[2024-01-24 11:26:03,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:03,074] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:03,075] [INFO] DQC Reference Directory: /var/lib/cwl/stg0e27d57e-470d-431c-a916-03692a064542/dqc_reference
[2024-01-24 11:26:04,244] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:04,245] [INFO] Task started: Prodigal
[2024-01-24 11:26:04,246] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bba82b3-fe28-4816-bfd2-49f9aafa80aa/GCF_016765675.1_ASM1676567v1_genomic.fna.gz | prodigal -d GCF_016765675.1_ASM1676567v1_genomic.fna/cds.fna -a GCF_016765675.1_ASM1676567v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:14,437] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:14,437] [INFO] Task started: HMMsearch
[2024-01-24 11:26:14,438] [INFO] Running command: hmmsearch --tblout GCF_016765675.1_ASM1676567v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0e27d57e-470d-431c-a916-03692a064542/dqc_reference/reference_markers.hmm GCF_016765675.1_ASM1676567v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:14,688] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:14,689] [INFO] Found 6/6 markers.
[2024-01-24 11:26:14,727] [INFO] Query marker FASTA was written to GCF_016765675.1_ASM1676567v1_genomic.fna/markers.fasta
[2024-01-24 11:26:14,727] [INFO] Task started: Blastn
[2024-01-24 11:26:14,727] [INFO] Running command: blastn -query GCF_016765675.1_ASM1676567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e27d57e-470d-431c-a916-03692a064542/dqc_reference/reference_markers.fasta -out GCF_016765675.1_ASM1676567v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:15,299] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:15,303] [INFO] Selected 27 target genomes.
[2024-01-24 11:26:15,303] [INFO] Target genome list was writen to GCF_016765675.1_ASM1676567v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:15,353] [INFO] Task started: fastANI
[2024-01-24 11:26:15,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bba82b3-fe28-4816-bfd2-49f9aafa80aa/GCF_016765675.1_ASM1676567v1_genomic.fna.gz --refList GCF_016765675.1_ASM1676567v1_genomic.fna/target_genomes.txt --output GCF_016765675.1_ASM1676567v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:34,486] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:34,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0e27d57e-470d-431c-a916-03692a064542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:34,487] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0e27d57e-470d-431c-a916-03692a064542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:34,503] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:26:34,503] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:26:34,503] [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	79.6086	545	1433	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	79.3188	589	1433	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	78.2057	317	1433	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	78.089	278	1433	95	below_threshold
Neobacillus vireti	strain=DSM 15602	GCA_001026695.1	220686	220686	type	True	78.0633	327	1433	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.0407	328	1433	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.9398	258	1433	95	below_threshold
Neobacillus vireti	strain=LMG 21834	GCA_000508325.2	220686	220686	type	True	77.9342	305	1433	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.9016	324	1433	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	77.8799	234	1433	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	77.857	329	1433	95	below_threshold
Neobacillus sedimentimangrovi	strain=FJAT-2464	GCA_010614825.1	2699460	2699460	type	True	77.795	247	1433	95	below_threshold
Neobacillus drentensis	strain=FJAT-10044	GCA_001636415.1	220684	220684	type	True	77.7377	281	1433	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	77.734	326	1433	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.7272	253	1433	95	below_threshold
Neobacillus drentensis	strain=NBRC 102427	GCA_001591445.1	220684	220684	type	True	77.6023	268	1433	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	77.5518	321	1433	95	below_threshold
Neobacillus massiliamazoniensis	strain=LF1	GCA_001048695.1	1499688	1499688	type	True	77.5166	272	1433	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	77.4936	55	1433	95	below_threshold
Sutcliffiella cohnii	strain=DSM 6307	GCA_002250055.1	33932	33932	type	True	77.4368	53	1433	95	below_threshold
Heyndrickxia vini	strain=JCM 19841	GCA_016772275.1	1476025	1476025	type	True	77.4004	81	1433	95	below_threshold
Bacillus acidicola	strain=FJAT-2406	GCA_001636425.1	209389	209389	type	True	77.2277	72	1433	95	below_threshold
Bacillus dafuensis	strain=FJAT-25496	GCA_007995155.1	1742359	1742359	type	True	76.965	128	1433	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:34,505] [INFO] DFAST Taxonomy check result was written to GCF_016765675.1_ASM1676567v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:34,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:34,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:34,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0e27d57e-470d-431c-a916-03692a064542/dqc_reference/checkm_data
[2024-01-24 11:26:34,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:34,549] [INFO] Task started: CheckM
[2024-01-24 11:26:34,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016765675.1_ASM1676567v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016765675.1_ASM1676567v1_genomic.fna/checkm_input GCF_016765675.1_ASM1676567v1_genomic.fna/checkm_result
[2024-01-24 11:27:08,240] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:08,242] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.30%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:08,261] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:08,261] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:08,261] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016765675.1_ASM1676567v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:08,262] [INFO] Task started: Blastn
[2024-01-24 11:27:08,262] [INFO] Running command: blastn -query GCF_016765675.1_ASM1676567v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0e27d57e-470d-431c-a916-03692a064542/dqc_reference/reference_markers_gtdb.fasta -out GCF_016765675.1_ASM1676567v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:09,067] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:09,070] [INFO] Selected 23 target genomes.
[2024-01-24 11:27:09,070] [INFO] Target genome list was writen to GCF_016765675.1_ASM1676567v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:09,094] [INFO] Task started: fastANI
[2024-01-24 11:27:09,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bba82b3-fe28-4816-bfd2-49f9aafa80aa/GCF_016765675.1_ASM1676567v1_genomic.fna.gz --refList GCF_016765675.1_ASM1676567v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016765675.1_ASM1676567v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:27,413] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:27,432] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:27,433] [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_016765675.1	s__Neobacillus sp016765675	100.0	1431	1433	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_014656545.1	s__Neobacillus sp014656545	79.6033	546	1433	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_016464375.1	s__Neobacillus renqingensis	79.5401	576	1433	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	79.3377	587	1433	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_018343535.1	s__Neobacillus sp018343535	78.216	315	1433	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_013248975.1	s__Neobacillus endophyticus	78.1065	273	1433	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	78.0858	325	1433	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	78.0153	327	1433	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	77.9076	232	1433	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_002860255.1	s__Neobacillus cucumis_A	77.8117	254	1433	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	77.7219	277	1433	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	77.7134	254	1433	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_001866655.1	s__Neobacillus sp001866655	77.6035	270	1433	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_016772275.1	s__Heyndrickxia vini	77.4415	80	1433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Heyndrickxia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409995.1	s__Neobacillus niacini_B	77.3924	220	1433	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_001636425.1	s__Bacillus_AE acidicola	77.13	71	1433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Bacillaceae_C;g__Bacillus_AE	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995155.1	s__Cytobacillus dafuensis	76.965	128	1433	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_000632715.1	s__Saccharococcus caldoxylosilyticus	76.7732	50	1433	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:27,434] [INFO] GTDB search result was written to GCF_016765675.1_ASM1676567v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:27,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:27,439] [INFO] DFAST_QC result json was written to GCF_016765675.1_ASM1676567v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:27,439] [INFO] DFAST_QC completed!
[2024-01-24 11:27:27,439] [INFO] Total running time: 0h1m24s