[2024-01-24 14:20:01,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:01,051] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:01,052] [INFO] DQC Reference Directory: /var/lib/cwl/stge4d2d921-a4c5-4338-a93c-afc160127836/dqc_reference
[2024-01-24 14:20:02,238] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:02,239] [INFO] Task started: Prodigal
[2024-01-24 14:20:02,239] [INFO] Running command: gunzip -c /var/lib/cwl/stga5fb3eb9-4664-43c0-baea-6e7a1f4410b5/GCF_003013395.1_ASM301339v1_genomic.fna.gz | prodigal -d GCF_003013395.1_ASM301339v1_genomic.fna/cds.fna -a GCF_003013395.1_ASM301339v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:22,673] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:22,674] [INFO] Task started: HMMsearch
[2024-01-24 14:20:22,674] [INFO] Running command: hmmsearch --tblout GCF_003013395.1_ASM301339v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4d2d921-a4c5-4338-a93c-afc160127836/dqc_reference/reference_markers.hmm GCF_003013395.1_ASM301339v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:23,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:23,012] [INFO] Found 6/6 markers.
[2024-01-24 14:20:23,064] [INFO] Query marker FASTA was written to GCF_003013395.1_ASM301339v1_genomic.fna/markers.fasta
[2024-01-24 14:20:23,065] [INFO] Task started: Blastn
[2024-01-24 14:20:23,065] [INFO] Running command: blastn -query GCF_003013395.1_ASM301339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4d2d921-a4c5-4338-a93c-afc160127836/dqc_reference/reference_markers.fasta -out GCF_003013395.1_ASM301339v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:23,631] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:23,657] [INFO] Selected 12 target genomes.
[2024-01-24 14:20:23,658] [INFO] Target genome list was writen to GCF_003013395.1_ASM301339v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:23,684] [INFO] Task started: fastANI
[2024-01-24 14:20:23,684] [INFO] Running command: fastANI --query /var/lib/cwl/stga5fb3eb9-4664-43c0-baea-6e7a1f4410b5/GCF_003013395.1_ASM301339v1_genomic.fna.gz --refList GCF_003013395.1_ASM301339v1_genomic.fna/target_genomes.txt --output GCF_003013395.1_ASM301339v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:40,289] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:40,290] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4d2d921-a4c5-4338-a93c-afc160127836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:40,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4d2d921-a4c5-4338-a93c-afc160127836/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:40,303] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:40,303] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:40,303] [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 fortis	strain=NRRL NRS-1210	GCA_003013395.1	2126352	2126352	type	True	100.0	2042	2050	95	conclusive
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	92.6565	1770	2050	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	92.6215	1800	2050	95	below_threshold
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	92.5967	1792	2050	95	below_threshold
Brevibacillus brevis	strain=NBRC 15304	GCA_006539845.1	1393	1393	suspected-type	True	92.5933	1756	2050	95	below_threshold
Brevibacillus brevis	strain=DSM 30	GCA_003385915.1	1393	1393	suspected-type	True	92.5561	1811	2050	95	below_threshold
Brevibacillus formosus	strain=DSM 9885	GCA_001012775.1	54913	54913	type	True	91.8654	1757	2050	95	below_threshold
Brevibacillus formosus	strain=NRRL NRS-863	GCA_003013405.1	54913	54913	type	True	91.8649	1739	2050	95	below_threshold
Brevibacillus formosus	strain=NBRC 15716	GCA_006540185.1	54913	54913	type	True	91.8387	1717	2050	95	below_threshold
Brevibacillus antibioticus	strain=TGS2-1	GCA_005217615.1	2570228	2570228	type	True	91.5433	1639	2050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:40,305] [INFO] DFAST Taxonomy check result was written to GCF_003013395.1_ASM301339v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:40,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:40,305] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:40,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4d2d921-a4c5-4338-a93c-afc160127836/dqc_reference/checkm_data
[2024-01-24 14:20:40,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:40,364] [INFO] Task started: CheckM
[2024-01-24 14:20:40,364] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003013395.1_ASM301339v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003013395.1_ASM301339v1_genomic.fna/checkm_input GCF_003013395.1_ASM301339v1_genomic.fna/checkm_result
[2024-01-24 14:21:42,218] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:42,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:42,245] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:42,245] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:42,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003013395.1_ASM301339v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:42,246] [INFO] Task started: Blastn
[2024-01-24 14:21:42,246] [INFO] Running command: blastn -query GCF_003013395.1_ASM301339v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4d2d921-a4c5-4338-a93c-afc160127836/dqc_reference/reference_markers_gtdb.fasta -out GCF_003013395.1_ASM301339v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:42,988] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:42,993] [INFO] Selected 9 target genomes.
[2024-01-24 14:21:42,993] [INFO] Target genome list was writen to GCF_003013395.1_ASM301339v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:43,001] [INFO] Task started: fastANI
[2024-01-24 14:21:43,001] [INFO] Running command: fastANI --query /var/lib/cwl/stga5fb3eb9-4664-43c0-baea-6e7a1f4410b5/GCF_003013395.1_ASM301339v1_genomic.fna.gz --refList GCF_003013395.1_ASM301339v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003013395.1_ASM301339v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:57,445] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:57,459] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:57,459] [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_003013395.1	s__Brevibacillus fortis	100.0	2042	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003013475.1	s__Brevibacillus porteri	92.6565	1770	2050	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	92.6502	1772	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.13	96.13	0.92	0.92	2	-
GCF_900637055.1	s__Brevibacillus brevis	92.6214	1800	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_001039275.2	s__Brevibacillus brevis_C	92.1897	1732	2050	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	91.8647	1739	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_013284355.1	s__Brevibacillus sp013284355	91.621	1755	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217615.1	s__Brevibacillus antibioticus	91.5433	1639	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010165.1	s__Brevibacillus brevis_D	91.2837	1756	2050	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:57,461] [INFO] GTDB search result was written to GCF_003013395.1_ASM301339v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:57,462] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:57,465] [INFO] DFAST_QC result json was written to GCF_003013395.1_ASM301339v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:57,465] [INFO] DFAST_QC completed!
[2024-01-24 14:21:57,465] [INFO] Total running time: 0h1m56s