[2024-01-25 19:05:05,768] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:05:05,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:05:05,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg394d785d-ef75-43cf-90e8-5ec595ceb510/dqc_reference
[2024-01-25 19:05:06,936] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:05:06,936] [INFO] Task started: Prodigal
[2024-01-25 19:05:06,937] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b465c6c-b26c-4f05-9927-dcc7a60b6d9b/GCF_009674765.1_ASM967476v1_genomic.fna.gz | prodigal -d GCF_009674765.1_ASM967476v1_genomic.fna/cds.fna -a GCF_009674765.1_ASM967476v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:05:16,536] [INFO] Task succeeded: Prodigal
[2024-01-25 19:05:16,536] [INFO] Task started: HMMsearch
[2024-01-25 19:05:16,536] [INFO] Running command: hmmsearch --tblout GCF_009674765.1_ASM967476v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg394d785d-ef75-43cf-90e8-5ec595ceb510/dqc_reference/reference_markers.hmm GCF_009674765.1_ASM967476v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:05:16,821] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:05:16,822] [INFO] Found 6/6 markers.
[2024-01-25 19:05:16,860] [INFO] Query marker FASTA was written to GCF_009674765.1_ASM967476v1_genomic.fna/markers.fasta
[2024-01-25 19:05:16,860] [INFO] Task started: Blastn
[2024-01-25 19:05:16,860] [INFO] Running command: blastn -query GCF_009674765.1_ASM967476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg394d785d-ef75-43cf-90e8-5ec595ceb510/dqc_reference/reference_markers.fasta -out GCF_009674765.1_ASM967476v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:17,413] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:17,416] [INFO] Selected 17 target genomes.
[2024-01-25 19:05:17,416] [INFO] Target genome list was writen to GCF_009674765.1_ASM967476v1_genomic.fna/target_genomes.txt
[2024-01-25 19:05:17,445] [INFO] Task started: fastANI
[2024-01-25 19:05:17,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b465c6c-b26c-4f05-9927-dcc7a60b6d9b/GCF_009674765.1_ASM967476v1_genomic.fna.gz --refList GCF_009674765.1_ASM967476v1_genomic.fna/target_genomes.txt --output GCF_009674765.1_ASM967476v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:05:34,540] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:34,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg394d785d-ef75-43cf-90e8-5ec595ceb510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:05:34,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg394d785d-ef75-43cf-90e8-5ec595ceb510/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:05:34,551] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:05:34,551] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:05:34,551] [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
Metabacillus idriensis	strain=DSM 19097	GCA_009674765.1	324768	324768	type	True	100.0	1612	1612	95	conclusive
Metabacillus idriensis	strain=DSM-19097	GCA_904423875.1	324768	324768	type	True	99.9977	1610	1612	95	conclusive
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	88.654	1235	1612	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	80.4112	696	1612	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	77.8588	78	1612	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	77.6512	174	1612	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	77.5571	133	1612	95	below_threshold
Metabacillus crassostreae	strain=DSM 24486	GCA_016908395.1	929098	929098	type	True	77.538	134	1612	95	below_threshold
Metabacillus endolithicus	strain=KCTC 33579	GCA_023078335.1	1535204	1535204	type	True	77.449	153	1612	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	77.4459	103	1612	95	below_threshold
Metabacillus litoralis	strain=SW-211	GCA_007994985.1	152268	152268	suspected-type	True	77.3563	140	1612	95	below_threshold
Bacillus oleivorans	strain=JC228	GCA_900207585.1	1448271	1448271	type	True	77.1943	63	1612	95	below_threshold
Bacillus swezeyi	strain=NRRL B-41294	GCA_001969815.1	1925020	1925020	type	True	77.0334	90	1612	95	below_threshold
Bacillus licheniformis	strain=DSM 13	GCA_022630555.1	1402	1402	type	True	76.8761	95	1612	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.8498	101	1612	95	below_threshold
Falsibacillus albus	strain=GY 10110	GCA_003668575.1	2478915	2478915	type	True	76.7276	93	1612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:05:34,553] [INFO] DFAST Taxonomy check result was written to GCF_009674765.1_ASM967476v1_genomic.fna/tc_result.tsv
[2024-01-25 19:05:34,553] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:05:34,553] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:05:34,553] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg394d785d-ef75-43cf-90e8-5ec595ceb510/dqc_reference/checkm_data
