[2024-01-24 11:58:20,742] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:20,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:20,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg3338fb7b-b723-4d52-b013-24fbe51a46b6/dqc_reference
[2024-01-24 11:58:21,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:21,974] [INFO] Task started: Prodigal
[2024-01-24 11:58:21,974] [INFO] Running command: gunzip -c /var/lib/cwl/stg04d15b8d-5ad1-47ae-ba02-f7f14be03677/GCF_003710985.1_ASM371098v1_genomic.fna.gz | prodigal -d GCF_003710985.1_ASM371098v1_genomic.fna/cds.fna -a GCF_003710985.1_ASM371098v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:58:36,842] [INFO] Task succeeded: Prodigal
[2024-01-24 11:58:36,843] [INFO] Task started: HMMsearch
[2024-01-24 11:58:36,843] [INFO] Running command: hmmsearch --tblout GCF_003710985.1_ASM371098v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3338fb7b-b723-4d52-b013-24fbe51a46b6/dqc_reference/reference_markers.hmm GCF_003710985.1_ASM371098v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:58:37,156] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:58:37,157] [INFO] Found 6/6 markers.
[2024-01-24 11:58:37,202] [INFO] Query marker FASTA was written to GCF_003710985.1_ASM371098v1_genomic.fna/markers.fasta
[2024-01-24 11:58:37,203] [INFO] Task started: Blastn
[2024-01-24 11:58:37,203] [INFO] Running command: blastn -query GCF_003710985.1_ASM371098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3338fb7b-b723-4d52-b013-24fbe51a46b6/dqc_reference/reference_markers.fasta -out GCF_003710985.1_ASM371098v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:58:37,791] [INFO] Task succeeded: Blastn
[2024-01-24 11:58:37,795] [INFO] Selected 19 target genomes.
[2024-01-24 11:58:37,795] [INFO] Target genome list was writen to GCF_003710985.1_ASM371098v1_genomic.fna/target_genomes.txt
[2024-01-24 11:58:37,809] [INFO] Task started: fastANI
[2024-01-24 11:58:37,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d15b8d-5ad1-47ae-ba02-f7f14be03677/GCF_003710985.1_ASM371098v1_genomic.fna.gz --refList GCF_003710985.1_ASM371098v1_genomic.fna/target_genomes.txt --output GCF_003710985.1_ASM371098v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:58:54,822] [INFO] Task succeeded: fastANI
[2024-01-24 11:58:54,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3338fb7b-b723-4d52-b013-24fbe51a46b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:58:54,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3338fb7b-b723-4d52-b013-24fbe51a46b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:58:54,840] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:58:54,840] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:58:54,840] [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 panacihumi	strain=JCM 15085	GCA_003710985.1	497735	497735	type	True	100.0	1656	1659	95	conclusive
Brevibacillus invocatus	strain=JCM 12215	GCA_003710915.1	173959	173959	type	True	80.9321	819	1659	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	79.0944	508	1659	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	79.0875	513	1659	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	78.9369	505	1659	95	below_threshold
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	78.9088	488	1659	95	below_threshold
Brevibacillus fortis	strain=NRRL NRS-1210	GCA_003013395.1	2126352	2126352	type	True	78.7864	407	1659	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	78.7841	406	1659	95	below_threshold
Brevibacillus reuszeri	strain=DSM 9887	GCA_001187725.1	54915	54915	type	True	78.7122	487	1659	95	below_threshold
Brevibacillus formosus	strain=NRRL NRS-863	GCA_003013405.1	54913	54913	type	True	78.693	417	1659	95	below_threshold
Brevibacillus reuszeri	strain=NBRC 15719	GCA_006540225.1	54915	54915	type	True	78.5747	475	1659	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	78.5698	493	1659	95	below_threshold
Brevibacillus centrosporus	strain=NRRL NRS 664	GCA_003710815.1	54910	54910	type	True	78.4867	509	1659	95	below_threshold
Brevibacillus nitrificans	strain=JCM 15774	GCA_003710965.1	651560	651560	type	True	78.4727	516	1659	95	below_threshold
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	78.4647	492	1659	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:58:54,841] [INFO] DFAST Taxonomy check result was written to GCF_003710985.1_ASM371098v1_genomic.fna/tc_result.tsv
[2024-01-24 11:58:54,842] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:58:54,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:58:54,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3338fb7b-b723-4d52-b013-24fbe51a46b6/dqc_reference/checkm_data
[2024-01-24 11:58:54,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:58:54,889] [INFO] Task started: CheckM
[2024-01-24 11:58:54,889] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710985.1_ASM371098v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710985.1_ASM371098v1_genomic.fna/checkm_input GCF_003710985.1_ASM371098v1_genomic.fna/checkm_result
[2024-01-24 11:59:40,622] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:40,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:40,645] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:40,645] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:40,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710985.1_ASM371098v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:40,646] [INFO] Task started: Blastn
[2024-01-24 11:59:40,646] [INFO] Running command: blastn -query GCF_003710985.1_ASM371098v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3338fb7b-b723-4d52-b013-24fbe51a46b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710985.1_ASM371098v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:41,413] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:41,417] [INFO] Selected 14 target genomes.
[2024-01-24 11:59:41,418] [INFO] Target genome list was writen to GCF_003710985.1_ASM371098v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:41,429] [INFO] Task started: fastANI
[2024-01-24 11:59:41,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg04d15b8d-5ad1-47ae-ba02-f7f14be03677/GCF_003710985.1_ASM371098v1_genomic.fna.gz --refList GCF_003710985.1_ASM371098v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710985.1_ASM371098v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:56,037] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:56,050] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:56,050] [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_003710985.1	s__Brevibacillus panacihumi	100.0	1656	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000503775.1	s__Brevibacillus panacihumi_A	94.5411	1514	1659	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	80.9241	820	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004117055.1	s__Brevibacillus agri	79.0787	514	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	79.0104	520	1659	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	78.9837	472	1659	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	78.9012	488	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002897295.1	s__Brevibacillus reuszeri_A	78.8091	493	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_003013395.1	s__Brevibacillus fortis	78.7864	407	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710905.1	s__Brevibacillus parabrevis	78.7154	514	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_001187725.1	s__Brevibacillus reuszeri	78.7122	487	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003710815.1	s__Brevibacillus centrosporus	78.5028	507	1659	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:56,052] [INFO] GTDB search result was written to GCF_003710985.1_ASM371098v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:56,052] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:56,055] [INFO] DFAST_QC result json was written to GCF_003710985.1_ASM371098v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:56,055] [INFO] DFAST_QC completed!
[2024-01-24 11:59:56,055] [INFO] Total running time: 0h1m35s