[2024-01-25 17:46:35,595] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:35,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:35,597] [INFO] DQC Reference Directory: /var/lib/cwl/stg89904dce-1fb7-4a30-8c9e-9b983f427c59/dqc_reference
[2024-01-25 17:46:36,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:36,858] [INFO] Task started: Prodigal
[2024-01-25 17:46:36,858] [INFO] Running command: gunzip -c /var/lib/cwl/stg5ac11069-d209-4e9d-b855-b0a375164d76/GCF_027563345.1_ASM2756334v1_genomic.fna.gz | prodigal -d GCF_027563345.1_ASM2756334v1_genomic.fna/cds.fna -a GCF_027563345.1_ASM2756334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:43,741] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:43,741] [INFO] Task started: HMMsearch
[2024-01-25 17:46:43,741] [INFO] Running command: hmmsearch --tblout GCF_027563345.1_ASM2756334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89904dce-1fb7-4a30-8c9e-9b983f427c59/dqc_reference/reference_markers.hmm GCF_027563345.1_ASM2756334v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:43,973] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:43,975] [INFO] Found 6/6 markers.
[2024-01-25 17:46:44,006] [INFO] Query marker FASTA was written to GCF_027563345.1_ASM2756334v1_genomic.fna/markers.fasta
[2024-01-25 17:46:44,006] [INFO] Task started: Blastn
[2024-01-25 17:46:44,006] [INFO] Running command: blastn -query GCF_027563345.1_ASM2756334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89904dce-1fb7-4a30-8c9e-9b983f427c59/dqc_reference/reference_markers.fasta -out GCF_027563345.1_ASM2756334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:44,580] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:44,584] [INFO] Selected 15 target genomes.
[2024-01-25 17:46:44,584] [INFO] Target genome list was writen to GCF_027563345.1_ASM2756334v1_genomic.fna/target_genomes.txt
[2024-01-25 17:46:44,590] [INFO] Task started: fastANI
[2024-01-25 17:46:44,590] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ac11069-d209-4e9d-b855-b0a375164d76/GCF_027563345.1_ASM2756334v1_genomic.fna.gz --refList GCF_027563345.1_ASM2756334v1_genomic.fna/target_genomes.txt --output GCF_027563345.1_ASM2756334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:57,124] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:57,124] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89904dce-1fb7-4a30-8c9e-9b983f427c59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:57,124] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89904dce-1fb7-4a30-8c9e-9b983f427c59/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:57,134] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:46:57,134] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:46:57,134] [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 psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	84.6023	911	1316	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	79.751	518	1316	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	79.7289	523	1316	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	79.4955	479	1316	95	below_threshold
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	79.4663	494	1316	95	below_threshold
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	79.3311	479	1316	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	79.1634	398	1316	95	below_threshold
Solibacillus cecembensis	strain=DSM 21993	GCA_001439635.1	459347	459347	type	True	77.3383	124	1316	95	below_threshold
Lysinibacillus cavernae	strain=SYSU K30005	GCA_009724685.1	2666135	2666135	type	True	77.2607	129	1316	95	below_threshold
Metabacillus bambusae	strain=BG109	GCA_017497975.1	2795218	2795218	type	True	76.9064	70	1316	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	76.7062	50	1316	95	below_threshold
Bacillus suaedaesalsae	strain=RD4P76	GCA_016890225.1	2810349	2810349	type	True	76.4812	57	1316	95	below_threshold
Bacillus gaemokensis	strain=JCM 15801	GCA_000712615.1	574375	574375	type	True	76.1195	63	1316	95	below_threshold
Bacillus gaemokensis	strain=KCTC 13318	GCA_001590835.1	574375	574375	type	True	76.0911	64	1316	95	below_threshold
Bacillus sanguinis	strain=BML-BC004	GCA_018332475.1	2817476	2817476	type	True	76.0833	59	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:57,135] [INFO] DFAST Taxonomy check result was written to GCF_027563345.1_ASM2756334v1_genomic.fna/tc_result.tsv
[2024-01-25 17:46:57,136] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:57,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:57,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89904dce-1fb7-4a30-8c9e-9b983f427c59/dqc_reference/checkm_data
[2024-01-25 17:46:57,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:57,178] [INFO] Task started: CheckM
[2024-01-25 17:46:57,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027563345.1_ASM2756334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027563345.1_ASM2756334v1_genomic.fna/checkm_input GCF_027563345.1_ASM2756334v1_genomic.fna/checkm_result
[2024-01-25 17:47:22,176] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:22,177] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:22,198] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:22,198] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:22,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027563345.1_ASM2756334v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:22,199] [INFO] Task started: Blastn
[2024-01-25 17:47:22,199] [INFO] Running command: blastn -query GCF_027563345.1_ASM2756334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg89904dce-1fb7-4a30-8c9e-9b983f427c59/dqc_reference/reference_markers_gtdb.fasta -out GCF_027563345.1_ASM2756334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:23,005] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:23,007] [INFO] Selected 8 target genomes.
[2024-01-25 17:47:23,008] [INFO] Target genome list was writen to GCF_027563345.1_ASM2756334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:23,016] [INFO] Task started: fastANI
[2024-01-25 17:47:23,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg5ac11069-d209-4e9d-b855-b0a375164d76/GCF_027563345.1_ASM2756334v1_genomic.fna.gz --refList GCF_027563345.1_ASM2756334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027563345.1_ASM2756334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:31,234] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:31,241] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:31,241] [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
GCA_900114885.1	s__Psychrobacillus psychrodurans	99.9936	1299	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.67	97.67	0.91	0.91	2	conclusive
GCF_018140925.1	s__Psychrobacillus sp018140925	87.653	1024	1316	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_900103605.1	s__Psychrobacillus sp900103605	84.6843	859	1316	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_900115805.1	s__Psychrobacillus psychrotolerans	84.5676	915	1316	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	79.7744	516	1316	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_900111345.1	s__Psychrobacillus sp900111345	79.753	505	1316	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_008973485.1	s__Psychrobacillus glaciei	79.3751	482	1316	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	79.1402	401	1316	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:31,242] [INFO] GTDB search result was written to GCF_027563345.1_ASM2756334v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:31,243] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:31,247] [INFO] DFAST_QC result json was written to GCF_027563345.1_ASM2756334v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:31,248] [INFO] DFAST_QC completed!
[2024-01-25 17:47:31,248] [INFO] Total running time: 0h0m56s