fna/cds.fna -a GCF_014646615.1_ASM1464661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:16,158] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:16,159] [INFO] Task started: HMMsearch
[2024-01-24 11:51:16,159] [INFO] Running command: hmmsearch --tblout GCF_014646615.1_ASM1464661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga57e31be-b49e-4bdd-a639-047206ea89f5/dqc_reference/reference_markers.hmm GCF_014646615.1_ASM1464661v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:16,489] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:16,491] [INFO] Found 6/6 markers.
[2024-01-24 11:51:16,527] [INFO] Query marker FASTA was written to GCF_014646615.1_ASM1464661v1_genomic.fna/markers.fasta
[2024-01-24 11:51:16,527] [INFO] Task started: Blastn
[2024-01-24 11:51:16,527] [INFO] Running command: blastn -query GCF_014646615.1_ASM1464661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga57e31be-b49e-4bdd-a639-047206ea89f5/dqc_reference/reference_markers.fasta -out GCF_014646615.1_ASM1464661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:17,208] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:17,212] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:17,213] [INFO] Target genome list was writen to GCF_014646615.1_ASM1464661v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:17,325] [INFO] Task started: fastANI
[2024-01-24 11:51:17,326] [INFO] Running command: fastANI --query /var/lib/cwl/stgfef6303e-fde0-4ebd-8d0e-c7a8e0bebacd/GCF_014646615.1_ASM1464661v1_genomic.fna.gz --refList GCF_014646615.1_ASM1464661v1_genomic.fna/target_genomes.txt --output GCF_014646615.1_ASM1464661v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:27,391] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:27,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga57e31be-b49e-4bdd-a639-047206ea89f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:27,393] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga57e31be-b49e-4bdd-a639-047206ea89f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:27,407] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:27,407] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:27,407] [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 voinovskiensis	strain=JCM 12111	GCA_014646615.1	230470	230470	type	True	100.0	1038	1040	95	conclusive
Anoxybacillus voinovskiensis	strain=DSM 17075	GCA_014196205.1	230470	230470	type	True	99.9931	1030	1040	95	conclusive
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	90.4368	853	1040	95	below_threshold
Anoxybacillus tepidamans	strain=DSM 16325	GCA_014201465.1	265948	265948	type	True	82.525	667	1040	95	below_threshold
Anoxybacillus ayderensis	strain=AB04	GCA_000833605.1	265546	265546	type	True	80.7657	357	1040	95	below_threshold
Anoxybacillus kamchatkensis	strain=DSM 14988	GCA_013761015.1	196180	196180	type	True	79.9777	324	1040	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	79.7764	346	1040	95	below_threshold
Anoxybacillus rupiensis	strain=DSM 17127	GCA_014196195.1	311460	311460	type	True	78.4899	388	1040	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	78.332	343	1040	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	78.095	366	1040	95	below_threshold
Geobacillus thermodenitrificans subsp. thermodenitrificans	strain=DSM 465	GCA_000496575.1	1511749	33940	type	True	77.2452	233	1040	95	below_threshold
Fredinandcohnia onubensis	strain=0911MAR22V3	GCA_002734215.1	1571209	1571209	type	True	76.2151	50	1040	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:27,409] [INFO] DFAST Taxonomy check result was written to GCF_014646615.1_ASM1464661v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:27,409] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:27,409] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:27,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga57e31be-b49e-4bdd-a639-047206ea89f5/dqc_reference/checkm_data
[2024-01-24 11:51:27,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:27,448] [INFO] Task started: CheckM
[2024-01-24 11:51:27,449] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646615.1_ASM1464661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646615.1_ASM1464661v1_genomic.fna/checkm_input GCF_014646615.1_ASM1464661v1_genomic.fna/checkm_result
[2024-01-24 11:51:57,529] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:57,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:57,563] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:57,563] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:57,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646615.1_ASM1464661v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:57,564] [INFO] Task started: Blastn
[2024-01-24 11:51:57,564] [INFO] Running command: blastn -query GCF_014646615.1_ASM1464661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga57e31be-b49e-4bdd-a639-047206ea89f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646615.1_ASM1464661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:58,677] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:58,682] [INFO] Selected 18 target genomes.
[2024-01-24 11:51:58,682] [INFO] Target genome list was writen to GCF_014646615.1_ASM1464661v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:58,699] [INFO] Task started: fastANI
[2024-01-24 11:51:58,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgfef6303e-fde0-4ebd-8d0e-c7a8e0bebacd/GCF_014646615.1_ASM1464661v1_genomic.fna.gz --refList GCF_014646615.1_ASM1464661v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646615.1_ASM1464661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:10,862] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:10,879] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:10,880] [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_014196205.1	s__Anoxybacillus_A voinovskiensis	99.9931	1030	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001634285.1	s__Anoxybacillus_A amylolyticus	90.4556	852	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201465.1	s__Anoxybacillus_A tepidamans	82.5586	663	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000833605.1	s__Anoxybacillus ayderensis	80.7908	360	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	97.55	97.17	0.91	0.88	8	-
GCA_002243705.1	s__Anoxybacillus flavithermus	80.2701	355	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.37	95.30	0.87	0.86	4	-
GCF_900111795.1	s__Anoxybacillus pushchinoensis	79.8929	293	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	95.71	95.71	0.84	0.84	2	-
GCF_001187595.1	s__Anoxybacillus gonensis	79.8124	356	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	98.51	96.49	0.91	0.88	6	-
GCF_000620165.1	s__Anoxybacillus_A tepidamans_A	79.4332	480	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013761245.1	s__Anoxybacillus_C caldiproteolyticus	78.623	391	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_C	95.0	99.29	99.25	0.94	0.93	3	-
GCF_014196195.1	s__Anoxybacillus_A rupiensis	78.4891	387	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	98.88	98.54	0.93	0.92	7	-
GCF_003688615.2	s__Parageobacillus toebii	78.3061	355	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_011761475.1	s__Saccharococcus thermophilus	78.1	346	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632515.1	s__Saccharococcus sp000632515	77.9798	363	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013760845.1	s__Anoxybacillus_B calidus	77.7762	290	1040	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_000496575.1	s__Geobacillus thermodenitrificans	77.2693	235	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	99.33	99.10	0.94	0.90	12	-
GCF_002734285.1	s__Fredinandcohnia onubensis_A	76.4711	52	1040	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:10,882] [INFO] GTDB search result was written to GCF_014646615.1_ASM1464661v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:10,882] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:10,886] [INFO] DFAST_QC result json was written to GCF_014646615.1_ASM1464661v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:10,886] [INFO] DFAST_QC completed!
[2024-01-24 11:52:10,886] [INFO] Total running time: 0h1m4s