[2024-01-24 14:39:14,649] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,666] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,666] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a49a297-0d42-4340-a937-e5e08bcabd93/dqc_reference
[2024-01-24 14:39:16,026] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,027] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg21c4450d-69b4-49af-a6a1-a274ac41a813/GCF_008973485.1_ASM897348v1_genomic.fna.gz | prodigal -d GCF_008973485.1_ASM897348v1_genomic.fna/cds.fna -a GCF_008973485.1_ASM897348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:24,911] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:24,911] [INFO] Task started: HMMsearch
[2024-01-24 14:39:24,911] [INFO] Running command: hmmsearch --tblout GCF_008973485.1_ASM897348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a49a297-0d42-4340-a937-e5e08bcabd93/dqc_reference/reference_markers.hmm GCF_008973485.1_ASM897348v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:25,222] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:25,223] [INFO] Found 6/6 markers.
[2024-01-24 14:39:25,263] [INFO] Query marker FASTA was written to GCF_008973485.1_ASM897348v1_genomic.fna/markers.fasta
[2024-01-24 14:39:25,264] [INFO] Task started: Blastn
[2024-01-24 14:39:25,264] [INFO] Running command: blastn -query GCF_008973485.1_ASM897348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a49a297-0d42-4340-a937-e5e08bcabd93/dqc_reference/reference_markers.fasta -out GCF_008973485.1_ASM897348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:25,885] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:25,890] [INFO] Selected 15 target genomes.
[2024-01-24 14:39:25,891] [INFO] Target genome list was writen to GCF_008973485.1_ASM897348v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:25,898] [INFO] Task started: fastANI
[2024-01-24 14:39:25,898] [INFO] Running command: fastANI --query /var/lib/cwl/stg21c4450d-69b4-49af-a6a1-a274ac41a813/GCF_008973485.1_ASM897348v1_genomic.fna.gz --refList GCF_008973485.1_ASM897348v1_genomic.fna/target_genomes.txt --output GCF_008973485.1_ASM897348v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:39,126] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:39,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a49a297-0d42-4340-a937-e5e08bcabd93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:39,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a49a297-0d42-4340-a937-e5e08bcabd93/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:39,144] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:39,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:39,144] [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
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	100.0	1446	1450	95	conclusive
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	80.8118	678	1450	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	80.1017	570	1450	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	79.9812	548	1450	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	79.9735	562	1450	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	79.5964	444	1450	95	below_threshold
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	79.3994	429	1450	95	below_threshold
Solibacillus merdavium	strain=Sa1YVA6	GCA_014836935.1	2762218	2762218	type	True	77.1985	89	1450	95	below_threshold
Solibacillus faecavium	strain=A46	GCA_014836905.1	2762221	2762221	type	True	77.1624	103	1450	95	below_threshold
Lysinibacillus composti	strain=MCCC 1A13240	GCA_003856865.1	720633	720633	type	True	77.0913	138	1450	95	below_threshold
Rummeliibacillus suwonensis	strain=G20	GCA_007896435.1	1306154	1306154	type	True	76.8826	111	1450	95	below_threshold
Bacillus salipaludis	strain=WN066	GCA_004358205.1	2547811	2547811	type	True	76.8772	81	1450	95	below_threshold
Kurthia massiliensis	strain=JC30	GCA_000285555.1	1033739	1033739	type	True	76.6296	75	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:39,146] [INFO] DFAST Taxonomy check result was written to GCF_008973485.1_ASM897348v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:39,147] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:39,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:39,148] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a49a297-0d42-4340-a937-e5e08bcabd93/dqc_reference/checkm_data
[2024-01-24 14:39:39,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:39,196] [INFO] Task started: CheckM
[2024-01-24 14:39:39,196] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008973485.1_ASM897348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008973485.1_ASM897348v1_genomic.fna/checkm_input GCF_008973485.1_ASM897348v1_genomic.fna/checkm_result
[2024-01-24 14:40:11,614] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:11,615] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:11,642] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:11,642] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:11,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008973485.1_ASM897348v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:11,643] [INFO] Task started: Blastn
[2024-01-24 14:40:11,643] [INFO] Running command: blastn -query GCF_008973485.1_ASM897348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7a49a297-0d42-4340-a937-e5e08bcabd93/dqc_reference/reference_markers_gtdb.fasta -out GCF_008973485.1_ASM897348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:12,461] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:12,465] [INFO] Selected 12 target genomes.
[2024-01-24 14:40:12,465] [INFO] Target genome list was writen to GCF_008973485.1_ASM897348v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:12,499] [INFO] Task started: fastANI
[2024-01-24 14:40:12,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg21c4450d-69b4-49af-a6a1-a274ac41a813/GCF_008973485.1_ASM897348v1_genomic.fna.gz --refList GCF_008973485.1_ASM897348v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008973485.1_ASM897348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:24,865] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:24,875] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:24,875] [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_008973485.1	s__Psychrobacillus glaciei	100.0	1447	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001278755.1	s__Psychrobacillus sp001278755	80.9975	685	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.52	97.52	0.91	0.91	2	-
GCF_006861825.1	s__Psychrobacillus vulpis	80.817	677	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861775.1	s__Psychrobacillus soli	80.1111	569	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018140925.1	s__Psychrobacillus sp018140925	80.011	500	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111345.1	s__Psychrobacillus sp900111345	79.9909	585	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861795.1	s__Psychrobacillus lasiicapitis	79.9798	547	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007676755.1	s__Psychrobacillus sp007676755	79.9145	577	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254155.1	s__Psychrobacillus insolitus	79.5913	444	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900114885.1	s__Psychrobacillus psychrodurans	79.5724	467	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.67	97.67	0.91	0.91	2	-
GCF_900115805.1	s__Psychrobacillus psychrotolerans	79.4037	428	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007896435.1	s__Rummeliibacillus suwonensis	76.9009	110	1450	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Rummeliibacillus	95.0	98.15	97.53	0.89	0.86	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:24,877] [INFO] GTDB search result was written to GCF_008973485.1_ASM897348v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:24,878] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:24,881] [INFO] DFAST_QC result json was written to GCF_008973485.1_ASM897348v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:24,881] [INFO] DFAST_QC completed!
[2024-01-24 14:40:24,881] [INFO] Total running time: 0h1m10s