[2024-01-24 13:58:10,293] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,294] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,295] [INFO] DQC Reference Directory: /var/lib/cwl/stg933c7646-8554-4da4-9e79-7db0d8831107/dqc_reference
[2024-01-24 13:58:11,388] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,388] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a1d9d32-88f5-46e0-bdd3-96002a1ea467/GCF_018343535.1_ASM1834353v1_genomic.fna.gz | prodigal -d GCF_018343535.1_ASM1834353v1_genomic.fna/cds.fna -a GCF_018343535.1_ASM1834353v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:23,948] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:23,948] [INFO] Task started: HMMsearch
[2024-01-24 13:58:23,948] [INFO] Running command: hmmsearch --tblout GCF_018343535.1_ASM1834353v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg933c7646-8554-4da4-9e79-7db0d8831107/dqc_reference/reference_markers.hmm GCF_018343535.1_ASM1834353v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:24,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:24,220] [INFO] Found 6/6 markers.
[2024-01-24 13:58:24,265] [INFO] Query marker FASTA was written to GCF_018343535.1_ASM1834353v1_genomic.fna/markers.fasta
[2024-01-24 13:58:24,265] [INFO] Task started: Blastn
[2024-01-24 13:58:24,266] [INFO] Running command: blastn -query GCF_018343535.1_ASM1834353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg933c7646-8554-4da4-9e79-7db0d8831107/dqc_reference/reference_markers.fasta -out GCF_018343535.1_ASM1834353v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,814] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,816] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:24,816] [INFO] Target genome list was writen to GCF_018343535.1_ASM1834353v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:24,821] [INFO] Task started: fastANI
[2024-01-24 13:58:24,822] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a1d9d32-88f5-46e0-bdd3-96002a1ea467/GCF_018343535.1_ASM1834353v1_genomic.fna.gz --refList GCF_018343535.1_ASM1834353v1_genomic.fna/target_genomes.txt --output GCF_018343535.1_ASM1834353v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:46,685] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:46,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg933c7646-8554-4da4-9e79-7db0d8831107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:46,686] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg933c7646-8554-4da4-9e79-7db0d8831107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:46,696] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:46,696] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:46,696] [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 rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	100.0	2099	2101	95	conclusive
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	93.2908	1583	2101	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	79.3271	518	2101	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	79.0039	502	2101	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	78.9709	480	2101	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	78.7272	486	2101	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	78.7266	393	2101	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	78.7192	462	2101	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	78.5953	448	2101	95	below_threshold
Neobacillus cucumis	strain=DSM 101566	GCA_016908975.1	1740721	1740721	type	True	78.5496	425	2101	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	78.5466	495	2101	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	78.524	381	2101	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	78.3988	348	2101	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	78.2866	475	2101	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	78.0259	183	2101	95	below_threshold
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	77.8369	71	2101	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.6565	272	2101	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:46,697] [INFO] DFAST Taxonomy check result was written to GCF_018343535.1_ASM1834353v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:46,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:46,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:46,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg933c7646-8554-4da4-9e79-7db0d8831107/dqc_reference/checkm_data
[2024-01-24 13:58:46,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:46,757] [INFO] Task started: CheckM
[2024-01-24 13:58:46,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018343535.1_ASM1834353v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018343535.1_ASM1834353v1_genomic.fna/checkm_input GCF_018343535.1_ASM1834353v1_genomic.fna/checkm_result
[2024-01-24 13:59:24,942] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:24,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:24,959] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:24,959] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:24,959] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018343535.1_ASM1834353v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:24,959] [INFO] Task started: Blastn
[2024-01-24 13:59:24,959] [INFO] Running command: blastn -query GCF_018343535.1_ASM1834353v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg933c7646-8554-4da4-9e79-7db0d8831107/dqc_reference/reference_markers_gtdb.fasta -out GCF_018343535.1_ASM1834353v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:25,723] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:25,726] [INFO] Selected 27 target genomes.
[2024-01-24 13:59:25,726] [INFO] Target genome list was writen to GCF_018343535.1_ASM1834353v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:25,739] [INFO] Task started: fastANI
[2024-01-24 13:59:25,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a1d9d32-88f5-46e0-bdd3-96002a1ea467/GCF_018343535.1_ASM1834353v1_genomic.fna.gz --refList GCF_018343535.1_ASM1834353v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018343535.1_ASM1834353v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:56,415] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:56,427] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:56,427] [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_018343535.1	s__Neobacillus sp018343535	100.0	2099	2101	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	conclusive
GCF_001510715.1	s__Neobacillus sp001510715	79.4925	681	2101	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_001636315.1	s__Neobacillus mesonae	79.342	516	2101	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_900177675.1	s__Neobacillus sp900177675	79.0775	486	2101	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	98.52	98.52	0.84	0.84	2	-
GCF_001026695.1	s__Neobacillus vireti	78.9514	481	2101	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_005154805.1	s__Neobacillus sp005154805	78.8319	504	2101	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_019219025.1	s__Neobacillus sp019219025	78.7833	475	2101	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_002860255.1	s__Neobacillus cucumis_A	78.7693	442	2101	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_014656545.1	s__Neobacillus sp014656545	78.7236	487	2101	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	78.6871	456	2101	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	78.6417	395	2101	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_001591805.1	s__Neobacillus novalis	78.5969	489	2101	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_016908975.1	s__Neobacillus cucumis	78.5242	426	2101	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_002585305.1	s__Neobacillus sp002585305	78.5118	440	2101	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_001048695.1	s__Neobacillus massiliamazoniensis	78.5095	380	2101	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_018613065.1	s__Neobacillus sp018613065	78.3884	472	2101	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	95.53	95.32	0.78	0.75	6	-
GCF_001591665.1	s__Neobacillus soli	78.2809	477	2101	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_016464375.1	s__Neobacillus renqingensis	77.8567	372	2101	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_001591485.1	s__Neobacillus fumarioli	77.6565	272	2101	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_002574545.1	s__Gottfriedia sp002574545	77.1115	64	2101	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Gottfriedia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014712675.1	s__Bacillus_AD faecalis	76.9551	83	2101	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Bacillus_AD	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:56,429] [INFO] GTDB search result was written to GCF_018343535.1_ASM1834353v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:56,429] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:56,432] [INFO] DFAST_QC result json was written to GCF_018343535.1_ASM1834353v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:56,433] [INFO] DFAST_QC completed!
[2024-01-24 13:59:56,433] [INFO] Total running time: 0h1m46s