[2024-01-24 14:46:56,319] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:56,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:56,326] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb869b19-6e7c-4765-93c1-a3788677181f/dqc_reference
[2024-01-24 14:46:57,630] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:57,631] [INFO] Task started: Prodigal
[2024-01-24 14:46:57,631] [INFO] Running command: gunzip -c /var/lib/cwl/stg5865c380-97c7-4327-b4f8-dd497d0a7a2a/GCF_003710825.1_ASM371082v1_genomic.fna.gz | prodigal -d GCF_003710825.1_ASM371082v1_genomic.fna/cds.fna -a GCF_003710825.1_ASM371082v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:18,732] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:18,732] [INFO] Task started: HMMsearch
[2024-01-24 14:47:18,733] [INFO] Running command: hmmsearch --tblout GCF_003710825.1_ASM371082v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb869b19-6e7c-4765-93c1-a3788677181f/dqc_reference/reference_markers.hmm GCF_003710825.1_ASM371082v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:19,101] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:19,103] [INFO] Found 6/6 markers.
[2024-01-24 14:47:19,161] [INFO] Query marker FASTA was written to GCF_003710825.1_ASM371082v1_genomic.fna/markers.fasta
[2024-01-24 14:47:19,162] [INFO] Task started: Blastn
[2024-01-24 14:47:19,162] [INFO] Running command: blastn -query GCF_003710825.1_ASM371082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb869b19-6e7c-4765-93c1-a3788677181f/dqc_reference/reference_markers.fasta -out GCF_003710825.1_ASM371082v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:19,823] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:19,834] [INFO] Selected 19 target genomes.
[2024-01-24 14:47:19,835] [INFO] Target genome list was writen to GCF_003710825.1_ASM371082v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:19,847] [INFO] Task started: fastANI
[2024-01-24 14:47:19,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg5865c380-97c7-4327-b4f8-dd497d0a7a2a/GCF_003710825.1_ASM371082v1_genomic.fna.gz --refList GCF_003710825.1_ASM371082v1_genomic.fna/target_genomes.txt --output GCF_003710825.1_ASM371082v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:39,386] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:39,387] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb869b19-6e7c-4765-93c1-a3788677181f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:39,387] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb869b19-6e7c-4765-93c1-a3788677181f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:39,399] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:39,399] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:39,400] [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 fluminis	strain=JCM 15716	GCA_003710825.1	511487	511487	type	True	100.0	2119	2120	95	conclusive
Brevibacillus nitrificans	strain=JCM 15774	GCA_003710965.1	651560	651560	type	True	77.6396	228	2120	95	below_threshold
Brevibacillus centrosporus	strain=NRRL NRS 664	GCA_003710815.1	54910	54910	type	True	77.6157	217	2120	95	below_threshold
Brevibacillus migulae	strain=CFH S0501	GCA_004521915.1	1644114	1644114	type	True	77.4064	206	2120	95	below_threshold
Brevibacillus gelatini	strain=DSM 100115	GCA_003710935.1	1655277	1655277	type	True	77.2753	204	2120	95	below_threshold
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	77.2142	211	2120	95	below_threshold
Brevibacillus composti	strain=FJAT-54423	GCA_016406105.1	2796470	2796470	type	True	77.1892	179	2120	95	below_threshold
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	77.1606	274	2120	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	76.9566	266	2120	95	below_threshold
Brevibacillus marinus	strain=SCSIO 07484	GCA_003963515.1	2496837	2496837	type	True	76.7457	127	2120	95	below_threshold
Paenibacillus macerans	strain=ATCC 8244	GCA_000746875.1	44252	44252	type	True	76.2708	60	2120	95	below_threshold
Paenibacillus glycinis	strain=T1	GCA_009909185.1	2697035	2697035	type	True	76.0309	62	2120	95	below_threshold
Paenibacillus cymbidii	strain=R196	GCA_004764705.1	1639034	1639034	type	True	75.8023	53	2120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:39,401] [INFO] DFAST Taxonomy check result was written to GCF_003710825.1_ASM371082v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:39,402] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:39,402] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:39,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb869b19-6e7c-4765-93c1-a3788677181f/dqc_reference/checkm_data
[2024-01-24 14:47:39,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:39,468] [INFO] Task started: CheckM
[2024-01-24 14:47:39,468] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710825.1_ASM371082v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710825.1_ASM371082v1_genomic.fna/checkm_input GCF_003710825.1_ASM371082v1_genomic.fna/checkm_result
[2024-01-24 14:48:38,274] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:38,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:38,299] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:38,299] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:38,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710825.1_ASM371082v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:38,300] [INFO] Task started: Blastn
[2024-01-24 14:48:38,301] [INFO] Running command: blastn -query GCF_003710825.1_ASM371082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb869b19-6e7c-4765-93c1-a3788677181f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710825.1_ASM371082v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:39,116] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:39,121] [INFO] Selected 21 target genomes.
[2024-01-24 14:48:39,121] [INFO] Target genome list was writen to GCF_003710825.1_ASM371082v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:39,157] [INFO] Task started: fastANI
[2024-01-24 14:48:39,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg5865c380-97c7-4327-b4f8-dd497d0a7a2a/GCF_003710825.1_ASM371082v1_genomic.fna.gz --refList GCF_003710825.1_ASM371082v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710825.1_ASM371082v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:57,045] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:57,063] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:57,063] [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_003710825.1	s__Brevibacillus_D fluminis	100.0	2119	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001187725.1	s__Brevibacillus reuszeri	78.7861	252	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	78.4083	281	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013405.1	s__Brevibacillus formosus	78.0287	197	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_003013395.1	s__Brevibacillus fortis	77.8306	208	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710815.1	s__Brevibacillus centrosporus	77.5577	219	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_004521915.1	s__CFH-S0501 sp004521915	77.4064	206	2120	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_003710915.1	s__Brevibacillus invocatus	77.3662	164	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710935.1	s__Brevibacillus gelatini	77.3024	206	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710865.1	s__Brevibacillus borstelensis	77.2573	184	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.53	99.39	0.94	0.92	8	-
GCF_003710905.1	s__Brevibacillus parabrevis	77.1635	271	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_018228725.1	s__Brevibacillus sp018228725	77.043	174	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013096935.1	s__Brevibacillus sp003388715	76.7029	168	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.49	99.45	0.95	0.95	3	-
GCF_002257645.1	s__Paenibacillus sp002257645	76.4426	71	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909185.1	s__Paenibacillus_Z glycinis	76.0309	62	2120	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__Paenibacillaceae;g__Paenibacillus_Z	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:57,065] [INFO] GTDB search result was written to GCF_003710825.1_ASM371082v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:57,065] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:57,068] [INFO] DFAST_QC result json was written to GCF_003710825.1_ASM371082v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:57,069] [INFO] DFAST_QC completed!
[2024-01-24 14:48:57,069] [INFO] Total running time: 0h2m1s