[2024-01-24 14:22:04,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:04,310] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:04,311] [INFO] DQC Reference Directory: /var/lib/cwl/stg102a96cf-dbe5-452f-8234-07fc65e3fa14/dqc_reference
[2024-01-24 14:22:05,627] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:05,628] [INFO] Task started: Prodigal
[2024-01-24 14:22:05,629] [INFO] Running command: gunzip -c /var/lib/cwl/stge02a767f-1cdd-4809-bbbe-8e246e82d0c5/GCF_006170445.1_ASM617044v1_genomic.fna.gz | prodigal -d GCF_006170445.1_ASM617044v1_genomic.fna/cds.fna -a GCF_006170445.1_ASM617044v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:27,409] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:27,410] [INFO] Task started: HMMsearch
[2024-01-24 14:22:27,410] [INFO] Running command: hmmsearch --tblout GCF_006170445.1_ASM617044v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg102a96cf-dbe5-452f-8234-07fc65e3fa14/dqc_reference/reference_markers.hmm GCF_006170445.1_ASM617044v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:27,740] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:27,742] [INFO] Found 6/6 markers.
[2024-01-24 14:22:27,791] [INFO] Query marker FASTA was written to GCF_006170445.1_ASM617044v1_genomic.fna/markers.fasta
[2024-01-24 14:22:27,792] [INFO] Task started: Blastn
[2024-01-24 14:22:27,792] [INFO] Running command: blastn -query GCF_006170445.1_ASM617044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg102a96cf-dbe5-452f-8234-07fc65e3fa14/dqc_reference/reference_markers.fasta -out GCF_006170445.1_ASM617044v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:28,373] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:28,376] [INFO] Selected 30 target genomes.
[2024-01-24 14:22:28,377] [INFO] Target genome list was writen to GCF_006170445.1_ASM617044v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:28,396] [INFO] Task started: fastANI
[2024-01-24 14:22:28,396] [INFO] Running command: fastANI --query /var/lib/cwl/stge02a767f-1cdd-4809-bbbe-8e246e82d0c5/GCF_006170445.1_ASM617044v1_genomic.fna.gz --refList GCF_006170445.1_ASM617044v1_genomic.fna/target_genomes.txt --output GCF_006170445.1_ASM617044v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:51,378] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:51,379] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg102a96cf-dbe5-452f-8234-07fc65e3fa14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:51,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg102a96cf-dbe5-452f-8234-07fc65e3fa14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:51,394] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:51,394] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:51,394] [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 antibioticus	strain=TGS2-1	GCA_005217615.1	2570228	2570228	type	True	77.5071	123	1901	95	below_threshold
Brevibacillus reuszeri	strain=DSM 9887	GCA_001187725.1	54915	54915	type	True	77.436	118	1901	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	77.376	140	1901	95	below_threshold
Brevibacillus migulae	strain=CFH S0501	GCA_004521915.1	1644114	1644114	type	True	77.2415	165	1901	95	below_threshold
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	77.2339	131	1901	95	below_threshold
Brevibacillus invocatus	strain=JCM 12215	GCA_003710915.1	173959	173959	type	True	77.1752	114	1901	95	below_threshold
Brevibacillus brevis	strain=NRRL NRS-604	GCA_003012835.1	1393	1393	suspected-type	True	77.0859	143	1901	95	below_threshold
Brevibacillus parabrevis	strain=NRRL NRS 605	GCA_003710905.1	54914	54914	type	True	77.0647	156	1901	95	below_threshold
Brevibacillus brevis	strain=DSM 30	GCA_003385915.1	1393	1393	suspected-type	True	77.0195	135	1901	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	76.9952	167	1901	95	below_threshold
Brevibacillus borstelensis	strain=NRRL NRS 818	GCA_003710865.1	45462	45462	type	True	76.9887	115	1901	95	below_threshold
Brevibacillus reuszeri	strain=NBRC 15719	GCA_006540225.1	54915	54915	type	True	76.9303	113	1901	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	76.9261	170	1901	95	below_threshold
Brevibacillus brevis	strain=NBRC 15304	GCA_006539845.1	1393	1393	suspected-type	True	76.8893	134	1901	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	76.7077	160	1901	95	below_threshold
Brevibacillus borstelensis	strain=NBRC 15714	GCA_006540165.1	45462	45462	type	True	76.6458	112	1901	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	76.644	165	1901	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:51,397] [INFO] DFAST Taxonomy check result was written to GCF_006170445.1_ASM617044v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:51,397] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:51,398] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:51,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg102a96cf-dbe5-452f-8234-07fc65e3fa14/dqc_reference/checkm_data
