[2024-01-24 15:10:33,242] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:33,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:33,244] [INFO] DQC Reference Directory: /var/lib/cwl/stge8a0d576-3584-45a5-9737-8f8086cb6696/dqc_reference
[2024-01-24 15:10:37,182] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:37,183] [INFO] Task started: Prodigal
[2024-01-24 15:10:37,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg6a9ea194-7920-451c-8c95-3727e951da73/GCF_014196095.1_ASM1419609v1_genomic.fna.gz | prodigal -d GCF_014196095.1_ASM1419609v1_genomic.fna/cds.fna -a GCF_014196095.1_ASM1419609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:45,498] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:45,498] [INFO] Task started: HMMsearch
[2024-01-24 15:10:45,499] [INFO] Running command: hmmsearch --tblout GCF_014196095.1_ASM1419609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8a0d576-3584-45a5-9737-8f8086cb6696/dqc_reference/reference_markers.hmm GCF_014196095.1_ASM1419609v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:45,773] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:45,775] [INFO] Found 6/6 markers.
[2024-01-24 15:10:45,807] [INFO] Query marker FASTA was written to GCF_014196095.1_ASM1419609v1_genomic.fna/markers.fasta
[2024-01-24 15:10:45,807] [INFO] Task started: Blastn
[2024-01-24 15:10:45,807] [INFO] Running command: blastn -query GCF_014196095.1_ASM1419609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a0d576-3584-45a5-9737-8f8086cb6696/dqc_reference/reference_markers.fasta -out GCF_014196095.1_ASM1419609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:47,260] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:47,264] [INFO] Selected 12 target genomes.
[2024-01-24 15:10:47,264] [INFO] Target genome list was writen to GCF_014196095.1_ASM1419609v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:47,339] [INFO] Task started: fastANI
[2024-01-24 15:10:47,339] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a9ea194-7920-451c-8c95-3727e951da73/GCF_014196095.1_ASM1419609v1_genomic.fna.gz --refList GCF_014196095.1_ASM1419609v1_genomic.fna/target_genomes.txt --output GCF_014196095.1_ASM1419609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:56,563] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:56,564] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8a0d576-3584-45a5-9737-8f8086cb6696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:56,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8a0d576-3584-45a5-9737-8f8086cb6696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:56,573] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:10:56,574] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:56,574] [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
Parageobacillus toebii	strain=DSM 14590	GCA_014196095.1	153151	153151	type	True	100.0	1065	1066	95	conclusive
Parageobacillus toebii	strain=DSM 14590	GCA_003688615.2	153151	153151	type	True	99.9974	1064	1066	95	conclusive
Parageobacillus toebii	strain=NBRC 107807	GCA_001598935.1	153151	153151	type	True	99.9959	1047	1066	95	conclusive
Parageobacillus thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	85.4361	828	1066	95	below_threshold
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	85.2984	815	1066	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=DSM 12041	GCA_014196025.1	81408	81408	type	True	84.9013	808	1066	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	84.6282	796	1066	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	77.6786	206	1066	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.5005	66	1066	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:56,575] [INFO] DFAST Taxonomy check result was written to GCF_014196095.1_ASM1419609v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:56,576] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:56,576] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:56,576] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8a0d576-3584-45a5-9737-8f8086cb6696/dqc_reference/checkm_data
[2024-01-24 15:10:56,577] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:56,613] [INFO] Task started: CheckM
[2024-01-24 15:10:56,613] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196095.1_ASM1419609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196095.1_ASM1419609v1_genomic.fna/checkm_input GCF_014196095.1_ASM1419609v1_genomic.fna/checkm_result
[2024-01-24 15:11:30,313] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:30,314] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:30,334] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:30,335] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:30,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196095.1_ASM1419609v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:30,336] [INFO] Task started: Blastn
[2024-01-24 15:11:30,336] [INFO] Running command: blastn -query GCF_014196095.1_ASM1419609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge8a0d576-3584-45a5-9737-8f8086cb6696/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196095.1_ASM1419609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:31,163] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:31,168] [INFO] Selected 7 target genomes.
[2024-01-24 15:11:31,168] [INFO] Target genome list was writen to GCF_014196095.1_ASM1419609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:31,177] [INFO] Task started: fastANI
[2024-01-24 15:11:31,177] [INFO] Running command: fastANI --query /var/lib/cwl/stg6a9ea194-7920-451c-8c95-3727e951da73/GCF_014196095.1_ASM1419609v1_genomic.fna.gz --refList GCF_014196095.1_ASM1419609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196095.1_ASM1419609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:38,413] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:38,424] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:38,425] [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_003688615.2	s__Parageobacillus toebii	99.9974	1064	1066	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	conclusive
GCF_001655645.1	s__Parageobacillus thermoglucosidasius_A	86.0106	847	1066	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111865.1	s__Parageobacillus thermantarcticus	85.9624	771	1066	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632515.1	s__Saccharococcus sp000632515	85.3502	820	1066	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001295365.1	s__Parageobacillus thermoglucosidasius	85.2943	814	1066	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	-
GCF_011761475.1	s__Saccharococcus thermophilus	84.9405	767	1066	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632715.1	s__Saccharococcus caldoxylosilyticus	84.6301	796	1066	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:38,426] [INFO] GTDB search result was written to GCF_014196095.1_ASM1419609v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:38,427] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:38,430] [INFO] DFAST_QC result json was written to GCF_014196095.1_ASM1419609v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:38,431] [INFO] DFAST_QC completed!
[2024-01-24 15:11:38,431] [INFO] Total running time: 0h1m5s