[2024-01-24 12:30:33,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:33,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:33,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg74408ae8-9a68-4e82-bb20-7c9ee9940c90/dqc_reference
[2024-01-24 12:30:35,013] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:35,014] [INFO] Task started: Prodigal
[2024-01-24 12:30:35,015] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cb71846-3baa-469b-a327-2611f3294a42/GCF_004124315.2_ASM412431v2_genomic.fna.gz | prodigal -d GCF_004124315.2_ASM412431v2_genomic.fna/cds.fna -a GCF_004124315.2_ASM412431v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:45,564] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:45,565] [INFO] Task started: HMMsearch
[2024-01-24 12:30:45,565] [INFO] Running command: hmmsearch --tblout GCF_004124315.2_ASM412431v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74408ae8-9a68-4e82-bb20-7c9ee9940c90/dqc_reference/reference_markers.hmm GCF_004124315.2_ASM412431v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:45,865] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:45,866] [INFO] Found 6/6 markers.
[2024-01-24 12:30:45,910] [INFO] Query marker FASTA was written to GCF_004124315.2_ASM412431v2_genomic.fna/markers.fasta
[2024-01-24 12:30:45,911] [INFO] Task started: Blastn
[2024-01-24 12:30:45,911] [INFO] Running command: blastn -query GCF_004124315.2_ASM412431v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg74408ae8-9a68-4e82-bb20-7c9ee9940c90/dqc_reference/reference_markers.fasta -out GCF_004124315.2_ASM412431v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:46,503] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:46,507] [INFO] Selected 12 target genomes.
[2024-01-24 12:30:46,508] [INFO] Target genome list was writen to GCF_004124315.2_ASM412431v2_genomic.fna/target_genomes.txt
[2024-01-24 12:30:46,514] [INFO] Task started: fastANI
[2024-01-24 12:30:46,514] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb71846-3baa-469b-a327-2611f3294a42/GCF_004124315.2_ASM412431v2_genomic.fna.gz --refList GCF_004124315.2_ASM412431v2_genomic.fna/target_genomes.txt --output GCF_004124315.2_ASM412431v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:57,418] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:57,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74408ae8-9a68-4e82-bb20-7c9ee9940c90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:57,419] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74408ae8-9a68-4e82-bb20-7c9ee9940c90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:57,432] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:30:57,432] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:30:57,432] [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 inaquosorum	strain=KCTC 13429	GCA_003148415.1	483913	483913	type	True	93.661	1249	1375	95	below_threshold
Bacillus inaquosorum	strain=KCTC 13429	GCA_000332645.1	483913	483913	type	True	93.6523	1215	1375	95	below_threshold
Bacillus spizizenii	strain=TU-B-10	GCA_000227465.1	96241	96241	type	True	93.5195	1259	1375	95	below_threshold
Bacillus spizizenii	strain=NBRC 101239	GCA_007989785.1	96241	96241	type	True	93.4556	1222	1375	95	below_threshold
Bacillus tequilensis	strain=NCTC13306	GCA_900445435.1	227866	227866	type	True	93.2938	1014	1375	95	below_threshold
Bacillus tequilensis	strain=KCTC 13622	GCA_000507145.1	227866	227866	type	True	93.2744	1156	1375	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009135.1	135461	1423	type	True	92.2175	1274	1375	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_002009095.1	135461	1423	type	True	92.2147	1275	1375	95	below_threshold
Bacillus subtilis subsp. subtilis	strain=168	GCA_024917115.1	135461	1423	type	True	92.2009	1273	1375	95	below_threshold
Bacillus vallismortis	strain=DV1-F-3	GCA_000245315.1	72361	72361	type	True	91.4999	1044	1375	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:57,433] [INFO] DFAST Taxonomy check result was written to GCF_004124315.2_ASM412431v2_genomic.fna/tc_result.tsv
[2024-01-24 12:30:57,434] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:57,434] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:57,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74408ae8-9a68-4e82-bb20-7c9ee9940c90/dqc_reference/checkm_data
[2024-01-24 12:30:57,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:57,476] [INFO] Task started: CheckM
[2024-01-24 12:30:57,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004124315.2_ASM412431v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004124315.2_ASM412431v2_genomic.fna/checkm_input GCF_004124315.2_ASM412431v2_genomic.fna/checkm_result
[2024-01-24 12:31:35,552] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:35,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:35,586] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:35,586] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:35,587] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004124315.2_ASM412431v2_genomic.fna/markers.fasta)
[2024-01-24 12:31:35,587] [INFO] Task started: Blastn
[2024-01-24 12:31:35,587] [INFO] Running command: blastn -query GCF_004124315.2_ASM412431v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg74408ae8-9a68-4e82-bb20-7c9ee9940c90/dqc_reference/reference_markers_gtdb.fasta -out GCF_004124315.2_ASM412431v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:36,402] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:36,406] [INFO] Selected 10 target genomes.
[2024-01-24 12:31:36,407] [INFO] Target genome list was writen to GCF_004124315.2_ASM412431v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:36,415] [INFO] Task started: fastANI
[2024-01-24 12:31:36,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cb71846-3baa-469b-a327-2611f3294a42/GCF_004124315.2_ASM412431v2_genomic.fna.gz --refList GCF_004124315.2_ASM412431v2_genomic.fna/target_genomes_gtdb.txt --output GCF_004124315.2_ASM412431v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:47,212] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:47,265] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:47,265] [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_004124315.1	s__Bacillus cabrialesii	99.97	1343	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	96.72	96.66	0.93	0.91	11	conclusive
GCA_000332645.1	s__Bacillus inaquosorum	93.6366	1216	1375	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	93.5138	1260	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.29	95.06	0.95	0.89	32	-
GCF_000507145.1	s__Bacillus tequilensis	93.2744	1156	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.71	97.42	0.93	0.92	4	-
GCF_002153395.1	s__Bacillus subtilis_G	92.289	1211	1375	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	92.2322	1270	1375	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	91.5676	1178	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.90	97.68	0.96	0.94	6	-
GCF_000196735.1	s__Bacillus amyloliquefaciens	81.2032	684	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.08	97.42	0.94	0.89	27	-
GCF_001584325.1	s__Bacillus nakamurai	81.0187	645	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.07	99.07	0.94	0.94	2	-
GCF_000981385.1	s__Metabacillus sp000981385	77.2064	87	1375	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Metabacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:47,267] [INFO] GTDB search result was written to GCF_004124315.2_ASM412431v2_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:47,268] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:47,275] [INFO] DFAST_QC result json was written to GCF_004124315.2_ASM412431v2_genomic.fna/dqc_result.json
[2024-01-24 12:31:47,275] [INFO] DFAST_QC completed!
[2024-01-24 12:31:47,275] [INFO] Total running time: 0h1m14s