[2024-01-25 18:48:35,635] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:48:35,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:48:35,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg8349ccf4-336a-4dec-9954-cd396143f6dc/dqc_reference
[2024-01-25 18:48:36,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:48:36,824] [INFO] Task started: Prodigal
[2024-01-25 18:48:36,824] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd4288ce-c932-4d67-9695-549620eb2faa/GCF_013760845.1_ASM1376084v1_genomic.fna.gz | prodigal -d GCF_013760845.1_ASM1376084v1_genomic.fna/cds.fna -a GCF_013760845.1_ASM1376084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:48:43,533] [INFO] Task succeeded: Prodigal
[2024-01-25 18:48:43,533] [INFO] Task started: HMMsearch
[2024-01-25 18:48:43,533] [INFO] Running command: hmmsearch --tblout GCF_013760845.1_ASM1376084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8349ccf4-336a-4dec-9954-cd396143f6dc/dqc_reference/reference_markers.hmm GCF_013760845.1_ASM1376084v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:48:43,769] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:48:43,770] [INFO] Found 6/6 markers.
[2024-01-25 18:48:43,798] [INFO] Query marker FASTA was written to GCF_013760845.1_ASM1376084v1_genomic.fna/markers.fasta
[2024-01-25 18:48:43,798] [INFO] Task started: Blastn
[2024-01-25 18:48:43,798] [INFO] Running command: blastn -query GCF_013760845.1_ASM1376084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8349ccf4-336a-4dec-9954-cd396143f6dc/dqc_reference/reference_markers.fasta -out GCF_013760845.1_ASM1376084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:44,361] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:44,364] [INFO] Selected 21 target genomes.
[2024-01-25 18:48:44,364] [INFO] Target genome list was writen to GCF_013760845.1_ASM1376084v1_genomic.fna/target_genomes.txt
[2024-01-25 18:48:44,376] [INFO] Task started: fastANI
[2024-01-25 18:48:44,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4288ce-c932-4d67-9695-549620eb2faa/GCF_013760845.1_ASM1376084v1_genomic.fna.gz --refList GCF_013760845.1_ASM1376084v1_genomic.fna/target_genomes.txt --output GCF_013760845.1_ASM1376084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:48:58,032] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:58,032] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8349ccf4-336a-4dec-9954-cd396143f6dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:48:58,033] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8349ccf4-336a-4dec-9954-cd396143f6dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:48:58,045] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:48:58,045] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:48:58,045] [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	100.0	1124	1125	95	conclusive
Anoxybacillus vitaminiphilus	strain=CGMCC 1.8979	GCA_003259935.1	581036	581036	type	True	88.8913	797	1125	95	below_threshold
Anoxybacillus caldiproteolyticus	strain=DSM 15730	GCA_013761245.1	247480	247480	type	True	80.8456	553	1125	95	below_threshold
Parageobacillus thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	78.6909	332	1125	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	78.6658	335	1125	95	below_threshold
Anoxybacillus tepidamans	strain=DSM 16325	GCA_014201465.1	265948	265948	type	True	78.5481	340	1125	95	below_threshold
Anoxybacillus amylolyticus	strain=DSM 15939	GCA_001634285.1	294699	294699	type	True	78.2609	297	1125	95	below_threshold
Anoxybacillus thermarum	strain=AF/04	GCA_000836725.1	404937	404937	type	True	78.2103	233	1125	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001418025.1	1325335	1325335	type	True	78.0861	233	1125	95	below_threshold
Anoxybacillus suryakundensis	strain=DSM 27374	GCA_001517225.1	1325335	1325335	type	True	78.0853	233	1125	95	below_threshold
Anoxybacillus kamchatkensis	strain=DSM 14988	GCA_013761015.1	196180	196180	type	True	78.0524	226	1125	95	below_threshold
Anoxybacillus voinovskiensis	strain=JCM 12111	GCA_014646615.1	230470	230470	type	True	77.9415	277	1125	95	below_threshold
Anoxybacillus voinovskiensis	strain=DSM 17075	GCA_014196205.1	230470	230470	type	True	77.8955	284	1125	95	below_threshold
Anoxybacillus tengchongensis	strain=DSM 23211	GCA_014201585.1	576944	576944	type	True	77.8432	233	1125	95	below_threshold
Bacillus kexueae	strain=KCTC 33881	GCA_022809095.1	2078952	2078952	type	True	77.2972	109	1125	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.0582	87	1125	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	76.9608	78	1125	95	below_threshold
Metabacillus iocasae	strain=DSM 104297	GCA_016909075.1	2291674	2291674	type	True	76.9402	120	1125	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	76.8925	95	1125	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	76.4798	78	1125	95	below_threshold
Sutcliffiella deserti	strain=DG-18	GCA_020037475.1	2875501	2875501	type	True	76.2814	53	1125	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:48:58,046] [INFO] DFAST Taxonomy check result was written to GCF_013760845.1_ASM1376084v1_genomic.fna/tc_result.tsv
