[2024-01-24 14:39:14,645] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:14,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:14,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg06c1bb45-b5b1-4e3b-85cc-04d67234ebfe/dqc_reference
[2024-01-24 14:39:16,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,023] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgfee59c05-9dc7-4445-b55c-f72a4c27d2d6/GCF_006540025.1_ASM654002v1_genomic.fna.gz | prodigal -d GCF_006540025.1_ASM654002v1_genomic.fna/cds.fna -a GCF_006540025.1_ASM654002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:33,023] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:33,024] [INFO] Task started: HMMsearch
[2024-01-24 14:39:33,024] [INFO] Running command: hmmsearch --tblout GCF_006540025.1_ASM654002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06c1bb45-b5b1-4e3b-85cc-04d67234ebfe/dqc_reference/reference_markers.hmm GCF_006540025.1_ASM654002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:33,435] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:33,437] [INFO] Found 6/6 markers.
[2024-01-24 14:39:33,487] [INFO] Query marker FASTA was written to GCF_006540025.1_ASM654002v1_genomic.fna/markers.fasta
[2024-01-24 14:39:33,487] [INFO] Task started: Blastn
[2024-01-24 14:39:33,487] [INFO] Running command: blastn -query GCF_006540025.1_ASM654002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06c1bb45-b5b1-4e3b-85cc-04d67234ebfe/dqc_reference/reference_markers.fasta -out GCF_006540025.1_ASM654002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:34,138] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:34,142] [INFO] Selected 9 target genomes.
[2024-01-24 14:39:34,142] [INFO] Target genome list was writen to GCF_006540025.1_ASM654002v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:34,149] [INFO] Task started: fastANI
[2024-01-24 14:39:34,149] [INFO] Running command: fastANI --query /var/lib/cwl/stgfee59c05-9dc7-4445-b55c-f72a4c27d2d6/GCF_006540025.1_ASM654002v1_genomic.fna.gz --refList GCF_006540025.1_ASM654002v1_genomic.fna/target_genomes.txt --output GCF_006540025.1_ASM654002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:43,835] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:43,835] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06c1bb45-b5b1-4e3b-85cc-04d67234ebfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:43,835] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06c1bb45-b5b1-4e3b-85cc-04d67234ebfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:43,843] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:39:43,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:43,844] [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
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	100.0	1617	1623	95	conclusive
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	99.9988	1620	1623	95	conclusive
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	99.9839	1623	1623	95	conclusive
Brevibacillus gelatini	strain=DSM 100115	GCA_003710935.1	1655277	1655277	type	True	90.6364	1188	1623	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	85.4707	1345	1623	95	below_threshold
Brevibacillus invocatus	strain=JCM 12215	GCA_003710915.1	173959	173959	type	True	78.6488	472	1623	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:43,845] [INFO] DFAST Taxonomy check result was written to GCF_006540025.1_ASM654002v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:43,846] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:43,846] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:43,846] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06c1bb45-b5b1-4e3b-85cc-04d67234ebfe/dqc_reference/checkm_data
[2024-01-24 14:39:43,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:43,905] [INFO] Task started: CheckM
[2024-01-24 14:39:43,906] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540025.1_ASM654002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540025.1_ASM654002v1_genomic.fna/checkm_input GCF_006540025.1_ASM654002v1_genomic.fna/checkm_result
[2024-01-24 14:40:32,749] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:32,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:32,773] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:32,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:32,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540025.1_ASM654002v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:32,774] [INFO] Task started: Blastn
[2024-01-24 14:40:32,774] [INFO] Running command: blastn -query GCF_006540025.1_ASM654002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06c1bb45-b5b1-4e3b-85cc-04d67234ebfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540025.1_ASM654002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:33,596] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:33,600] [INFO] Selected 11 target genomes.
[2024-01-24 14:40:33,600] [INFO] Target genome list was writen to GCF_006540025.1_ASM654002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:33,604] [INFO] Task started: fastANI
[2024-01-24 14:40:33,604] [INFO] Running command: fastANI --query /var/lib/cwl/stgfee59c05-9dc7-4445-b55c-f72a4c27d2d6/GCF_006540025.1_ASM654002v1_genomic.fna.gz --refList GCF_006540025.1_ASM654002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540025.1_ASM654002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:46,074] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:46,086] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:46,087] [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_004117055.1	s__Brevibacillus agri	99.9839	1623	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	conclusive
GCF_003710935.1	s__Brevibacillus gelatini	90.6112	1190	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710905.1	s__Brevibacillus parabrevis	85.4237	1346	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_003013395.1	s__Brevibacillus fortis	80.4997	797	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039275.2	s__Brevibacillus brevis_C	80.4574	819	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_003013405.1	s__Brevibacillus formosus	80.4148	819	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_000010165.1	s__Brevibacillus brevis_D	80.3957	786	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_013284355.1	s__Brevibacillus sp013284355	80.3916	799	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897295.1	s__Brevibacillus reuszeri_A	79.9181	738	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_003710815.1	s__Brevibacillus centrosporus	79.7838	623	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	79.5719	695	1623	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:40:46,088] [INFO] GTDB search result was written to GCF_006540025.1_ASM654002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:46,089] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:46,092] [INFO] DFAST_QC result json was written to GCF_006540025.1_ASM654002v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:46,092] [INFO] DFAST_QC completed!
[2024-01-24 14:40:46,092] [INFO] Total running time: 0h1m31s