[2024-01-25 17:39:35,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,498] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,498] [INFO] DQC Reference Directory: /var/lib/cwl/stga7f07a4f-f113-474a-b332-2c10db8b1707/dqc_reference
[2024-01-25 17:39:36,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,685] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,685] [INFO] Running command: gunzip -c /var/lib/cwl/stge255607c-2c76-459e-ba8a-a70bb985bbe7/GCF_031316635.1_ASM3131663v1_genomic.fna.gz | prodigal -d GCF_031316635.1_ASM3131663v1_genomic.fna/cds.fna -a GCF_031316635.1_ASM3131663v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:45,396] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:45,397] [INFO] Task started: HMMsearch
[2024-01-25 17:39:45,397] [INFO] Running command: hmmsearch --tblout GCF_031316635.1_ASM3131663v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7f07a4f-f113-474a-b332-2c10db8b1707/dqc_reference/reference_markers.hmm GCF_031316635.1_ASM3131663v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:45,652] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:45,653] [INFO] Found 6/6 markers.
[2024-01-25 17:39:45,685] [INFO] Query marker FASTA was written to GCF_031316635.1_ASM3131663v1_genomic.fna/markers.fasta
[2024-01-25 17:39:45,686] [INFO] Task started: Blastn
[2024-01-25 17:39:45,686] [INFO] Running command: blastn -query GCF_031316635.1_ASM3131663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7f07a4f-f113-474a-b332-2c10db8b1707/dqc_reference/reference_markers.fasta -out GCF_031316635.1_ASM3131663v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:46,245] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:46,248] [INFO] Selected 10 target genomes.
[2024-01-25 17:39:46,248] [INFO] Target genome list was writen to GCF_031316635.1_ASM3131663v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:46,252] [INFO] Task started: fastANI
[2024-01-25 17:39:46,253] [INFO] Running command: fastANI --query /var/lib/cwl/stge255607c-2c76-459e-ba8a-a70bb985bbe7/GCF_031316635.1_ASM3131663v1_genomic.fna.gz --refList GCF_031316635.1_ASM3131663v1_genomic.fna/target_genomes.txt --output GCF_031316635.1_ASM3131663v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:55,421] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:55,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7f07a4f-f113-474a-b332-2c10db8b1707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:55,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7f07a4f-f113-474a-b332-2c10db8b1707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:55,428] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 17:39:55,428] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 17:39:55,429] [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 mojavensis	strain=RO-H-1 = KCTC 3706	GCA_000507105.1	72360	72360	type	True	99.9924	1299	1303	95	inconclusive
Bacillus mojavensis	strain=RO-H-1	GCA_014499005.1	72360	72360	type	True	99.9905	1298	1303	95	inconclusive
Bacillus mojavensis	strain=RO-H-1	GCA_000245335.1	72360	72360	type	True	99.9547	1287	1303	95	inconclusive
Bacillus halotolerans	strain=ATCC 25096	GCA_001517105.1	260554	260554	type	True	95.4866	1213	1303	95	inconclusive
Bacillus halotolerans	strain=FJAT-2398	GCA_001637525.1	260554	260554	type	True	95.4633	1223	1303	95	inconclusive
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	87.1566	1147	1303	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	86.7685	962	1303	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	86.5995	992	1303	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:55,430] [INFO] DFAST Taxonomy check result was written to GCF_031316635.1_ASM3131663v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:55,432] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:55,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:55,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7f07a4f-f113-474a-b332-2c10db8b1707/dqc_reference/checkm_data
[2024-01-25 17:39:55,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:55,473] [INFO] Task started: CheckM
[2024-01-25 17:39:55,473] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031316635.1_ASM3131663v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031316635.1_ASM3131663v1_genomic.fna/checkm_input GCF_031316635.1_ASM3131663v1_genomic.fna/checkm_result
[2024-01-25 17:40:26,077] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:26,079] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:26,108] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:26,108] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:26,109] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031316635.1_ASM3131663v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:26,110] [INFO] Task started: Blastn
[2024-01-25 17:40:26,110] [INFO] Running command: blastn -query GCF_031316635.1_ASM3131663v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7f07a4f-f113-474a-b332-2c10db8b1707/dqc_reference/reference_markers_gtdb.fasta -out GCF_031316635.1_ASM3131663v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:26,948] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:26,951] [INFO] Selected 9 target genomes.
[2024-01-25 17:40:26,951] [INFO] Target genome list was writen to GCF_031316635.1_ASM3131663v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:26,959] [INFO] Task started: fastANI
[2024-01-25 17:40:26,959] [INFO] Running command: fastANI --query /var/lib/cwl/stge255607c-2c76-459e-ba8a-a70bb985bbe7/GCF_031316635.1_ASM3131663v1_genomic.fna.gz --refList GCF_031316635.1_ASM3131663v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031316635.1_ASM3131663v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:35,859] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:35,866] [INFO] Found 9 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-25 17:40:35,867] [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_000245335.1	s__Bacillus mojavensis	99.9547	1287	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4726	99.54	98.69	0.98	0.95	4	inconclusive
GCF_001517105.1	s__Bacillus halotolerans	95.4866	1213	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.4726	98.36	97.72	0.93	0.91	37	inconclusive
GCA_000332645.1	s__Bacillus inaquosorum	88.2211	1180	1303	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	87.9957	1157	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCF_004124315.1	s__Bacillus cabrialesii	87.5371	1164	1303	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	87.2614	1128	1303	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	87.1731	1159	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.63	95.03	0.95	0.86	485	-
GCF_000507145.1	s__Bacillus tequilensis	86.868	1079	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_001584335.1	s__Bacillus atrophaeus	82.0986	920	1303	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.59	97.38	0.93	0.89	38	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:35,868] [INFO] GTDB search result was written to GCF_031316635.1_ASM3131663v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:35,869] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:35,879] [INFO] DFAST_QC result json was written to GCF_031316635.1_ASM3131663v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:35,880] [INFO] DFAST_QC completed!
[2024-01-25 17:40:35,880] [INFO] Total running time: 0h1m0s