[2024-01-24 14:22:51,400] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:51,454] [INFO] Task started: CheckM
[2024-01-24 14:22:51,454] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006170445.1_ASM617044v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006170445.1_ASM617044v1_genomic.fna/checkm_input GCF_006170445.1_ASM617044v1_genomic.fna/checkm_result
[2024-01-24 14:23:54,174] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:54,176] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:54,204] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:54,205] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:54,205] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006170445.1_ASM617044v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:54,206] [INFO] Task started: Blastn
[2024-01-24 14:23:54,206] [INFO] Running command: blastn -query GCF_006170445.1_ASM617044v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg102a96cf-dbe5-452f-8234-07fc65e3fa14/dqc_reference/reference_markers_gtdb.fasta -out GCF_006170445.1_ASM617044v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:54,987] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:54,990] [INFO] Selected 24 target genomes.
[2024-01-24 14:23:54,990] [INFO] Target genome list was writen to GCF_006170445.1_ASM617044v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:55,008] [INFO] Task started: fastANI
[2024-01-24 14:23:55,009] [INFO] Running command: fastANI --query /var/lib/cwl/stge02a767f-1cdd-4809-bbbe-8e246e82d0c5/GCF_006170445.1_ASM617044v1_genomic.fna.gz --refList GCF_006170445.1_ASM617044v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006170445.1_ASM617044v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:19,053] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:19,072] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:19,072] [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_006170445.1	s__Brevibacillus_B sp006170445	100.0	1901	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000010165.1	s__Brevibacillus brevis_D	77.6597	132	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_005217615.1	s__Brevibacillus antibioticus	77.4965	122	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187725.1	s__Brevibacillus reuszeri	77.4544	118	1901	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	77.3735	152	1901	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	77.3481	145	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_900637055.1	s__Brevibacillus brevis	77.3454	140	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_003710915.1	s__Brevibacillus invocatus	77.2193	112	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521915.1	s__CFH-S0501 sp004521915	77.2159	166	1901	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_013284355.1	s__Brevibacillus sp013284355	77.1681	135	1901	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	77.0623	115	1901	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	76.9953	155	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_004117055.1	s__Brevibacillus agri	76.9249	169	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_000503775.1	s__Brevibacillus panacihumi_A	76.8954	121	1901	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	76.8258	101	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_C	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000454065.1	s__Brevibacillus thermoruber	76.6633	154	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.54	98.43	0.91	0.89	5	-
GCF_013096935.1	s__Brevibacillus sp003388715	76.5853	147	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.49	99.45	0.95	0.95	3	-
GCA_017656235.1	s__SCSIO-07484 sp017656235	76.5224	93	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__SCSIO-07484	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000722545.1	s__Paenibacillus_G tyrfis	75.8066	51	1901	d__Bacteria;p__Firmicutes;c__Bacilli;o__Paenibacillales;f__NBRC-103111;g__Paenibacillus_G	95.0	98.07	98.07	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:19,074] [INFO] GTDB search result was written to GCF_006170445.1_ASM617044v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:19,074] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:19,079] [INFO] DFAST_QC result json was written to GCF_006170445.1_ASM617044v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:19,079] [INFO] DFAST_QC completed!
[2024-01-24 14:24:19,079] [INFO] Total running time: 0h2m15s