[2024-01-24 11:51:19,605] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:19,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:19,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d3645e4-a65d-4bae-8747-179b32879f81/dqc_reference
[2024-01-24 11:51:20,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:20,799] [INFO] Task started: Prodigal
[2024-01-24 11:51:20,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg40dc5b89-4498-4be4-ba24-4a2cf332f0ec/GCF_016464375.1_ASM1646437v1_genomic.fna.gz | prodigal -d GCF_016464375.1_ASM1646437v1_genomic.fna/cds.fna -a GCF_016464375.1_ASM1646437v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:30,558] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:30,559] [INFO] Task started: HMMsearch
[2024-01-24 11:51:30,559] [INFO] Running command: hmmsearch --tblout GCF_016464375.1_ASM1646437v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d3645e4-a65d-4bae-8747-179b32879f81/dqc_reference/reference_markers.hmm GCF_016464375.1_ASM1646437v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:30,872] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:30,873] [INFO] Found 6/6 markers.
[2024-01-24 11:51:30,915] [INFO] Query marker FASTA was written to GCF_016464375.1_ASM1646437v1_genomic.fna/markers.fasta
[2024-01-24 11:51:30,916] [INFO] Task started: Blastn
[2024-01-24 11:51:30,916] [INFO] Running command: blastn -query GCF_016464375.1_ASM1646437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d3645e4-a65d-4bae-8747-179b32879f81/dqc_reference/reference_markers.fasta -out GCF_016464375.1_ASM1646437v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:31,512] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:31,517] [INFO] Selected 19 target genomes.
[2024-01-24 11:51:31,517] [INFO] Target genome list was writen to GCF_016464375.1_ASM1646437v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:31,561] [INFO] Task started: fastANI
[2024-01-24 11:51:31,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg40dc5b89-4498-4be4-ba24-4a2cf332f0ec/GCF_016464375.1_ASM1646437v1_genomic.fna.gz --refList GCF_016464375.1_ASM1646437v1_genomic.fna/target_genomes.txt --output GCF_016464375.1_ASM1646437v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:47,063] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:47,064] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d3645e4-a65d-4bae-8747-179b32879f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:47,064] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d3645e4-a65d-4bae-8747-179b32879f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:47,081] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:51:47,081] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:51:47,081] [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	80.3945	647	1465	95	below_threshold
Neobacillus mesonae	strain=FJAT-13985	GCA_001636315.1	1193713	1193713	type	True	80.1095	647	1465	95	below_threshold
Neobacillus soli	strain=DSM 15604	GCA_002335815.1	220688	220688	type	True	78.0509	373	1465	95	below_threshold
Neobacillus soli	strain=NBRC 102451	GCA_001591665.1	220688	220688	type	True	78.0075	363	1465	95	below_threshold
Neobacillus novalis	strain=FJAT-14227	GCA_001636395.1	220687	220687	type	True	78.0038	423	1465	95	below_threshold
Neobacillus novalis	strain=NBRC 102450	GCA_001591805.1	220687	220687	type	True	77.9702	414	1465	95	below_threshold
Neobacillus citreus	strain=FJAT-50051	GCA_018343545.2	2833578	2833578	type	True	77.8693	349	1465	95	below_threshold
Neobacillus fumarioli	strain=NBRC 102428	GCA_001591485.1	105229	105229	type	True	77.8527	287	1465	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	77.8365	360	1465	95	below_threshold
Neobacillus jeddahensis	strain=JCE	GCA_000612625.1	1461580	1461580	type	True	77.7739	328	1465	95	below_threshold
Neobacillus endophyticus	strain=BRMEA1	GCA_013248975.1	2738405	2738405	type	True	77.664	312	1465	95	below_threshold
Neobacillus dielmonensis	strain=FF4	GCA_000612665.1	1347369	1347369	type	True	77.5718	278	1465	95	below_threshold
Neobacillus thermocopriae	strain=SgZ-7	GCA_010975035.1	1215031	1215031	type	True	77.4426	250	1465	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.6452	144	1465	95	below_threshold
Peribacillus loiseleuriae	strain=FJAT-27997	GCA_001183985.1	1679170	1679170	type	True	76.2006	90	1465	95	below_threshold
Pseudoneobacillus rhizosphaerae	strain=CIP 111885	GCA_917563885.1	2880968	2880968	type	True	76.1697	114	1465	95	below_threshold
Bacillus massiliogorillae	strain=G2	GCA_000380245.2	1243664	1243664	type	True	75.8737	65	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:47,083] [INFO] DFAST Taxonomy check result was written to GCF_016464375.1_ASM1646437v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:47,083] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:47,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:47,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d3645e4-a65d-4bae-8747-179b32879f81/dqc_reference/checkm_data
[2024-01-24 11:51:47,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:47,134] [INFO] Task started: CheckM
[2024-01-24 11:51:47,135] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016464375.1_ASM1646437v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016464375.1_ASM1646437v1_genomic.fna/checkm_input GCF_016464375.1_ASM1646437v1_genomic.fna/checkm_result
[2024-01-24 11:52:20,829] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:20,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:20,856] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:20,856] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:20,857] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016464375.1_ASM1646437v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:20,857] [INFO] Task started: Blastn
[2024-01-24 11:52:20,857] [INFO] Running command: blastn -query GCF_016464375.1_ASM1646437v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d3645e4-a65d-4bae-8747-179b32879f81/dqc_reference/reference_markers_gtdb.fasta -out GCF_016464375.1_ASM1646437v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:21,608] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:21,613] [INFO] Selected 19 target genomes.
[2024-01-24 11:52:21,613] [INFO] Target genome list was writen to GCF_016464375.1_ASM1646437v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:21,642] [INFO] Task started: fastANI
[2024-01-24 11:52:21,642] [INFO] Running command: fastANI --query /var/lib/cwl/stg40dc5b89-4498-4be4-ba24-4a2cf332f0ec/GCF_016464375.1_ASM1646437v1_genomic.fna.gz --refList GCF_016464375.1_ASM1646437v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016464375.1_ASM1646437v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:40,226] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:40,257] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:40,258] [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_016464375.1	s__Neobacillus renqingensis	100.0	1464	1465	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	80.3921	648	1465	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	80.0817	651	1465	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_016765675.1	s__Neobacillus sp016765675	79.696	568	1465	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	79.1011	421	1465	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_005154805.1	s__Neobacillus sp005154805	78.2099	396	1465	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_001591665.1	s__Neobacillus soli	78.0105	364	1465	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_001510715.1	s__Neobacillus sp001510715	77.884	335	1465	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	77.852	287	1465	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_018343535.1	s__Neobacillus sp018343535	77.7904	363	1465	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_000612625.1	s__Neobacillus jeddahensis	77.7739	328	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	99.99	99.99	0.99	0.99	3	-
GCF_013248975.1	s__Neobacillus endophyticus	77.6852	310	1465	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_000612665.1	s__Neobacillus dielmonensis	77.5833	277	1465	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	77.4733	332	1465	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	77.4296	252	1465	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_013409995.1	s__Neobacillus niacini_B	77.3122	242	1465	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_000294775.2	s__Cytobacillus oceanisediminis_B	76.5892	128	1465	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	-
GCF_001510645.1	s__Peribacillus sp001510645	75.9626	75	1465	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Peribacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:40,261] [INFO] GTDB search result was written to GCF_016464375.1_ASM1646437v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:40,262] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:40,268] [INFO] DFAST_QC result json was written to GCF_016464375.1_ASM1646437v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:40,268] [INFO] DFAST_QC completed!
[2024-01-24 11:52:40,268] [INFO] Total running time: 0h1m21s