[2024-01-24 11:59:05,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg83235a36-487d-4cc3-84fa-dbb5ebb4b05b/dqc_reference
[2024-01-24 11:59:06,309] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,310] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,311] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e900b85-06ea-438a-a558-74da8b4f7695/GCF_006540225.1_ASM654022v1_genomic.fna.gz | prodigal -d GCF_006540225.1_ASM654022v1_genomic.fna/cds.fna -a GCF_006540225.1_ASM654022v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:25,470] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:25,471] [INFO] Task started: HMMsearch
[2024-01-24 11:59:25,471] [INFO] Running command: hmmsearch --tblout GCF_006540225.1_ASM654022v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg83235a36-487d-4cc3-84fa-dbb5ebb4b05b/dqc_reference/reference_markers.hmm GCF_006540225.1_ASM654022v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:25,826] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:25,827] [INFO] Found 6/6 markers.
[2024-01-24 11:59:25,890] [INFO] Query marker FASTA was written to GCF_006540225.1_ASM654022v1_genomic.fna/markers.fasta
[2024-01-24 11:59:25,891] [INFO] Task started: Blastn
[2024-01-24 11:59:25,891] [INFO] Running command: blastn -query GCF_006540225.1_ASM654022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83235a36-487d-4cc3-84fa-dbb5ebb4b05b/dqc_reference/reference_markers.fasta -out GCF_006540225.1_ASM654022v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:26,469] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:26,474] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:26,474] [INFO] Target genome list was writen to GCF_006540225.1_ASM654022v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:26,495] [INFO] Task started: fastANI
[2024-01-24 11:59:26,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e900b85-06ea-438a-a558-74da8b4f7695/GCF_006540225.1_ASM654022v1_genomic.fna.gz --refList GCF_006540225.1_ASM654022v1_genomic.fna/target_genomes.txt --output GCF_006540225.1_ASM654022v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:39,718] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:39,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg83235a36-487d-4cc3-84fa-dbb5ebb4b05b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:39,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg83235a36-487d-4cc3-84fa-dbb5ebb4b05b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:39,729] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:39,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:39,729] [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 reuszeri	strain=NBRC 15719	GCA_006540225.1	54915	54915	type	True	100.0	2278	2282	95	conclusive
Brevibacillus reuszeri	strain=DSM 9887	GCA_001187725.1	54915	54915	type	True	99.9975	2282	2282	95	conclusive
Brevibacillus fortis	strain=NRRL NRS-1210	GCA_003013395.1	2126352	2126352	type	True	80.0447	750	2282	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	80.0176	710	2282	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	80.0148	699	2282	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	79.9648	729	2282	95	below_threshold
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	79.8564	775	2282	95	below_threshold
Brevibacillus antibioticus	strain=TGS2-1	GCA_005217615.1	2570228	2570228	type	True	79.8068	770	2282	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	79.792	784	2282	95	below_threshold
Brevibacillus brevis	strain=NBRC 15304	GCA_006539845.1	1393	1393	suspected-type	True	79.7861	762	2282	95	below_threshold
Brevibacillus centrosporus	strain=NRRL NRS 664	GCA_003710815.1	54910	54910	type	True	79.7311	686	2282	95	below_threshold
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	79.662	678	2282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:39,731] [INFO] DFAST Taxonomy check result was written to GCF_006540225.1_ASM654022v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:39,732] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:39,732] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:39,733] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg83235a36-487d-4cc3-84fa-dbb5ebb4b05b/dqc_reference/checkm_data
[2024-01-24 11:59:39,733] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:39,801] [INFO] Task started: CheckM
[2024-01-24 11:59:39,801] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540225.1_ASM654022v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540225.1_ASM654022v1_genomic.fna/checkm_input GCF_006540225.1_ASM654022v1_genomic.fna/checkm_result
[2024-01-24 12:00:36,468] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:36,469] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 12.88%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:36,498] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:36,499] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:36,499] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540225.1_ASM654022v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:36,499] [INFO] Task started: Blastn
[2024-01-24 12:00:36,500] [INFO] Running command: blastn -query GCF_006540225.1_ASM654022v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg83235a36-487d-4cc3-84fa-dbb5ebb4b05b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540225.1_ASM654022v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:37,228] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:37,232] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:37,233] [INFO] Target genome list was writen to GCF_006540225.1_ASM654022v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:37,244] [INFO] Task started: fastANI
[2024-01-24 12:00:37,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e900b85-06ea-438a-a558-74da8b4f7695/GCF_006540225.1_ASM654022v1_genomic.fna.gz --refList GCF_006540225.1_ASM654022v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540225.1_ASM654022v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:53,332] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:53,345] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:53,345] [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_001187725.1	s__Brevibacillus reuszeri	99.9975	2282	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002897295.1	s__Brevibacillus reuszeri_A	87.2939	1782	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_003013395.1	s__Brevibacillus fortis	80.0447	750	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284355.1	s__Brevibacillus sp013284355	79.9848	768	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117055.1	s__Brevibacillus agri	79.9779	728	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_003710905.1	s__Brevibacillus parabrevis	79.9343	773	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_003013475.1	s__Brevibacillus porteri	79.8957	773	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
GCF_000282075.1	s__Brevibacillus sp000282075	79.8221	790	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.13	96.13	0.92	0.92	2	-
GCF_001039275.2	s__Brevibacillus brevis_C	79.8135	789	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.38	97.50	0.95	0.94	3	-
GCF_005217615.1	s__Brevibacillus antibioticus	79.8037	769	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900637055.1	s__Brevibacillus brevis	79.7987	783	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_003710815.1	s__Brevibacillus centrosporus	79.7222	686	2282	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_003710935.1	s__Brevibacillus gelatini	79.7166	602	2282	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 12:00:53,347] [INFO] GTDB search result was written to GCF_006540225.1_ASM654022v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:53,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:53,351] [INFO] DFAST_QC result json was written to GCF_006540225.1_ASM654022v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:53,351] [INFO] DFAST_QC completed!
[2024-01-24 12:00:53,352] [INFO] Total running time: 0h1m48s