[2024-01-24 13:36:31,189] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:31,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:31,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg97ec325f-6d3c-4269-a0a6-4851817e21cf/dqc_reference
[2024-01-24 13:36:32,556] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:32,557] [INFO] Task started: Prodigal
[2024-01-24 13:36:32,557] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd549db9-b2f7-4a12-bc55-bc5a23f703ef/GCF_018343665.1_ASM1834366v1_genomic.fna.gz | prodigal -d GCF_018343665.1_ASM1834366v1_genomic.fna/cds.fna -a GCF_018343665.1_ASM1834366v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:43,344] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:43,344] [INFO] Task started: HMMsearch
[2024-01-24 13:36:43,345] [INFO] Running command: hmmsearch --tblout GCF_018343665.1_ASM1834366v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97ec325f-6d3c-4269-a0a6-4851817e21cf/dqc_reference/reference_markers.hmm GCF_018343665.1_ASM1834366v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:43,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:43,675] [INFO] Found 6/6 markers.
[2024-01-24 13:36:43,726] [INFO] Query marker FASTA was written to GCF_018343665.1_ASM1834366v1_genomic.fna/markers.fasta
[2024-01-24 13:36:43,727] [INFO] Task started: Blastn
[2024-01-24 13:36:43,727] [INFO] Running command: blastn -query GCF_018343665.1_ASM1834366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ec325f-6d3c-4269-a0a6-4851817e21cf/dqc_reference/reference_markers.fasta -out GCF_018343665.1_ASM1834366v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:36:44,315] [INFO] Task succeeded: Blastn
[2024-01-24 13:36:44,319] [INFO] Selected 23 target genomes.
[2024-01-24 13:36:44,319] [INFO] Target genome list was writen to GCF_018343665.1_ASM1834366v1_genomic.fna/target_genomes.txt
[2024-01-24 13:36:44,336] [INFO] Task started: fastANI
[2024-01-24 13:36:44,337] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd549db9-b2f7-4a12-bc55-bc5a23f703ef/GCF_018343665.1_ASM1834366v1_genomic.fna.gz --refList GCF_018343665.1_ASM1834366v1_genomic.fna/target_genomes.txt --output GCF_018343665.1_ASM1834366v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:07,407] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:07,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97ec325f-6d3c-4269-a0a6-4851817e21cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:07,408] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97ec325f-6d3c-4269-a0a6-4851817e21cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:07,426] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:07,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:07,427] [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
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	93.0631	1317	1767	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	79.9811	609	1767	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	79.0571	541	1767	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	78.8071	205	1767	95	below_threshold
Cytobacillus praedii	strain=FJAT-25547	GCA_001439605.1	1742358	1742358	type	True	78.7866	516	1767	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.1877	188	1767	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	78.1759	405	1767	95	below_threshold
Peribacillus frigoritolerans	strain=FJAT-2396	GCA_001636405.1	450367	450367	type	True	78.0343	112	1767	95	below_threshold
Bacillus dakarensis	strain=Marseille-P3515	GCA_900156875.1	1926278	1926278	type	True	77.8243	191	1767	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_017809215.1	38875	38875	type	True	77.6419	145	1767	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	77.3928	163	1767	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	77.2964	169	1767	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_019915265.1	2672567	2672567	type	True	77.2706	153	1767	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.267	165	1767	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_003055085.1	46224	46224	type	True	77.2451	110	1767	95	below_threshold
Sutcliffiella halmapala	strain=DSM 8723	GCA_002019665.1	79882	79882	type	True	77.2202	108	1767	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_002009555.1	38875	38875	type	True	77.1824	126	1767	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	77.1441	172	1767	95	below_threshold
Heyndrickxia sporothermodurans	strain=DSM 10599	GCA_016785185.1	46224	46224	type	True	77.0917	120	1767	95	below_threshold
Bacillus aquiflavi	strain=3H-10	GCA_011008855.1	2672567	2672567	type	True	76.9467	152	1767	95	below_threshold
Bacillus andreraoultii	strain=SIT1	GCA_001244735.1	1499685	1499685	type	True	76.8284	73	1767	95	below_threshold
Bacillus nitratireducens	strain=4049	GCA_001884135.1	2026193	2026193	type	True	76.7706	102	1767	95	below_threshold
Ureibacillus chungkukjangi	strain=2RL32	GCA_003049615.1	1202712	1202712	type	True	76.6215	77	1767	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:07,428] [INFO] DFAST Taxonomy check result was written to GCF_018343665.1_ASM1834366v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:07,429] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:07,429] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:07,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97ec325f-6d3c-4269-a0a6-4851817e21cf/dqc_reference/checkm_data
[2024-01-24 13:37:07,431] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:07,485] [INFO] Task started: CheckM
[2024-01-24 13:37:07,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018343665.1_ASM1834366v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018343665.1_ASM1834366v1_genomic.fna/checkm_input GCF_018343665.1_ASM1834366v1_genomic.fna/checkm_result
[2024-01-24 13:37:46,302] [INFO] Task succeeded: CheckM
[2024-01-24 13:37:46,303] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:37:46,325] [INFO] ===== Completeness check finished =====
[2024-01-24 13:37:46,325] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:37:46,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018343665.1_ASM1834366v1_genomic.fna/markers.fasta)
[2024-01-24 13:37:46,326] [INFO] Task started: Blastn
[2024-01-24 13:37:46,326] [INFO] Running command: blastn -query GCF_018343665.1_ASM1834366v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97ec325f-6d3c-4269-a0a6-4851817e21cf/dqc_reference/reference_markers_gtdb.fasta -out GCF_018343665.1_ASM1834366v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:47,111] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:47,114] [INFO] Selected 14 target genomes.
[2024-01-24 13:37:47,115] [INFO] Target genome list was writen to GCF_018343665.1_ASM1834366v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:37:47,132] [INFO] Task started: fastANI
[2024-01-24 13:37:47,133] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd549db9-b2f7-4a12-bc55-bc5a23f703ef/GCF_018343665.1_ASM1834366v1_genomic.fna.gz --refList GCF_018343665.1_ASM1834366v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018343665.1_ASM1834366v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:04,086] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:04,105] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:04,105] [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_018343665.1	s__Cytobacillus sp018343665	100.0	1767	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007995155.1	s__Cytobacillus dafuensis	93.0579	1318	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_008923245.1	s__Cytobacillus depressus	80.0048	610	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001509555.1	s__Cytobacillus sp001509555	79.5485	586	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420595.1	s__Cytobacillus solani	79.0198	543	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.54	99.49	0.95	0.94	3	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	78.8482	504	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001439605.1	s__Cytobacillus praedii	78.7812	518	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.20	99.20	0.93	0.93	2	-
GCF_019039215.1	s__Cytobacillus sp019039215	78.7552	476	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017874625.1	s__Cytobacillus eiseniae	78.1284	408	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613035.1	s__Cytobacillus sp018613035	77.9793	271	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	99.97	99.97	0.97	0.97	2	-
GCF_002019635.1	s__Metabacillus halosaccharovorans	77.788	145	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	95.47	95.47	0.86	0.86	2	-
GCF_011008845.1	s__Bacillus_BS mesophilus	77.2147	78	1767	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__SA4;g__Bacillus_BS	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:04,107] [INFO] GTDB search result was written to GCF_018343665.1_ASM1834366v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:04,107] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:04,111] [INFO] DFAST_QC result json was written to GCF_018343665.1_ASM1834366v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:04,112] [INFO] DFAST_QC completed!
[2024-01-24 13:38:04,112] [INFO] Total running time: 0h1m33s