[2024-01-24 14:38:47,908] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:38:47,910] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:38:47,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b5c95ce-1df6-4131-9ebd-d29ae2384226/dqc_reference
[2024-01-24 14:38:50,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:38:50,450] [INFO] Task started: Prodigal
[2024-01-24 14:38:50,450] [INFO] Running command: gunzip -c /var/lib/cwl/stga840a946-f68f-4738-91da-7d374ef3f189/GCF_004521915.1_ASM452191v1_genomic.fna.gz | prodigal -d GCF_004521915.1_ASM452191v1_genomic.fna/cds.fna -a GCF_004521915.1_ASM452191v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:06,698] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:06,699] [INFO] Task started: HMMsearch
[2024-01-24 14:39:06,699] [INFO] Running command: hmmsearch --tblout GCF_004521915.1_ASM452191v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b5c95ce-1df6-4131-9ebd-d29ae2384226/dqc_reference/reference_markers.hmm GCF_004521915.1_ASM452191v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:07,133] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:07,134] [INFO] Found 6/6 markers.
[2024-01-24 14:39:07,180] [INFO] Query marker FASTA was written to GCF_004521915.1_ASM452191v1_genomic.fna/markers.fasta
[2024-01-24 14:39:07,181] [INFO] Task started: Blastn
[2024-01-24 14:39:07,181] [INFO] Running command: blastn -query GCF_004521915.1_ASM452191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5c95ce-1df6-4131-9ebd-d29ae2384226/dqc_reference/reference_markers.fasta -out GCF_004521915.1_ASM452191v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:07,785] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:07,789] [INFO] Selected 25 target genomes.
[2024-01-24 14:39:07,789] [INFO] Target genome list was writen to GCF_004521915.1_ASM452191v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:07,798] [INFO] Task started: fastANI
[2024-01-24 14:39:07,798] [INFO] Running command: fastANI --query /var/lib/cwl/stga840a946-f68f-4738-91da-7d374ef3f189/GCF_004521915.1_ASM452191v1_genomic.fna.gz --refList GCF_004521915.1_ASM452191v1_genomic.fna/target_genomes.txt --output GCF_004521915.1_ASM452191v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:30,920] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:30,920] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b5c95ce-1df6-4131-9ebd-d29ae2384226/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:30,921] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b5c95ce-1df6-4131-9ebd-d29ae2384226/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:30,935] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:30,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:30,935] [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 migulae	strain=CFH S0501	GCA_004521915.1	1644114	1644114	type	True	100.0	1715	1718	95	conclusive
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	77.5989	194	1718	95	below_threshold
Brevibacillus nitrificans	strain=JCM 15774	GCA_003710965.1	651560	651560	type	True	77.4509	232	1718	95	below_threshold
Brevibacillus centrosporus	strain=NRRL NRS 664	GCA_003710815.1	54910	54910	type	True	77.4146	213	1718	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	77.3331	214	1718	95	below_threshold
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	77.3089	211	1718	95	below_threshold
Brevibacillus reuszeri	strain=DSM 9887	GCA_001187725.1	54915	54915	type	True	77.2924	189	1718	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	77.2851	215	1718	95	below_threshold
Brevibacillus gelatini	strain=DSM 100115	GCA_003710935.1	1655277	1655277	type	True	77.2727	204	1718	95	below_threshold
Brevibacillus borstelensis	strain=NRRL NRS 818	GCA_003710865.1	45462	45462	type	True	77.2245	202	1718	95	below_threshold
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	77.1712	222	1718	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	77.1687	210	1718	95	below_threshold
Brevibacillus composti	strain=FJAT-54423	GCA_016406105.1	2796470	2796470	type	True	77.1315	202	1718	95	below_threshold
Brevibacillus borstelensis	strain=NBRC 15714	GCA_006540165.1	45462	45462	type	True	77.0517	201	1718	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	77.0452	220	1718	95	below_threshold
Brevibacillus massiliensis	strain=phR	GCA_000311785.1	1118054	1118054	type	True	76.6856	146	1718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:30,937] [INFO] DFAST Taxonomy check result was written to GCF_004521915.1_ASM452191v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:30,938] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:30,938] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:30,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b5c95ce-1df6-4131-9ebd-d29ae2384226/dqc_reference/checkm_data
[2024-01-24 14:39:30,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:30,992] [INFO] Task started: CheckM
[2024-01-24 14:39:30,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004521915.1_ASM452191v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004521915.1_ASM452191v1_genomic.fna/checkm_input GCF_004521915.1_ASM452191v1_genomic.fna/checkm_result
[2024-01-24 14:40:22,547] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:22,548] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:22,574] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:22,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:22,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004521915.1_ASM452191v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:22,576] [INFO] Task started: Blastn
[2024-01-24 14:40:22,576] [INFO] Running command: blastn -query GCF_004521915.1_ASM452191v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b5c95ce-1df6-4131-9ebd-d29ae2384226/dqc_reference/reference_markers_gtdb.fasta -out GCF_004521915.1_ASM452191v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:23,473] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:23,481] [INFO] Selected 24 target genomes.
[2024-01-24 14:40:23,481] [INFO] Target genome list was writen to GCF_004521915.1_ASM452191v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:23,497] [INFO] Task started: fastANI
[2024-01-24 14:40:23,497] [INFO] Running command: fastANI --query /var/lib/cwl/stga840a946-f68f-4738-91da-7d374ef3f189/GCF_004521915.1_ASM452191v1_genomic.fna.gz --refList GCF_004521915.1_ASM452191v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004521915.1_ASM452191v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:40:46,871] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:46,884] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:40:46,884] [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_004521915.1	s__CFH-S0501 sp004521915	100.0	1715	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__CFH-S0501	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011059135.1	s__CFH-S0501 sp011059135	77.8133	296	1718	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_016811915.1	s__Brevibacillus choshinensis_A	77.7286	244	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001420695.1	s__Brevibacillus choshinensis	77.6395	195	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000503775.1	s__Brevibacillus panacihumi_A	77.5522	204	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013395.1	s__Brevibacillus fortis	77.5286	169	1718	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	77.4228	210	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_002897295.1	s__Brevibacillus reuszeri_A	77.3438	172	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_004117055.1	s__Brevibacillus agri	77.2984	214	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_001187725.1	s__Brevibacillus reuszeri	77.2932	190	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003710935.1	s__Brevibacillus gelatini	77.2596	203	1718	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	77.229	199	1718	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	77.1837	221	1718	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	77.0869	202	1718	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000311785.1	s__Brevibacillus_C massiliensis	76.6869	146	1718	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 14:40:46,886] [INFO] GTDB search result was written to GCF_004521915.1_ASM452191v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:40:46,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:40:46,890] [INFO] DFAST_QC result json was written to GCF_004521915.1_ASM452191v1_genomic.fna/dqc_result.json
[2024-01-24 14:40:46,890] [INFO] DFAST_QC completed!
[2024-01-24 14:40:46,891] [INFO] Total running time: 0h1m59s