[2024-01-24 13:17:05,525] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,527] [INFO] DQC Reference Directory: /var/lib/cwl/stgdaefb9b9-40da-459d-ada9-4bf9e72426bb/dqc_reference
[2024-01-24 13:17:06,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,884] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,884] [INFO] Running command: gunzip -c /var/lib/cwl/stg50ce12dd-1f85-4714-b3c3-098515f52446/GCF_003254445.1_ASM325444v1_genomic.fna.gz | prodigal -d GCF_003254445.1_ASM325444v1_genomic.fna/cds.fna -a GCF_003254445.1_ASM325444v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:16,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:16,150] [INFO] Task started: HMMsearch
[2024-01-24 13:17:16,150] [INFO] Running command: hmmsearch --tblout GCF_003254445.1_ASM325444v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdaefb9b9-40da-459d-ada9-4bf9e72426bb/dqc_reference/reference_markers.hmm GCF_003254445.1_ASM325444v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:16,466] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:16,467] [INFO] Found 6/6 markers.
[2024-01-24 13:17:16,510] [INFO] Query marker FASTA was written to GCF_003254445.1_ASM325444v1_genomic.fna/markers.fasta
[2024-01-24 13:17:16,510] [INFO] Task started: Blastn
[2024-01-24 13:17:16,511] [INFO] Running command: blastn -query GCF_003254445.1_ASM325444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaefb9b9-40da-459d-ada9-4bf9e72426bb/dqc_reference/reference_markers.fasta -out GCF_003254445.1_ASM325444v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:17,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:17,173] [INFO] Selected 12 target genomes.
[2024-01-24 13:17:17,173] [INFO] Target genome list was writen to GCF_003254445.1_ASM325444v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:17,179] [INFO] Task started: fastANI
[2024-01-24 13:17:17,179] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ce12dd-1f85-4714-b3c3-098515f52446/GCF_003254445.1_ASM325444v1_genomic.fna.gz --refList GCF_003254445.1_ASM325444v1_genomic.fna/target_genomes.txt --output GCF_003254445.1_ASM325444v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:27,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:27,502] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdaefb9b9-40da-459d-ada9-4bf9e72426bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:27,502] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdaefb9b9-40da-459d-ada9-4bf9e72426bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:27,512] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:17:27,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:27,513] [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 safensis subsp. osmophilus	strain=BC09	GCA_003254445.1	1982610	561879	type	True	100.0	1293	1297	95	conclusive
Bacillus safensis	strain=FO-36b	GCA_000691165.1	561879	561879	type	True	95.7963	1126	1297	95	conclusive
Bacillus safensis	strain=FO-36b	GCA_003097715.1	561879	561879	type	True	95.7762	1131	1297	95	conclusive
Bacillus australimaris	strain=NH7I_1	GCA_001307105.1	1326968	1326968	type	True	93.1284	1110	1297	95	below_threshold
Bacillus pumilus	strain=ATCC 7061	GCA_000172815.1	1408	1408	suspected-type	True	91.3999	1110	1297	95	below_threshold
Bacillus pumilus	strain=NCTC10337	GCA_900186955.1	1408	1408	suspected-type	True	91.3932	1119	1297	95	below_threshold
Bacillus altitudinis	strain=41KF2b	GCA_000691145.1	293387	293387	type	True	89.1084	1089	1297	95	below_threshold
Metabacillus dongyingensis	strain=BY2G20	GCA_019933155.2	2874282	2874282	type	True	77.5415	93	1297	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	77.4633	59	1297	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	77.0726	92	1297	95	below_threshold
Anoxybacillus kestanbolensis	strain=NCIMB 13971	GCA_023653015.1	227476	227476	type	True	76.5591	50	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:27,520] [INFO] DFAST Taxonomy check result was written to GCF_003254445.1_ASM325444v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:27,521] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:27,521] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:27,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdaefb9b9-40da-459d-ada9-4bf9e72426bb/dqc_reference/checkm_data
[2024-01-24 13:17:27,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:27,582] [INFO] Task started: CheckM
[2024-01-24 13:17:27,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003254445.1_ASM325444v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003254445.1_ASM325444v1_genomic.fna/checkm_input GCF_003254445.1_ASM325444v1_genomic.fna/checkm_result
[2024-01-24 13:18:01,703] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:01,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:01,724] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:01,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:01,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003254445.1_ASM325444v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:01,726] [INFO] Task started: Blastn
[2024-01-24 13:18:01,726] [INFO] Running command: blastn -query GCF_003254445.1_ASM325444v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdaefb9b9-40da-459d-ada9-4bf9e72426bb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003254445.1_ASM325444v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:02,487] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:02,494] [INFO] Selected 8 target genomes.
[2024-01-24 13:18:02,494] [INFO] Target genome list was writen to GCF_003254445.1_ASM325444v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:02,503] [INFO] Task started: fastANI
[2024-01-24 13:18:02,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg50ce12dd-1f85-4714-b3c3-098515f52446/GCF_003254445.1_ASM325444v1_genomic.fna.gz --refList GCF_003254445.1_ASM325444v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003254445.1_ASM325444v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:10,025] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:10,032] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:10,033] [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_000691165.1	s__Bacillus safensis	95.7963	1126	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.22	95.80	0.94	0.90	99	conclusive
GCF_001307105.1	s__Bacillus australimaris	93.1284	1110	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900186955.1	s__Bacillus pumilus	91.3802	1120	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	95.74	95.13	0.93	0.87	168	-
GCF_014764715.1	s__Bacillus sp014764715	90.8525	1077	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003431975.1	s__Bacillus pumilus_N	90.8029	1102	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	99.39	99.09	0.95	0.93	4	-
GCF_000715205.1	s__Bacillus zhangzhouensis	90.7189	1084	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	97.04	95.33	0.94	0.92	3	-
GCF_002744245.1	s__Bacillus pumilus_M	89.4621	1037	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000691145.1	s__Bacillus altitudinis	89.1084	1089	1297	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae;g__Bacillus	95.0	98.17	97.02	0.95	0.92	117	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:10,034] [INFO] GTDB search result was written to GCF_003254445.1_ASM325444v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:10,035] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:10,038] [INFO] DFAST_QC result json was written to GCF_003254445.1_ASM325444v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:10,039] [INFO] DFAST_QC completed!
[2024-01-24 13:18:10,039] [INFO] Total running time: 0h1m5s