[2024-01-24 10:47:06,550] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,553] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d52cca5-8c8b-44b1-8737-768e98f07717/dqc_reference
[2024-01-24 10:47:12,100] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,104] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,104] [INFO] Running command: gunzip -c /var/lib/cwl/stg14484a05-777c-4fb4-8e06-985435c8a0ee/GCF_021245735.1_ASM2124573v1_genomic.fna.gz | prodigal -d GCF_021245735.1_ASM2124573v1_genomic.fna/cds.fna -a GCF_021245735.1_ASM2124573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:22,830] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:22,831] [INFO] Task started: HMMsearch
[2024-01-24 10:47:22,831] [INFO] Running command: hmmsearch --tblout GCF_021245735.1_ASM2124573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d52cca5-8c8b-44b1-8737-768e98f07717/dqc_reference/reference_markers.hmm GCF_021245735.1_ASM2124573v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:23,128] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:23,130] [INFO] Found 6/6 markers.
[2024-01-24 10:47:23,167] [INFO] Query marker FASTA was written to GCF_021245735.1_ASM2124573v1_genomic.fna/markers.fasta
[2024-01-24 10:47:23,168] [INFO] Task started: Blastn
[2024-01-24 10:47:23,168] [INFO] Running command: blastn -query GCF_021245735.1_ASM2124573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d52cca5-8c8b-44b1-8737-768e98f07717/dqc_reference/reference_markers.fasta -out GCF_021245735.1_ASM2124573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:23,771] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:23,774] [INFO] Selected 29 target genomes.
[2024-01-24 10:47:23,774] [INFO] Target genome list was writen to GCF_021245735.1_ASM2124573v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,806] [INFO] Task started: fastANI
[2024-01-24 10:47:23,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg14484a05-777c-4fb4-8e06-985435c8a0ee/GCF_021245735.1_ASM2124573v1_genomic.fna.gz --refList GCF_021245735.1_ASM2124573v1_genomic.fna/target_genomes.txt --output GCF_021245735.1_ASM2124573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:46,045] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:46,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d52cca5-8c8b-44b1-8737-768e98f07717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:46,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d52cca5-8c8b-44b1-8737-768e98f07717/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:46,057] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:47:46,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:47:46,058] [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 laterosporus	strain=DSM 25	GCA_002706795.1	1465	1465	suspected-type	True	78.6043	284	1599	95	below_threshold
Brevibacillus laterosporus	strain=DSM 25	GCA_000374385.1	1465	1465	suspected-type	True	78.513	280	1599	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	77.7624	92	1599	95	below_threshold
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	77.6614	88	1599	95	below_threshold
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	77.5028	91	1599	95	below_threshold
Brevibacillus migulae	strain=CFH S0501	GCA_004521915.1	1644114	1644114	type	True	77.2513	63	1599	95	below_threshold
Brevibacillus formosus	strain=NRRL NRS-863	GCA_003013405.1	54913	54913	type	True	77.1725	96	1599	95	below_threshold
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	77.1106	63	1599	95	below_threshold
Brevibacillus fortis	strain=NRRL NRS-1210	GCA_003013395.1	2126352	2126352	type	True	77.0852	99	1599	95	below_threshold
Brevibacillus formosus	strain=NBRC 15716	GCA_006540185.1	54913	54913	type	True	76.7555	92	1599	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	76.7116	61	1599	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:46,060] [INFO] DFAST Taxonomy check result was written to GCF_021245735.1_ASM2124573v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:46,061] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:46,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:46,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d52cca5-8c8b-44b1-8737-768e98f07717/dqc_reference/checkm_data
[2024-01-24 10:47:46,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:46,110] [INFO] Task started: CheckM
[2024-01-24 10:47:46,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021245735.1_ASM2124573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021245735.1_ASM2124573v1_genomic.fna/checkm_input GCF_021245735.1_ASM2124573v1_genomic.fna/checkm_result
[2024-01-24 10:48:22,809] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:22,810] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:22,830] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:22,830] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:22,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021245735.1_ASM2124573v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:22,831] [INFO] Task started: Blastn
[2024-01-24 10:48:22,831] [INFO] Running command: blastn -query GCF_021245735.1_ASM2124573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d52cca5-8c8b-44b1-8737-768e98f07717/dqc_reference/reference_markers_gtdb.fasta -out GCF_021245735.1_ASM2124573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:23,566] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:23,570] [INFO] Selected 31 target genomes.
[2024-01-24 10:48:23,570] [INFO] Target genome list was writen to GCF_021245735.1_ASM2124573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:23,616] [INFO] Task started: fastANI
[2024-01-24 10:48:23,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg14484a05-777c-4fb4-8e06-985435c8a0ee/GCF_021245735.1_ASM2124573v1_genomic.fna.gz --refList GCF_021245735.1_ASM2124573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021245735.1_ASM2124573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:48,384] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,396] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:48:48,396] [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_007833815.1	s__Brevibacillus_B laterosporus_D	79.0273	310	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_B	95.0	98.56	97.15	0.92	0.89	5	-
GCF_000219535.2	s__Brevibacillus_B halotolerans	78.7244	277	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_B	95.0	98.52	96.28	0.94	0.91	14	-
GCF_002706795.1	s__Brevibacillus_B laterosporus	78.6192	283	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_B	95.0	98.75	97.98	0.92	0.88	16	-
GCF_001420695.1	s__Brevibacillus choshinensis	77.588	90	1599	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	77.5875	90	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_002559665.1	s__Bacillus_A cereus_AV	77.3511	64	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013475.1	s__Brevibacillus porteri	77.3315	98	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
GCF_003013405.1	s__Brevibacillus formosus	77.1781	95	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_004521915.1	s__CFH-S0501 sp004521915	77.1716	62	1599	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__CFH-S0501	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710905.1	s__Brevibacillus parabrevis	77.1076	63	1599	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	77.0852	99	1599	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	76.8633	86	1599	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 10:48:48,399] [INFO] GTDB search result was written to GCF_021245735.1_ASM2124573v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:48,399] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:48,403] [INFO] DFAST_QC result json was written to GCF_021245735.1_ASM2124573v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:48,403] [INFO] DFAST_QC completed!
[2024-01-24 10:48:48,404] [INFO] Total running time: 0h1m42s