[2024-01-25 19:05:34,554] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:05:34,606] [INFO] Task started: CheckM
[2024-01-25 19:05:34,606] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009674765.1_ASM967476v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009674765.1_ASM967476v1_genomic.fna/checkm_input GCF_009674765.1_ASM967476v1_genomic.fna/checkm_result
[2024-01-25 19:06:07,734] [INFO] Task succeeded: CheckM
[2024-01-25 19:06:07,736] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:06:07,761] [INFO] ===== Completeness check finished =====
[2024-01-25 19:06:07,761] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:06:07,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009674765.1_ASM967476v1_genomic.fna/markers.fasta)
[2024-01-25 19:06:07,762] [INFO] Task started: Blastn
[2024-01-25 19:06:07,762] [INFO] Running command: blastn -query GCF_009674765.1_ASM967476v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg394d785d-ef75-43cf-90e8-5ec595ceb510/dqc_reference/reference_markers_gtdb.fasta -out GCF_009674765.1_ASM967476v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:08,533] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:08,536] [INFO] Selected 21 target genomes.
[2024-01-25 19:06:08,536] [INFO] Target genome list was writen to GCF_009674765.1_ASM967476v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:06:08,549] [INFO] Task started: fastANI
[2024-01-25 19:06:08,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b465c6c-b26c-4f05-9927-dcc7a60b6d9b/GCF_009674765.1_ASM967476v1_genomic.fna.gz --refList GCF_009674765.1_ASM967476v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009674765.1_ASM967476v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:06:27,197] [INFO] Task succeeded: fastANI
[2024-01-25 19:06:27,209] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:06:27,209] [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_009674765.1	s__Bacillus_P idriensis	100.0	1612	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.40	95.01	0.92	0.87	5	conclusive
GCF_014235785.1	s__Bacillus_P sp002858905	82.2622	805	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	98.85	98.20	0.93	0.90	4	-
GCF_000708755.2	s__Bacillus_P indicus	80.4362	694	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus_P	95.0	97.93	97.85	0.93	0.91	3	-
GCF_002577655.1	s__Metabacillus sp002577655	78.3954	158	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	77.8267	116	1612	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_018283675.1	s__Metabacillus_B sp018283675	77.538	132	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000009045.1	s__Bacillus subtilis	77.4749	102	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_003600835.1	s__Pseudobacillus sp003600835	77.4229	56	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038755.1	s__Cytobacillus firmus_B	77.3917	111	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	97.85	96.97	0.92	0.91	5	-
GCF_017303275.1	s__Cytobacillus sp017303275	77.3811	130	1612	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_007994985.1	s__Metabacillus litoralis	77.3022	145	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900207585.1	s__Bacillus_BF oleivorans	77.1943	63	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__JC228;f__JC228;g__Bacillus_BF	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003816055.1	s__Metabacillus_B sp003816055	77.179	150	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093085.1	s__Bacillus sp010093085	77.0912	103	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969815.1	s__Bacillus swezeyi	77.0334	90	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_000011645.1	s__Bacillus licheniformis	76.9218	97	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	99.64	99.26	0.97	0.81	213	-
GCF_000732485.2	s__Metabacillus_B sp000732485	76.8921	154	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969855.1	s__Bacillus haynesii	76.8708	88	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4556	97.08	96.53	0.93	0.92	6	-
GCF_001956215.1	s__Cytobacillus sp001956215	76.792	112	1612	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_013303125.1	s__Calidifontibacillus erzurumensis	76.3513	58	1612	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_C;f__Bacillaceae_J;g__Calidifontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:06:27,211] [INFO] GTDB search result was written to GCF_009674765.1_ASM967476v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:06:27,211] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:06:27,215] [INFO] DFAST_QC result json was written to GCF_009674765.1_ASM967476v1_genomic.fna/dqc_result.json
[2024-01-25 19:06:27,215] [INFO] DFAST_QC completed!
[2024-01-25 19:06:27,215] [INFO] Total running time: 0h1m21s