[2024-01-24 14:14:03,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:03,730] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:03,730] [INFO] DQC Reference Directory: /var/lib/cwl/stg4fa52453-2fd7-4823-9620-f5a9adae6a43/dqc_reference
[2024-01-24 14:14:04,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:04,973] [INFO] Task started: Prodigal
[2024-01-24 14:14:04,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg75415488-f61b-4573-9bb3-e578de494280/GCF_900445435.1_59178_C01_genomic.fna.gz | prodigal -d GCF_900445435.1_59178_C01_genomic.fna/cds.fna -a GCF_900445435.1_59178_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:14:14,913] [INFO] Task succeeded: Prodigal
[2024-01-24 14:14:14,914] [INFO] Task started: HMMsearch
[2024-01-24 14:14:14,914] [INFO] Running command: hmmsearch --tblout GCF_900445435.1_59178_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4fa52453-2fd7-4823-9620-f5a9adae6a43/dqc_reference/reference_markers.hmm GCF_900445435.1_59178_C01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:14:15,242] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:14:15,243] [INFO] Found 6/6 markers.
[2024-01-24 14:14:15,276] [INFO] Query marker FASTA was written to GCF_900445435.1_59178_C01_genomic.fna/markers.fasta
[2024-01-24 14:14:15,276] [INFO] Task started: Blastn
[2024-01-24 14:14:15,277] [INFO] Running command: blastn -query GCF_900445435.1_59178_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa52453-2fd7-4823-9620-f5a9adae6a43/dqc_reference/reference_markers.fasta -out GCF_900445435.1_59178_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:15,918] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:15,921] [INFO] Selected 10 target genomes.
[2024-01-24 14:14:15,921] [INFO] Target genome list was writen to GCF_900445435.1_59178_C01_genomic.fna/target_genomes.txt
[2024-01-24 14:14:15,931] [INFO] Task started: fastANI
[2024-01-24 14:14:15,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg75415488-f61b-4573-9bb3-e578de494280/GCF_900445435.1_59178_C01_genomic.fna.gz --refList GCF_900445435.1_59178_C01_genomic.fna/target_genomes.txt --output GCF_900445435.1_59178_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:14:25,344] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:25,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4fa52453-2fd7-4823-9620-f5a9adae6a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:14:25,344] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4fa52453-2fd7-4823-9620-f5a9adae6a43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:14:25,352] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:14:25,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:14:25,353] [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
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	100.0	1192	1200	95	conclusive
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	99.9763	1132	1200	95	conclusive
Bacillus inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	92.3961	1023	1200	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	92.2614	1003	1200	95	below_threshold
Bacillus spizizenii	strain=TU-B-10	GCA_000227465.1	96241	96241	type	True	92.2474	1005	1200	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	92.166	976	1200	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	91.4384	1007	1200	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	91.4327	1024	1200	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	90.4101	891	1200	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:14:25,354] [INFO] DFAST Taxonomy check result was written to GCF_900445435.1_59178_C01_genomic.fna/tc_result.tsv
[2024-01-24 14:14:25,355] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:14:25,355] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:14:25,355] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4fa52453-2fd7-4823-9620-f5a9adae6a43/dqc_reference/checkm_data
[2024-01-24 14:14:25,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:14:25,391] [INFO] Task started: CheckM
[2024-01-24 14:14:25,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445435.1_59178_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445435.1_59178_C01_genomic.fna/checkm_input GCF_900445435.1_59178_C01_genomic.fna/checkm_result
[2024-01-24 14:14:59,880] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:59,881] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 8.80%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:59,901] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:59,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:59,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445435.1_59178_C01_genomic.fna/markers.fasta)
[2024-01-24 14:14:59,902] [INFO] Task started: Blastn
[2024-01-24 14:14:59,902] [INFO] Running command: blastn -query GCF_900445435.1_59178_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg4fa52453-2fd7-4823-9620-f5a9adae6a43/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445435.1_59178_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:00,795] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:00,799] [INFO] Selected 7 target genomes.
[2024-01-24 14:15:00,799] [INFO] Target genome list was writen to GCF_900445435.1_59178_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:00,816] [INFO] Task started: fastANI
[2024-01-24 14:15:00,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg75415488-f61b-4573-9bb3-e578de494280/GCF_900445435.1_59178_C01_genomic.fna.gz --refList GCF_900445435.1_59178_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445435.1_59178_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:08,096] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:08,106] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:15:08,106] [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_000507145.1	s__Bacillus tequilensis	99.9763	1132	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	conclusive
GCF_004124315.1	s__Bacillus cabrialesii	93.2793	1005	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCA_000332645.1	s__Bacillus inaquosorum	92.2614	1003	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.81	0.94	0.91	20	-
GCF_000227465.1	s__Bacillus spizizenii	92.2534	1006	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCF_000009045.1	s__Bacillus subtilis	91.4115	1032	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_002153395.1	s__Bacillus subtilis_G	91.2491	996	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_010093085.1	s__Bacillus sp010093085	90.4623	946	1200	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:08,109] [INFO] GTDB search result was written to GCF_900445435.1_59178_C01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:08,110] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:08,113] [INFO] DFAST_QC result json was written to GCF_900445435.1_59178_C01_genomic.fna/dqc_result.json
[2024-01-24 14:15:08,113] [INFO] DFAST_QC completed!
[2024-01-24 14:15:08,113] [INFO] Total running time: 0h1m4s