[2024-01-24 12:22:13,295] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:13,297] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:13,297] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8524455-ee6c-4ac4-a03c-85d59e3429d0/dqc_reference
[2024-01-24 12:22:14,982] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:14,983] [INFO] Task started: Prodigal
[2024-01-24 12:22:14,983] [INFO] Running command: gunzip -c /var/lib/cwl/stg433f2f95-6811-4bec-873b-8f743aef2f18/GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/cds.fna -a GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:26,949] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:26,950] [INFO] Task started: HMMsearch
[2024-01-24 12:22:26,950] [INFO] Running command: hmmsearch --tblout GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8524455-ee6c-4ac4-a03c-85d59e3429d0/dqc_reference/reference_markers.hmm GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:27,297] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:27,298] [INFO] Found 6/6 markers.
[2024-01-24 12:22:27,345] [INFO] Query marker FASTA was written to GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:22:27,346] [INFO] Task started: Blastn
[2024-01-24 12:22:27,346] [INFO] Running command: blastn -query GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8524455-ee6c-4ac4-a03c-85d59e3429d0/dqc_reference/reference_markers.fasta -out GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:27,955] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:27,958] [INFO] Selected 18 target genomes.
[2024-01-24 12:22:27,959] [INFO] Target genome list was writen to GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:22:27,965] [INFO] Task started: fastANI
[2024-01-24 12:22:27,965] [INFO] Running command: fastANI --query /var/lib/cwl/stg433f2f95-6811-4bec-873b-8f743aef2f18/GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna.gz --refList GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:42,599] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:42,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8524455-ee6c-4ac4-a03c-85d59e3429d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:42,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8524455-ee6c-4ac4-a03c-85d59e3429d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:42,610] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:42,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:42,611] [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
Fictibacillus enclensis	strain=NIO-1003	GCA_900094955.1	1017270	1017270	type	True	100.0	1496	1496	95	conclusive
Fictibacillus enclensis	strain=NIO-1003	GCA_001457035.1	1017270	1017270	type	True	100.0	1496	1496	95	conclusive
Fictibacillus solisalsi	strain=CGMCC 1.6854	GCA_900103485.1	459525	459525	type	True	92.5465	1331	1496	95	below_threshold
Fictibacillus arsenicus	strain=Con a/3	GCA_001999465.1	255247	255247	type	True	77.8783	127	1496	95	below_threshold
Fictibacillus halophilus	strain=KCTC 33758	GCA_016401385.1	1610490	1610490	type	True	77.7023	109	1496	95	below_threshold
Fictibacillus aquaticus	strain=GDSW-R2A3	GCA_002245695.1	2021314	2021314	type	True	77.4846	111	1496	95	below_threshold
Fictibacillus barbaricus	strain=DSM 14730	GCA_017052555.1	182136	182136	type	True	77.2691	137	1496	95	below_threshold
Fictibacillus barbaricus	strain=CCM 4982	GCA_014635025.1	182136	182136	type	True	77.2216	132	1496	95	below_threshold
Metabacillus indicus	strain=LMG 22858	GCA_000708755.2	246786	246786	type	True	76.6695	56	1496	95	below_threshold
Neobacillus rhizophilus	strain=FJAT-49825	GCA_018343535.1	2833579	2833579	type	True	76.5889	63	1496	95	below_threshold
Metabacillus flavus	strain=KIGAM252	GCA_018283675.1	2823519	2823519	type	True	76.5834	57	1496	95	below_threshold
Peribacillus deserti	strain=DSM 105482	GCA_016909175.1	673318	673318	type	True	76.4494	51	1496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:42,613] [INFO] DFAST Taxonomy check result was written to GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:22:42,613] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:42,614] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:42,614] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8524455-ee6c-4ac4-a03c-85d59e3429d0/dqc_reference/checkm_data
[2024-01-24 12:22:42,615] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:42,660] [INFO] Task started: CheckM
[2024-01-24 12:22:42,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/checkm_input GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:23:23,252] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:23,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,278] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:23,279] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:23,279] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:23:23,280] [INFO] Task started: Blastn
[2024-01-24 12:23:23,280] [INFO] Running command: blastn -query GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8524455-ee6c-4ac4-a03c-85d59e3429d0/dqc_reference/reference_markers_gtdb.fasta -out GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,026] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,030] [INFO] Selected 17 target genomes.
[2024-01-24 12:23:24,030] [INFO] Target genome list was writen to GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:24,045] [INFO] Task started: fastANI
[2024-01-24 12:23:24,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg433f2f95-6811-4bec-873b-8f743aef2f18/GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna.gz --refList GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:36,693] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,708] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:36,708] [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_001457035.1	s__Fictibacillus_C enclensis	100.0	1496	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus_C	95.0	99.48	98.95	0.97	0.95	3	conclusive
GCF_900103485.1	s__Fictibacillus_C solisalsi	92.5392	1332	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001510655.1	s__Fictibacillus_C sp001510655	80.3028	695	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus_C	95.0	98.06	97.97	0.90	0.90	3	-
GCF_001999465.1	s__Fictibacillus arsenicus	77.8003	130	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016401385.1	s__Fictibacillus halophilus	77.5784	111	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245695.1	s__Fictibacillus aquaticus	77.5079	110	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642935.1	s__Fictibacillus arsenicus_B	77.3958	127	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216955.1	s__Fictibacillus sp004216955	77.3014	130	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__Fictibacillaceae;g__Fictibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015234585.1	s__Anaerobacillus_A hwajinpoensis_B	76.9838	50	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_G;f__HB172195;g__Anaerobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000294775.2	s__Cytobacillus oceanisediminis_B	76.9454	64	1496	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	76.5509	58	1496	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_018343535.1	s__Neobacillus sp018343535	76.4918	66	1496	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_000732485.2	s__Metabacillus_B sp000732485	76.292	60	1496	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,710] [INFO] GTDB search result was written to GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:36,710] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:36,713] [INFO] DFAST_QC result json was written to GCF_900094955.1_IMG-taxon_2616645019_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:23:36,714] [INFO] DFAST_QC completed!
[2024-01-24 12:23:36,714] [INFO] Total running time: 0h1m23s