[2024-01-24 12:14:34,073] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:34,081] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:34,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg309538b1-4fc4-42b4-968d-b5983e5f1eff/dqc_reference
[2024-01-24 12:14:35,343] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,344] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,344] [INFO] Running command: gunzip -c /var/lib/cwl/stgadf94030-ea8b-48f0-99a0-7f83c29a3ada/GCF_004376175.1_ASM437617v1_genomic.fna.gz | prodigal -d GCF_004376175.1_ASM437617v1_genomic.fna/cds.fna -a GCF_004376175.1_ASM437617v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:43,538] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:43,538] [INFO] Task started: HMMsearch
[2024-01-24 12:14:43,538] [INFO] Running command: hmmsearch --tblout GCF_004376175.1_ASM437617v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg309538b1-4fc4-42b4-968d-b5983e5f1eff/dqc_reference/reference_markers.hmm GCF_004376175.1_ASM437617v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:43,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:43,863] [INFO] Found 6/6 markers.
[2024-01-24 12:14:43,896] [INFO] Query marker FASTA was written to GCF_004376175.1_ASM437617v1_genomic.fna/markers.fasta
[2024-01-24 12:14:43,896] [INFO] Task started: Blastn
[2024-01-24 12:14:43,897] [INFO] Running command: blastn -query GCF_004376175.1_ASM437617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309538b1-4fc4-42b4-968d-b5983e5f1eff/dqc_reference/reference_markers.fasta -out GCF_004376175.1_ASM437617v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:44,442] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:44,444] [INFO] Selected 23 target genomes.
[2024-01-24 12:14:44,444] [INFO] Target genome list was writen to GCF_004376175.1_ASM437617v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:44,608] [INFO] Task started: fastANI
[2024-01-24 12:14:44,608] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf94030-ea8b-48f0-99a0-7f83c29a3ada/GCF_004376175.1_ASM437617v1_genomic.fna.gz --refList GCF_004376175.1_ASM437617v1_genomic.fna/target_genomes.txt --output GCF_004376175.1_ASM437617v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:00,823] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:00,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg309538b1-4fc4-42b4-968d-b5983e5f1eff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:00,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg309538b1-4fc4-42b4-968d-b5983e5f1eff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:00,831] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:00,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:00,831] [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
Halalkalibacterium halodurans	strain=DSM 497	GCA_004376175.1	86665	86665	type	True	100.0	1301	1313	95	conclusive
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	79.2639	115	1313	95	below_threshold
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	78.3454	107	1313	95	below_threshold
Alkalihalobacillus patagoniensis	strain=DSM 16117	GCA_002019705.1	228576	228576	type	True	78.1996	54	1313	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=KCTC 13244	GCA_001590785.1	519424	519424	type	True	77.6894	72	1313	95	below_threshold
Bacillus shivajii	strain=JCM 32183	GCA_020519665.1	1983719	1983719	type	True	77.6426	57	1313	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.3108	70	1313	95	below_threshold
Alkalihalobacillus trypoxylicola	strain=NBRC 102646	GCA_001592025.1	519424	519424	type	True	76.8758	66	1313	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	76.6603	92	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:00,832] [INFO] DFAST Taxonomy check result was written to GCF_004376175.1_ASM437617v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:00,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:00,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:00,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg309538b1-4fc4-42b4-968d-b5983e5f1eff/dqc_reference/checkm_data
[2024-01-24 12:15:00,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:00,875] [INFO] Task started: CheckM
[2024-01-24 12:15:00,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004376175.1_ASM437617v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004376175.1_ASM437617v1_genomic.fna/checkm_input GCF_004376175.1_ASM437617v1_genomic.fna/checkm_result
[2024-01-24 12:15:29,575] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:29,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:29,587] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:29,587] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:29,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004376175.1_ASM437617v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:29,587] [INFO] Task started: Blastn
[2024-01-24 12:15:29,588] [INFO] Running command: blastn -query GCF_004376175.1_ASM437617v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg309538b1-4fc4-42b4-968d-b5983e5f1eff/dqc_reference/reference_markers_gtdb.fasta -out GCF_004376175.1_ASM437617v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:30,367] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:30,369] [INFO] Selected 27 target genomes.
[2024-01-24 12:15:30,370] [INFO] Target genome list was writen to GCF_004376175.1_ASM437617v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:30,382] [INFO] Task started: fastANI
[2024-01-24 12:15:30,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgadf94030-ea8b-48f0-99a0-7f83c29a3ada/GCF_004376175.1_ASM437617v1_genomic.fna.gz --refList GCF_004376175.1_ASM437617v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004376175.1_ASM437617v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:48,458] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:48,465] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:48,465] [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_004376175.1	s__Bacillus_M halodurans	100.0	1301	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_M	95.0	98.72	98.59	0.83	0.82	4	conclusive
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	79.2639	115	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787375.1	s__Bacillus_L okhensis	78.3454	107	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019705.1	s__Bacillus_H patagoniensis	78.1869	53	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156385.1	s__45385 sp002156385	77.8875	108	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590785.1	s__Alkalihalobacillus trypoxylicola	77.6894	72	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	98.48	96.97	0.95	0.90	3	-
GCF_017745675.1	s__Bacillus_BH sp017745675	77.5074	82	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	77.3108	70	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	76.7088	90	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	76.5883	74	1313	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:48,466] [INFO] GTDB search result was written to GCF_004376175.1_ASM437617v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:48,467] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:48,469] [INFO] DFAST_QC result json was written to GCF_004376175.1_ASM437617v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:48,469] [INFO] DFAST_QC completed!
[2024-01-24 12:15:48,469] [INFO] Total running time: 0h1m14s