[2024-01-24 15:18:23,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:23,393] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:23,393] [INFO] DQC Reference Directory: /var/lib/cwl/stg59afa36b-d6ac-4127-97a1-2977cc95018c/dqc_reference
[2024-01-24 15:18:25,002] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:25,003] [INFO] Task started: Prodigal
[2024-01-24 15:18:25,004] [INFO] Running command: gunzip -c /var/lib/cwl/stg331924fd-5a7d-47f0-8c64-787548e27ea7/GCF_016406105.1_ASM1640610v1_genomic.fna.gz | prodigal -d GCF_016406105.1_ASM1640610v1_genomic.fna/cds.fna -a GCF_016406105.1_ASM1640610v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:39,164] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:39,164] [INFO] Task started: HMMsearch
[2024-01-24 15:18:39,164] [INFO] Running command: hmmsearch --tblout GCF_016406105.1_ASM1640610v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg59afa36b-d6ac-4127-97a1-2977cc95018c/dqc_reference/reference_markers.hmm GCF_016406105.1_ASM1640610v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:39,552] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:39,554] [INFO] Found 6/6 markers.
[2024-01-24 15:18:39,596] [INFO] Query marker FASTA was written to GCF_016406105.1_ASM1640610v1_genomic.fna/markers.fasta
[2024-01-24 15:18:39,596] [INFO] Task started: Blastn
[2024-01-24 15:18:39,596] [INFO] Running command: blastn -query GCF_016406105.1_ASM1640610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59afa36b-d6ac-4127-97a1-2977cc95018c/dqc_reference/reference_markers.fasta -out GCF_016406105.1_ASM1640610v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:40,324] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:40,357] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:40,358] [INFO] Target genome list was writen to GCF_016406105.1_ASM1640610v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:40,369] [INFO] Task started: fastANI
[2024-01-24 15:18:40,369] [INFO] Running command: fastANI --query /var/lib/cwl/stg331924fd-5a7d-47f0-8c64-787548e27ea7/GCF_016406105.1_ASM1640610v1_genomic.fna.gz --refList GCF_016406105.1_ASM1640610v1_genomic.fna/target_genomes.txt --output GCF_016406105.1_ASM1640610v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:54,752] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:54,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg59afa36b-d6ac-4127-97a1-2977cc95018c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:54,753] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg59afa36b-d6ac-4127-97a1-2977cc95018c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:54,765] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:54,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:54,766] [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 composti	strain=FJAT-54423	GCA_016406105.1	2796470	2796470	type	True	100.0	1485	1488	95	conclusive
Brevibacillus borstelensis	strain=NRRL NRS 818	GCA_003710865.1	45462	45462	type	True	80.0582	731	1488	95	below_threshold
Brevibacillus borstelensis	strain=NBRC 15714	GCA_006540165.1	45462	45462	type	True	79.9465	736	1488	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	78.8644	409	1488	95	below_threshold
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	78.4731	279	1488	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	78.3374	396	1488	95	below_threshold
Brevibacillus panacihumi	strain=JCM 15085	GCA_003710985.1	497735	497735	type	True	78.2453	349	1488	95	below_threshold
Brevibacillus marinus	strain=SCSIO 07484	GCA_003963515.1	2496837	2496837	type	True	78.2301	213	1488	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	78.0844	379	1488	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	78.0495	237	1488	95	below_threshold
Brevibacillus invocatus	strain=JCM 12215	GCA_003710915.1	173959	173959	type	True	77.9323	299	1488	95	below_threshold
Brevibacillus massiliensis	strain=phR	GCA_000311785.1	1118054	1118054	type	True	77.3785	198	1488	95	below_threshold
Brevibacillus migulae	strain=CFH S0501	GCA_004521915.1	1644114	1644114	type	True	76.9653	212	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:54,767] [INFO] DFAST Taxonomy check result was written to GCF_016406105.1_ASM1640610v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:54,768] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:54,768] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:54,769] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg59afa36b-d6ac-4127-97a1-2977cc95018c/dqc_reference/checkm_data
[2024-01-24 15:18:54,770] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:54,816] [INFO] Task started: CheckM
[2024-01-24 15:18:54,817] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016406105.1_ASM1640610v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016406105.1_ASM1640610v1_genomic.fna/checkm_input GCF_016406105.1_ASM1640610v1_genomic.fna/checkm_result
[2024-01-24 15:19:36,994] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:36,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:37,024] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:37,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:37,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016406105.1_ASM1640610v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:37,025] [INFO] Task started: Blastn
[2024-01-24 15:19:37,025] [INFO] Running command: blastn -query GCF_016406105.1_ASM1640610v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg59afa36b-d6ac-4127-97a1-2977cc95018c/dqc_reference/reference_markers_gtdb.fasta -out GCF_016406105.1_ASM1640610v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:37,788] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:37,793] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:37,793] [INFO] Target genome list was writen to GCF_016406105.1_ASM1640610v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:37,801] [INFO] Task started: fastANI
[2024-01-24 15:19:37,801] [INFO] Running command: fastANI --query /var/lib/cwl/stg331924fd-5a7d-47f0-8c64-787548e27ea7/GCF_016406105.1_ASM1640610v1_genomic.fna.gz --refList GCF_016406105.1_ASM1640610v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016406105.1_ASM1640610v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:46,593] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:46,606] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:46,606] [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_018228725.1	s__Brevibacillus sp018228725	99.9797	1469	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.98	99.98	0.98	0.98	2	conclusive
GCF_003710865.1	s__Brevibacillus borstelensis	80.0364	734	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.53	99.39	0.94	0.92	8	-
GCF_000503775.1	s__Brevibacillus panacihumi_A	79.2213	363	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454065.1	s__Brevibacillus thermoruber	79.001	555	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.54	98.43	0.91	0.89	5	-
GCF_004117055.1	s__Brevibacillus agri	78.8703	409	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_013096935.1	s__Brevibacillus sp003388715	78.6803	477	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.49	99.45	0.95	0.95	3	-
GCF_003710985.1	s__Brevibacillus panacihumi	78.2662	348	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710915.1	s__Brevibacillus invocatus	77.9014	296	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000311785.1	s__Brevibacillus_C massiliensis	77.3785	198	1488	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_C	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:46,608] [INFO] GTDB search result was written to GCF_016406105.1_ASM1640610v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:46,608] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:46,613] [INFO] DFAST_QC result json was written to GCF_016406105.1_ASM1640610v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:46,613] [INFO] DFAST_QC completed!
[2024-01-24 15:19:46,614] [INFO] Total running time: 0h1m23s