[2024-01-24 13:28:29,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:29,099] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:29,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d24621b-20d8-414e-b925-387e21dc2679/dqc_reference
[2024-01-24 13:28:30,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:30,361] [INFO] Task started: Prodigal
[2024-01-24 13:28:30,361] [INFO] Running command: gunzip -c /var/lib/cwl/stg81797d2a-af39-40a3-a2c5-4187e1de071c/GCF_014656545.1_ASM1465654v1_genomic.fna.gz | prodigal -d GCF_014656545.1_ASM1465654v1_genomic.fna/cds.fna -a GCF_014656545.1_ASM1465654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:42,012] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:42,012] [INFO] Task started: HMMsearch
[2024-01-24 13:28:42,012] [INFO] Running command: hmmsearch --tblout GCF_014656545.1_ASM1465654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d24621b-20d8-414e-b925-387e21dc2679/dqc_reference/reference_markers.hmm GCF_014656545.1_ASM1465654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:42,350] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:42,351] [INFO] Found 6/6 markers.
[2024-01-24 13:28:42,396] [INFO] Query marker FASTA was written to GCF_014656545.1_ASM1465654v1_genomic.fna/markers.fasta
[2024-01-24 13:28:42,396] [INFO] Task started: Blastn
[2024-01-24 13:28:42,397] [INFO] Running command: blastn -query GCF_014656545.1_ASM1465654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d24621b-20d8-414e-b925-387e21dc2679/dqc_reference/reference_markers.fasta -out GCF_014656545.1_ASM1465654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:43,002] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:43,006] [INFO] Selected 18 target genomes.
[2024-01-24 13:28:43,006] [INFO] Target genome list was writen to GCF_014656545.1_ASM1465654v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:43,014] [INFO] Task started: fastANI
[2024-01-24 13:28:43,014] [INFO] Running command: fastANI --query /var/lib/cwl/stg81797d2a-af39-40a3-a2c5-4187e1de071c/GCF_014656545.1_ASM1465654v1_genomic.fna.gz --refList GCF_014656545.1_ASM1465654v1_genomic.fna/target_genomes.txt --output GCF_014656545.1_ASM1465654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:59,549] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:59,550] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d24621b-20d8-414e-b925-387e21dc2679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:59,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d24621b-20d8-414e-b925-387e21dc2679/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:59,565] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:59,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:59,565] [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
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	100.0	1811	1818	95	conclusive
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	84.3764	1269	1818	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.6644	464	1818	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	78.6321	453	1818	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.5771	486	1818	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	78.5399	488	1818	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	78.3645	428	1818	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	78.2264	341	1818	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	78.1904	296	1818	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	78.07	293	1818	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	78.0431	351	1818	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	78.0073	388	1818	95	below_threshold
Neobacillus niacini	strain=NBRC 15566	GCA_001591505.1	86668	86668	suspected-type	True	77.8755	380	1818	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	77.8729	289	1818	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.5335	161	1818	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	77.2663	170	1818	95	below_threshold
Heyndrickxia oleronia	strain=DSM 9356	GCA_025263665.1	38875	38875	type	True	77.1159	112	1818	95	below_threshold
Robertmurraya siralis	strain=171544	GCA_005502275.1	77777	77777	type	True	76.6533	123	1818	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:59,567] [INFO] DFAST Taxonomy check result was written to GCF_014656545.1_ASM1465654v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:59,567] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:59,567] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:59,568] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d24621b-20d8-414e-b925-387e21dc2679/dqc_reference/checkm_data
[2024-01-24 13:28:59,569] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:59,621] [INFO] Task started: CheckM
[2024-01-24 13:28:59,621] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014656545.1_ASM1465654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014656545.1_ASM1465654v1_genomic.fna/checkm_input GCF_014656545.1_ASM1465654v1_genomic.fna/checkm_result
[2024-01-24 13:29:39,073] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:39,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:39,098] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:39,099] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:39,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014656545.1_ASM1465654v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:39,100] [INFO] Task started: Blastn
[2024-01-24 13:29:39,100] [INFO] Running command: blastn -query GCF_014656545.1_ASM1465654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d24621b-20d8-414e-b925-387e21dc2679/dqc_reference/reference_markers_gtdb.fasta -out GCF_014656545.1_ASM1465654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:39,954] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:39,960] [INFO] Selected 18 target genomes.
[2024-01-24 13:29:39,960] [INFO] Target genome list was writen to GCF_014656545.1_ASM1465654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:39,983] [INFO] Task started: fastANI
[2024-01-24 13:29:39,983] [INFO] Running command: fastANI --query /var/lib/cwl/stg81797d2a-af39-40a3-a2c5-4187e1de071c/GCF_014656545.1_ASM1465654v1_genomic.fna.gz --refList GCF_014656545.1_ASM1465654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014656545.1_ASM1465654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:59,025] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:59,044] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:59,044] [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_014656545.1	s__Neobacillus sp014656545	100.0	1811	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001636315.1	s__Neobacillus mesonae	84.3702	1270	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.98	98.98	0.94	0.94	2	-
GCF_016464375.1	s__Neobacillus renqingensis	80.2238	669	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016765675.1	s__Neobacillus sp016765675	79.6187	543	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000752035.1	s__Neobacillus rubiinfantis	78.6408	412	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001591805.1	s__Neobacillus novalis	78.6139	455	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018343535.1	s__Neobacillus sp018343535	78.5769	485	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.05	99.05	0.95	0.95	2	-
GCF_001866655.1	s__Neobacillus sp001866655	78.5468	407	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001026695.1	s__Neobacillus vireti	78.396	455	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002585305.1	s__Neobacillus sp002585305	78.29	383	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	97.64	95.53	0.90	0.84	3	-
GCF_016107705.1	s__Neobacillus cucumis_B	78.2696	390	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018613415.1	s__Neobacillus sp018613415	78.2594	390	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248975.1	s__Neobacillus endophyticus	78.1792	346	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759675.1	s__Neobacillus niacini_A	78.1507	400	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001048695.1	s__Neobacillus massiliamazoniensis	78.0239	352	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002567005.1	s__Neobacillus sp002567005	77.9746	359	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010975035.1	s__Neobacillus thermocopriae	77.8737	287	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.41	95.38	0.92	0.91	3	-
GCF_004341175.1	s__Neobacillus sp004341175	77.8043	345	1818	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:59,046] [INFO] GTDB search result was written to GCF_014656545.1_ASM1465654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:59,047] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:59,051] [INFO] DFAST_QC result json was written to GCF_014656545.1_ASM1465654v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:59,051] [INFO] DFAST_QC completed!
[2024-01-24 13:29:59,051] [INFO] Total running time: 0h1m30s