[2024-01-24 12:47:12,188] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:12,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:12,191] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa02ca6a-0a93-41f6-8648-d30013784d81/dqc_reference
[2024-01-24 12:47:13,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:13,726] [INFO] Task started: Prodigal
[2024-01-24 12:47:13,727] [INFO] Running command: gunzip -c /var/lib/cwl/stg11132d24-3bf4-4f5e-a91a-51de710ec3ec/GCF_007989785.1_ASM798978v1_genomic.fna.gz | prodigal -d GCF_007989785.1_ASM798978v1_genomic.fna/cds.fna -a GCF_007989785.1_ASM798978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:24,697] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:24,697] [INFO] Task started: HMMsearch
[2024-01-24 12:47:24,698] [INFO] Running command: hmmsearch --tblout GCF_007989785.1_ASM798978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa02ca6a-0a93-41f6-8648-d30013784d81/dqc_reference/reference_markers.hmm GCF_007989785.1_ASM798978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:24,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:24,990] [INFO] Found 6/6 markers.
[2024-01-24 12:47:25,026] [INFO] Query marker FASTA was written to GCF_007989785.1_ASM798978v1_genomic.fna/markers.fasta
[2024-01-24 12:47:25,027] [INFO] Task started: Blastn
[2024-01-24 12:47:25,027] [INFO] Running command: blastn -query GCF_007989785.1_ASM798978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa02ca6a-0a93-41f6-8648-d30013784d81/dqc_reference/reference_markers.fasta -out GCF_007989785.1_ASM798978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:25,721] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:25,725] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:25,725] [INFO] Target genome list was writen to GCF_007989785.1_ASM798978v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:25,732] [INFO] Task started: fastANI
[2024-01-24 12:47:25,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg11132d24-3bf4-4f5e-a91a-51de710ec3ec/GCF_007989785.1_ASM798978v1_genomic.fna.gz --refList GCF_007989785.1_ASM798978v1_genomic.fna/target_genomes.txt --output GCF_007989785.1_ASM798978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:37,596] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:37,596] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa02ca6a-0a93-41f6-8648-d30013784d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:37,597] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa02ca6a-0a93-41f6-8648-d30013784d81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:37,606] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:37,606] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:37,606] [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 spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	100.0	1350	1351	95	conclusive
Bacillus spizizenii	strain=TU-B-10	GCA_000227465.1	96241	96241	type	True	99.9996	1350	1351	95	conclusive
Bacillus inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	94.2307	1251	1351	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	94.2054	1249	1351	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	92.7178	1228	1351	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	92.7127	1232	1351	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	92.3001	1045	1351	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	92.0858	988	1351	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_003966255.1	2492960	2492960	type	True	76.8772	52	1351	95	below_threshold
Bacillus yapensis	strain=XXST-01	GCA_005280205.1	2492960	2492960	type	True	76.8772	52	1351	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:37,608] [INFO] DFAST Taxonomy check result was written to GCF_007989785.1_ASM798978v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:37,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:37,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:37,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa02ca6a-0a93-41f6-8648-d30013784d81/dqc_reference/checkm_data
[2024-01-24 12:47:37,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:37,651] [INFO] Task started: CheckM
[2024-01-24 12:47:37,651] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989785.1_ASM798978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989785.1_ASM798978v1_genomic.fna/checkm_input GCF_007989785.1_ASM798978v1_genomic.fna/checkm_result
[2024-01-24 12:48:15,268] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:15,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:15,294] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:15,295] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:15,296] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989785.1_ASM798978v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:15,296] [INFO] Task started: Blastn
[2024-01-24 12:48:15,296] [INFO] Running command: blastn -query GCF_007989785.1_ASM798978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa02ca6a-0a93-41f6-8648-d30013784d81/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989785.1_ASM798978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:16,366] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:16,370] [INFO] Selected 10 target genomes.
[2024-01-24 12:48:16,370] [INFO] Target genome list was writen to GCF_007989785.1_ASM798978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:16,378] [INFO] Task started: fastANI
[2024-01-24 12:48:16,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg11132d24-3bf4-4f5e-a91a-51de710ec3ec/GCF_007989785.1_ASM798978v1_genomic.fna.gz --refList GCF_007989785.1_ASM798978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989785.1_ASM798978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:25,645] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:25,660] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:25,660] [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_000227465.1	s__Bacillus spizizenii	99.9996	1350	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	conclusive
GCA_000332645.1	s__Bacillus inaquosorum	94.1991	1250	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.57	97.81	0.94	0.91	20	-
GCF_004124315.1	s__Bacillus cabrialesii	93.4946	1233	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	-
GCF_002153395.1	s__Bacillus subtilis_G	93.1014	1221	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	97.72	0.95	0.93	3	-
GCF_000009045.1	s__Bacillus subtilis	92.7231	1236	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_004116955.1	s__Bacillus vallismortis	92.3367	1167	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	-
GCF_000507145.1	s__Bacillus tequilensis	92.2185	1132	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_001969815.1	s__Bacillus swezeyi	79.2361	393	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.68	96.91	0.92	0.90	5	-
GCF_002744245.1	s__Bacillus pumilus_M	78.3265	208	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900186955.1	s__Bacillus pumilus	78.3116	203	1351	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	95.74	95.13	0.93	0.87	168	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:25,662] [INFO] GTDB search result was written to GCF_007989785.1_ASM798978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:25,664] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:25,667] [INFO] DFAST_QC result json was written to GCF_007989785.1_ASM798978v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:25,668] [INFO] DFAST_QC completed!
[2024-01-24 12:48:25,668] [INFO] Total running time: 0h1m13s