[2024-01-25 18:48:58,047] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:48:58,047] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:48:58,047] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8349ccf4-336a-4dec-9954-cd396143f6dc/dqc_reference/checkm_data
[2024-01-25 18:48:58,048] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:48:58,085] [INFO] Task started: CheckM
[2024-01-25 18:48:58,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013760845.1_ASM1376084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013760845.1_ASM1376084v1_genomic.fna/checkm_input GCF_013760845.1_ASM1376084v1_genomic.fna/checkm_result
[2024-01-25 18:49:23,124] [INFO] Task succeeded: CheckM
[2024-01-25 18:49:23,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:49:23,141] [INFO] ===== Completeness check finished =====
[2024-01-25 18:49:23,142] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:49:23,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013760845.1_ASM1376084v1_genomic.fna/markers.fasta)
[2024-01-25 18:49:23,143] [INFO] Task started: Blastn
[2024-01-25 18:49:23,143] [INFO] Running command: blastn -query GCF_013760845.1_ASM1376084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8349ccf4-336a-4dec-9954-cd396143f6dc/dqc_reference/reference_markers_gtdb.fasta -out GCF_013760845.1_ASM1376084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:23,932] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:23,935] [INFO] Selected 18 target genomes.
[2024-01-25 18:49:23,935] [INFO] Target genome list was writen to GCF_013760845.1_ASM1376084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:49:23,950] [INFO] Task started: fastANI
[2024-01-25 18:49:23,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4288ce-c932-4d67-9695-549620eb2faa/GCF_013760845.1_ASM1376084v1_genomic.fna.gz --refList GCF_013760845.1_ASM1376084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013760845.1_ASM1376084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:49:35,429] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:35,440] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:49:35,441] [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_013760845.1	s__Anoxybacillus_B calidus	100.0	1124	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003259935.1	s__Anoxybacillus_B vitaminiphilus	88.8731	798	1125	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_013761245.1	s__Anoxybacillus_C caldiproteolyticus	80.8496	553	1125	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_004341205.1	s__Thermolongibacillus altinsuensis	79.8957	391	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Thermolongibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632515.1	s__Saccharococcus sp000632515	79.2482	354	1125	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	79.2289	368	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCA_017656295.1	s__JACDOC01 sp017656295	78.7096	164	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__JACDOC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201465.1	s__Anoxybacillus_A tepidamans	78.5481	340	1125	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_011761475.1	s__Saccharococcus thermophilus	78.5243	292	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634285.1	s__Anoxybacillus_A amylolyticus	78.2401	298	1125	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_000836725.1	s__Anoxybacillus thermarum	78.2108	233	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196205.1	s__Anoxybacillus_A voinovskiensis	77.8797	284	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014201585.1	s__Anoxybacillus tengchongensis	77.8569	232	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	96.46	96.29	0.90	0.87	4	-
GCF_900111795.1	s__Anoxybacillus pushchinoensis	77.7458	229	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Anoxybacillus	95.0	95.71	95.71	0.84	0.84	2	-
GCF_000161455.1	s__Bacillus_A pseudomycoides	77.2242	90	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.62	95.81	0.91	0.85	116	-
GCF_001293645.1	s__Sutcliffiella_A sp001293645	77.1304	58	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_I;g__Sutcliffiella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002551815.1	s__Bacillus_A sp002551815	76.8197	85	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	99.80	99.69	0.94	0.92	5	-
GCF_002797395.1	s__45385 sp002797395	76.7835	55	1125	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:49:35,442] [INFO] GTDB search result was written to GCF_013760845.1_ASM1376084v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:49:35,443] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:49:35,447] [INFO] DFAST_QC result json was written to GCF_013760845.1_ASM1376084v1_genomic.fna/dqc_result.json
[2024-01-25 18:49:35,447] [INFO] DFAST_QC completed!
[2024-01-25 18:49:35,447] [INFO] Total running time: 0h0m60s