[2024-01-25 20:24:05,709] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:24:05,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:24:05,710] [INFO] DQC Reference Directory: /var/lib/cwl/stgc312bca2-84c5-49bc-ae1c-6dfe5f8754bb/dqc_reference
[2024-01-25 20:24:06,804] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:24:06,805] [INFO] Task started: Prodigal
[2024-01-25 20:24:06,805] [INFO] Running command: gunzip -c /var/lib/cwl/stgef9274aa-cf06-4262-bf9e-f5068e6d0683/GCF_001700985.1_ASM170098v1_genomic.fna.gz | prodigal -d GCF_001700985.1_ASM170098v1_genomic.fna/cds.fna -a GCF_001700985.1_ASM170098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:16,355] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:16,355] [INFO] Task started: HMMsearch
[2024-01-25 20:24:16,355] [INFO] Running command: hmmsearch --tblout GCF_001700985.1_ASM170098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc312bca2-84c5-49bc-ae1c-6dfe5f8754bb/dqc_reference/reference_markers.hmm GCF_001700985.1_ASM170098v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:16,591] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:16,592] [INFO] Found 6/6 markers.
[2024-01-25 20:24:16,622] [INFO] Query marker FASTA was written to GCF_001700985.1_ASM170098v1_genomic.fna/markers.fasta
[2024-01-25 20:24:16,622] [INFO] Task started: Blastn
[2024-01-25 20:24:16,622] [INFO] Running command: blastn -query GCF_001700985.1_ASM170098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc312bca2-84c5-49bc-ae1c-6dfe5f8754bb/dqc_reference/reference_markers.fasta -out GCF_001700985.1_ASM170098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:17,160] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:17,163] [INFO] Selected 11 target genomes.
[2024-01-25 20:24:17,163] [INFO] Target genome list was writen to GCF_001700985.1_ASM170098v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:17,171] [INFO] Task started: fastANI
[2024-01-25 20:24:17,171] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9274aa-cf06-4262-bf9e-f5068e6d0683/GCF_001700985.1_ASM170098v1_genomic.fna.gz --refList GCF_001700985.1_ASM170098v1_genomic.fna/target_genomes.txt --output GCF_001700985.1_ASM170098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:27,636] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:27,636] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc312bca2-84c5-49bc-ae1c-6dfe5f8754bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:27,637] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc312bca2-84c5-49bc-ae1c-6dfe5f8754bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:27,643] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2024-01-25 20:24:27,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:27,643] [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 thermoglucosidasius	strain=NCIMB 11955	GCA_001700985.1	1426	1426	type	True	100.0	1333	1333	95	conclusive
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_001295365.1	1426	1426	type	True	99.9966	1291	1333	95	conclusive
Parageobacillus thermoglucosidasius	strain=DSM 2542	GCA_000966225.1	1426	1426	type	True	99.9538	1268	1333	95	conclusive
Parageobacillus thermoglucosidasius	strain=NBRC 107763	GCA_000648295.1	1426	1426	type	True	99.9459	1259	1333	95	conclusive
Parageobacillus thermantarcticus	strain=M1	GCA_900111865.1	186116	186116	type	True	90.0357	888	1333	95	below_threshold
Parageobacillus caldoxylosilyticus	strain=NBRC 107762	GCA_000632715.1	81408	81408	type	True	83.5202	825	1333	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:27,645] [INFO] DFAST Taxonomy check result was written to GCF_001700985.1_ASM170098v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:27,645] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:27,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:27,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc312bca2-84c5-49bc-ae1c-6dfe5f8754bb/dqc_reference/checkm_data
[2024-01-25 20:24:27,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:27,686] [INFO] Task started: CheckM
[2024-01-25 20:24:27,686] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001700985.1_ASM170098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001700985.1_ASM170098v1_genomic.fna/checkm_input GCF_001700985.1_ASM170098v1_genomic.fna/checkm_result
[2024-01-25 20:24:58,777] [INFO] Task succeeded: CheckM
[2024-01-25 20:24:58,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:24:58,806] [INFO] ===== Completeness check finished =====
[2024-01-25 20:24:58,806] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:24:58,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001700985.1_ASM170098v1_genomic.fna/markers.fasta)
[2024-01-25 20:24:58,807] [INFO] Task started: Blastn
[2024-01-25 20:24:58,807] [INFO] Running command: blastn -query GCF_001700985.1_ASM170098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc312bca2-84c5-49bc-ae1c-6dfe5f8754bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_001700985.1_ASM170098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:59,737] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:59,739] [INFO] Selected 8 target genomes.
[2024-01-25 20:24:59,739] [INFO] Target genome list was writen to GCF_001700985.1_ASM170098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:24:59,763] [INFO] Task started: fastANI
[2024-01-25 20:24:59,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgef9274aa-cf06-4262-bf9e-f5068e6d0683/GCF_001700985.1_ASM170098v1_genomic.fna.gz --refList GCF_001700985.1_ASM170098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001700985.1_ASM170098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:25:07,324] [INFO] Task succeeded: fastANI
[2024-01-25 20:25:07,342] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:25:07,343] [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_001295365.1	s__Parageobacillus thermoglucosidasius	99.9966	1291	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	99.38	98.69	0.94	0.85	16	conclusive
GCF_001655645.1	s__Parageobacillus thermoglucosidasius_A	91.0453	1048	1333	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	90.0326	888	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688615.2	s__Parageobacillus toebii	85.5426	878	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Parageobacillus	95.0	98.34	97.52	0.87	0.80	15	-
GCF_000632715.1	s__Saccharococcus caldoxylosilyticus	83.521	824	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	98.78	97.71	0.91	0.87	7	-
GCF_011761475.1	s__Saccharococcus thermophilus	83.1438	740	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000632515.1	s__Saccharococcus sp000632515	83.1245	828	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Anoxybacillaceae;g__Saccharococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009183655.1	s__Pseudobacillus aerolatus	76.5799	69	1333	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__Domibacillaceae;g__Pseudobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:25:07,344] [INFO] GTDB search result was written to GCF_001700985.1_ASM170098v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:25:07,345] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:25:07,347] [INFO] DFAST_QC result json was written to GCF_001700985.1_ASM170098v1_genomic.fna/dqc_result.json
[2024-01-25 20:25:07,347] [INFO] DFAST_QC completed!
[2024-01-25 20:25:07,347] [INFO] Total running time: 0h1m2s