[2024-01-24 11:34:43,100] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:43,106] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:43,106] [INFO] DQC Reference Directory: /var/lib/cwl/stg9009a282-af0f-45dd-97ef-e4646f079d88/dqc_reference
[2024-01-24 11:34:44,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,498] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,498] [INFO] Running command: gunzip -c /var/lib/cwl/stga6b4dcc3-4e7e-4cbf-8707-59a8ace85db9/GCF_007830235.1_ASM783023v1_genomic.fna.gz | prodigal -d GCF_007830235.1_ASM783023v1_genomic.fna/cds.fna -a GCF_007830235.1_ASM783023v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:57,721] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:57,721] [INFO] Task started: HMMsearch
[2024-01-24 11:34:57,721] [INFO] Running command: hmmsearch --tblout GCF_007830235.1_ASM783023v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9009a282-af0f-45dd-97ef-e4646f079d88/dqc_reference/reference_markers.hmm GCF_007830235.1_ASM783023v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:34:58,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:34:58,080] [INFO] Found 6/6 markers.
[2024-01-24 11:34:58,150] [INFO] Query marker FASTA was written to GCF_007830235.1_ASM783023v1_genomic.fna/markers.fasta
[2024-01-24 11:34:58,150] [INFO] Task started: Blastn
[2024-01-24 11:34:58,150] [INFO] Running command: blastn -query GCF_007830235.1_ASM783023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9009a282-af0f-45dd-97ef-e4646f079d88/dqc_reference/reference_markers.fasta -out GCF_007830235.1_ASM783023v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:34:58,804] [INFO] Task succeeded: Blastn
[2024-01-24 11:34:58,807] [INFO] Selected 23 target genomes.
[2024-01-24 11:34:58,807] [INFO] Target genome list was writen to GCF_007830235.1_ASM783023v1_genomic.fna/target_genomes.txt
[2024-01-24 11:34:58,816] [INFO] Task started: fastANI
[2024-01-24 11:34:58,816] [INFO] Running command: fastANI --query /var/lib/cwl/stga6b4dcc3-4e7e-4cbf-8707-59a8ace85db9/GCF_007830235.1_ASM783023v1_genomic.fna.gz --refList GCF_007830235.1_ASM783023v1_genomic.fna/target_genomes.txt --output GCF_007830235.1_ASM783023v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:19,083] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:19,084] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9009a282-af0f-45dd-97ef-e4646f079d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:19,084] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9009a282-af0f-45dd-97ef-e4646f079d88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:19,102] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:19,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:19,103] [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
Cytobacillus firmus	strain=NBRC 15306	GCA_001591465.1	1399	1399	suspected-type	True	81.3106	826	1856	95	below_threshold
Cytobacillus firmus	strain=NCTC10335	GCA_900445365.1	1399	1399	suspected-type	True	81.2847	879	1856	95	below_threshold
Cytobacillus horneckiae	strain=1P01SC	GCA_002835735.1	549687	549687	type	True	78.2496	219	1856	95	below_threshold
Cytobacillus eiseniae	strain=DSM 26675	GCA_017874625.1	762947	762947	type	True	77.9241	221	1856	95	below_threshold
Cytobacillus depressus	strain=BZ1	GCA_008923245.1	1602942	1602942	type	True	77.9058	290	1856	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	77.6499	174	1856	95	below_threshold
Robertmurraya massiliosenegalensis	strain=JC6	GCA_000311725.1	1287657	1287657	type	True	77.5774	161	1856	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.5666	160	1856	95	below_threshold
Lederbergia citri	strain=FJAT-49780	GCA_018343625.1	2833580	2833580	type	True	77.3177	79	1856	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.2821	172	1856	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.2666	150	1856	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.245	152	1856	95	below_threshold
Margalitia camelliae	strain=7578-1	GCA_002844575.1	1707093	1707093	type	True	77.2031	88	1856	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.1787	148	1856	95	below_threshold
Lederbergia citrisecundus	strain=FJAT-49732	GCA_018343695.1	2833583	2833583	type	True	77.0271	89	1856	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	76.9626	166	1856	95	below_threshold
Peribacillus psychrosaccharolyticus	strain=ATCC 23296	GCA_000305495.2	1407	1407	type	True	76.8898	84	1856	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	76.8266	87	1856	95	below_threshold
Neobacillus piezotolerans	strain=YLB-04	GCA_003362805.1	2259171	2259171	type	True	76.8164	118	1856	95	below_threshold
Siminovitchia fortis	strain=DSM 16012	GCA_003605365.2	254758	254758	type	True	76.4703	59	1856	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:19,105] [INFO] DFAST Taxonomy check result was written to GCF_007830235.1_ASM783023v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:19,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:19,106] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:19,106] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9009a282-af0f-45dd-97ef-e4646f079d88/dqc_reference/checkm_data
[2024-01-24 11:35:19,107] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:19,163] [INFO] Task started: CheckM
[2024-01-24 11:35:19,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830235.1_ASM783023v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830235.1_ASM783023v1_genomic.fna/checkm_input GCF_007830235.1_ASM783023v1_genomic.fna/checkm_result
[2024-01-24 11:36:01,713] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:01,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:01,730] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:01,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:01,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830235.1_ASM783023v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:01,731] [INFO] Task started: Blastn
[2024-01-24 11:36:01,732] [INFO] Running command: blastn -query GCF_007830235.1_ASM783023v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9009a282-af0f-45dd-97ef-e4646f079d88/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830235.1_ASM783023v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:02,495] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:02,499] [INFO] Selected 7 target genomes.
[2024-01-24 11:36:02,500] [INFO] Target genome list was writen to GCF_007830235.1_ASM783023v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:02,505] [INFO] Task started: fastANI
[2024-01-24 11:36:02,505] [INFO] Running command: fastANI --query /var/lib/cwl/stga6b4dcc3-4e7e-4cbf-8707-59a8ace85db9/GCF_007830235.1_ASM783023v1_genomic.fna.gz --refList GCF_007830235.1_ASM783023v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830235.1_ASM783023v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:13,129] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:13,141] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:13,142] [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_007830235.1	s__Cytobacillus oceanisediminis	100.0	1856	1856	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_003182355.1	s__Cytobacillus oceanisediminis_A	94.2007	1522	1856	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	89.8113	1302	1856	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_000518885.1	s__Cytobacillus sp000518885	83.8903	1202	1856	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_004366035.1	s__Cytobacillus oceanisediminis_C	81.822	1059	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001274725.1	s__Cytobacillus globisporus	81.7757	971	1856	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_000294775.2	s__Cytobacillus oceanisediminis_B	81.5719	1031	1856	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	98.75	98.26	0.86	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,143] [INFO] GTDB search result was written to GCF_007830235.1_ASM783023v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:13,144] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:13,147] [INFO] DFAST_QC result json was written to GCF_007830235.1_ASM783023v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:13,147] [INFO] DFAST_QC completed!
[2024-01-24 11:36:13,148] [INFO] Total running time: 0h1m30s