[2024-01-25 19:24:45,019] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:24:45,021] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:24:45,021] [INFO] DQC Reference Directory: /var/lib/cwl/stg50b1765a-c983-4630-90f8-8e3c1b0fbc50/dqc_reference
[2024-01-25 19:24:48,242] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:24:48,243] [INFO] Task started: Prodigal
[2024-01-25 19:24:48,243] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fce4e31-3771-43fb-98ea-14291e8a637e/GCF_014196205.1_ASM1419620v1_genomic.fna.gz | prodigal -d GCF_014196205.1_ASM1419620v1_genomic.fna/cds.fna -a GCF_014196205.1_ASM1419620v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:24:55,453] [INFO] Task succeeded: Prodigal
[2024-01-25 19:24:55,454] [INFO] Task started: HMMsearch
[2024-01-25 19:24:55,454] [INFO] Running command: hmmsearch --tblout GCF_014196205.1_ASM1419620v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50b1765a-c983-4630-90f8-8e3c1b0fbc50/dqc_reference/reference_markers.hmm GCF_014196205.1_ASM1419620v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:24:55,673] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:24:55,675] [INFO] Found 6/6 markers.
[2024-01-25 19:24:55,713] [INFO] Query marker FASTA was written to GCF_014196205.1_ASM1419620v1_genomic.fna/markers.fasta
[2024-01-25 19:24:55,714] [INFO] Task started: Blastn
[2024-01-25 19:24:55,714] [INFO] Running command: blastn -query GCF_014196205.1_ASM1419620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b1765a-c983-4630-90f8-8e3c1b0fbc50/dqc_reference/reference_markers.fasta -out GCF_014196205.1_ASM1419620v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:24:56,330] [INFO] Task succeeded: Blastn
[2024-01-25 19:24:56,333] [INFO] Selected 15 target genomes.
[2024-01-25 19:24:56,333] [INFO] Target genome list was writen to GCF_014196205.1_ASM1419620v1_genomic.fna/target_genomes.txt
[2024-01-25 19:24:56,454] [INFO] Task started: fastANI
[2024-01-25 19:24:56,454] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fce4e31-3771-43fb-98ea-14291e8a637e/GCF_014196205.1_ASM1419620v1_genomic.fna.gz --refList GCF_014196205.1_ASM1419620v1_genomic.fna/target_genomes.txt --output GCF_014196205.1_ASM1419620v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:25:06,951] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:06,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50b1765a-c983-4630-90f8-8e3c1b0fbc50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:25:06,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50b1765a-c983-4630-90f8-8e3c1b0fbc50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:25:06,962] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:25:06,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:25:06,962] [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=DSM 17075	GCA_014196205.1	230470	230470	type	True	100.0	1043	1047	95	conclusive
Anoxybacillus voinovskiensis	strain=JCM 12111	GCA_014646615.1	230470	230470	type	True	99.9863	1020	1047	95	conclusive
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	90.4183	852	1047	95	below_threshold
Anoxybacillus tepidamans	strain=DSM 16325	GCA_014201465.1	265948	265948	type	True	82.5075	681	1047	95	below_threshold
Anoxybacillus ayderensis	strain=AB04	GCA_000833605.1	265546	265546	type	True	80.7183	360	1047	95	below_threshold
Anoxybacillus kamchatkensis	strain=DSM 14988	GCA_013761015.1	196180	196180	type	True	79.9519	327	1047	95	below_threshold
Anoxybacillus gonensis	strain=G2	GCA_000770375.1	198467	198467	suspected-type	True	79.7708	360	1047	95	below_threshold
Anoxybacillus rupiensis	strain=DSM 17127	GCA_014196195.1	311460	311460	type	True	78.7434	375	1047	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	78.0841	354	1047	95	below_threshold
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	78.0599	361	1047	95	below_threshold
Geobacillus thermodenitrificans subsp. thermodenitrificans	strain=DSM 465	GCA_000496575.1	1511749	33940	type	True	77.1399	231	1047	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:25:06,964] [INFO] DFAST Taxonomy check result was written to GCF_014196205.1_ASM1419620v1_genomic.fna/tc_result.tsv
[2024-01-25 19:25:06,966] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:25:06,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:25:06,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50b1765a-c983-4630-90f8-8e3c1b0fbc50/dqc_reference/checkm_data
[2024-01-25 19:25:06,967] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:25:07,009] [INFO] Task started: CheckM
[2024-01-25 19:25:07,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196205.1_ASM1419620v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196205.1_ASM1419620v1_genomic.fna/checkm_input GCF_014196205.1_ASM1419620v1_genomic.fna/checkm_result
[2024-01-25 19:25:32,618] [INFO] Task succeeded: CheckM
[2024-01-25 19:25:32,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:25:32,641] [INFO] ===== Completeness check finished =====
[2024-01-25 19:25:32,641] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:25:32,642] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196205.1_ASM1419620v1_genomic.fna/markers.fasta)
[2024-01-25 19:25:32,642] [INFO] Task started: Blastn
[2024-01-25 19:25:32,642] [INFO] Running command: blastn -query GCF_014196205.1_ASM1419620v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50b1765a-c983-4630-90f8-8e3c1b0fbc50/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196205.1_ASM1419620v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:25:33,650] [INFO] Task succeeded: Blastn
[2024-01-25 19:25:33,652] [INFO] Selected 18 target genomes.
[2024-01-25 19:25:33,653] [INFO] Target genome list was writen to GCF_014196205.1_ASM1419620v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:25:33,667] [INFO] Task started: fastANI
[2024-01-25 19:25:33,667] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fce4e31-3771-43fb-98ea-14291e8a637e/GCF_014196205.1_ASM1419620v1_genomic.fna.gz --refList GCF_014196205.1_ASM1419620v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196205.1_ASM1419620v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:25:46,402] [INFO] Task succeeded: fastANI
[2024-01-25 19:25:46,412] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:25:46,412] [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	100.0	1043	1047	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	90.4226	851	1047	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	82.5571	675	1047	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	80.7638	358	1047	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	80.2934	351	1047	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	80.205	289	1047	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	79.6985	362	1047	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	79.4715	482	1047	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_014196195.1	s__Anoxybacillus_A rupiensis	78.7439	376	1047	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_013761245.1	s__Anoxybacillus_C caldiproteolyticus	78.6094	390	1047	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_003688615.2	s__Parageobacillus toebii	78.0522	366	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_011761475.1	s__Saccharococcus thermophilus	78.0465	352	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_000632515.1	s__Saccharococcus sp000632515	78.0144	349	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_013760845.1	s__Anoxybacillus_B calidus	77.7071	296	1047	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	77.1283	232	1047	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Geobacillus	95.0	99.33	99.10	0.94	0.90	12	-
--------------------------------------------------------------------------------
[2024-01-25 19:25:46,413] [INFO] GTDB search result was written to GCF_014196205.1_ASM1419620v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:25:46,413] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:25:46,416] [INFO] DFAST_QC result json was written to GCF_014196205.1_ASM1419620v1_genomic.fna/dqc_result.json
[2024-01-25 19:25:46,417] [INFO] DFAST_QC completed!
[2024-01-25 19:25:46,417] [INFO] Total running time: 0h1m1s