[2024-01-24 11:27:04,630] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:27:04,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:27:04,633] [INFO] DQC Reference Directory: /var/lib/cwl/stg4af780c4-b632-406b-b0a8-ae793dbcc6fd/dqc_reference
[2024-01-24 11:27:05,832] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:27:05,832] [INFO] Task started: Prodigal
[2024-01-24 11:27:05,833] [INFO] Running command: gunzip -c /var/lib/cwl/stg154f1ab2-992e-463b-95f9-7e99a6b4a126/GCF_003710865.1_ASM371086v1_genomic.fna.gz | prodigal -d GCF_003710865.1_ASM371086v1_genomic.fna/cds.fna -a GCF_003710865.1_ASM371086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:20,873] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:20,873] [INFO] Task started: HMMsearch
[2024-01-24 11:27:20,874] [INFO] Running command: hmmsearch --tblout GCF_003710865.1_ASM371086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4af780c4-b632-406b-b0a8-ae793dbcc6fd/dqc_reference/reference_markers.hmm GCF_003710865.1_ASM371086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:21,176] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:21,177] [INFO] Found 6/6 markers.
[2024-01-24 11:27:21,219] [INFO] Query marker FASTA was written to GCF_003710865.1_ASM371086v1_genomic.fna/markers.fasta
[2024-01-24 11:27:21,219] [INFO] Task started: Blastn
[2024-01-24 11:27:21,220] [INFO] Running command: blastn -query GCF_003710865.1_ASM371086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4af780c4-b632-406b-b0a8-ae793dbcc6fd/dqc_reference/reference_markers.fasta -out GCF_003710865.1_ASM371086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:21,797] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:21,800] [INFO] Selected 18 target genomes.
[2024-01-24 11:27:21,801] [INFO] Target genome list was writen to GCF_003710865.1_ASM371086v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:21,808] [INFO] Task started: fastANI
[2024-01-24 11:27:21,808] [INFO] Running command: fastANI --query /var/lib/cwl/stg154f1ab2-992e-463b-95f9-7e99a6b4a126/GCF_003710865.1_ASM371086v1_genomic.fna.gz --refList GCF_003710865.1_ASM371086v1_genomic.fna/target_genomes.txt --output GCF_003710865.1_ASM371086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:37,088] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:37,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4af780c4-b632-406b-b0a8-ae793dbcc6fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:37,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4af780c4-b632-406b-b0a8-ae793dbcc6fd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:37,105] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:27:37,105] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:37,105] [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 borstelensis	strain=NRRL NRS 818	GCA_003710865.1	45462	45462	type	True	100.0	1703	1707	95	conclusive
Brevibacillus borstelensis	strain=NBRC 15714	GCA_006540165.1	45462	45462	type	True	99.9733	1643	1707	95	conclusive
Brevibacillus composti	strain=FJAT-54423	GCA_016406105.1	2796470	2796470	type	True	80.1991	707	1707	95	below_threshold
Brevibacillus panacihumi	strain=JCM 15085	GCA_003710985.1	497735	497735	type	True	78.6972	355	1707	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	78.443	414	1707	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	78.3246	407	1707	95	below_threshold
Brevibacillus invocatus	strain=JCM 12215	GCA_003710915.1	173959	173959	type	True	78.1738	289	1707	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	78.1465	302	1707	95	below_threshold
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	78.0667	310	1707	95	below_threshold
Brevibacillus nitrificans	strain=JCM 15774	GCA_003710965.1	651560	651560	type	True	77.9327	368	1707	95	below_threshold
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	77.6635	366	1707	95	below_threshold
Brevibacillus fluminis	strain=JCM 15716	GCA_003710825.1	511487	511487	type	True	77.4585	171	1707	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:37,107] [INFO] DFAST Taxonomy check result was written to GCF_003710865.1_ASM371086v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:37,107] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:37,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:37,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4af780c4-b632-406b-b0a8-ae793dbcc6fd/dqc_reference/checkm_data
[2024-01-24 11:27:37,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:37,159] [INFO] Task started: CheckM
[2024-01-24 11:27:37,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710865.1_ASM371086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710865.1_ASM371086v1_genomic.fna/checkm_input GCF_003710865.1_ASM371086v1_genomic.fna/checkm_result
[2024-01-24 11:28:23,220] [INFO] Task succeeded: CheckM
[2024-01-24 11:28:23,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:28:23,240] [INFO] ===== Completeness check finished =====
[2024-01-24 11:28:23,240] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:28:23,241] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710865.1_ASM371086v1_genomic.fna/markers.fasta)
[2024-01-24 11:28:23,241] [INFO] Task started: Blastn
[2024-01-24 11:28:23,241] [INFO] Running command: blastn -query GCF_003710865.1_ASM371086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4af780c4-b632-406b-b0a8-ae793dbcc6fd/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710865.1_ASM371086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:28:24,007] [INFO] Task succeeded: Blastn
[2024-01-24 11:28:24,011] [INFO] Selected 15 target genomes.
[2024-01-24 11:28:24,011] [INFO] Target genome list was writen to GCF_003710865.1_ASM371086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:28:24,023] [INFO] Task started: fastANI
[2024-01-24 11:28:24,024] [INFO] Running command: fastANI --query /var/lib/cwl/stg154f1ab2-992e-463b-95f9-7e99a6b4a126/GCF_003710865.1_ASM371086v1_genomic.fna.gz --refList GCF_003710865.1_ASM371086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710865.1_ASM371086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:28:39,111] [INFO] Task succeeded: fastANI
[2024-01-24 11:28:39,124] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:28:39,124] [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_003710865.1	s__Brevibacillus borstelensis	100.0	1703	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.53	99.39	0.94	0.92	8	conclusive
GCF_018228725.1	s__Brevibacillus sp018228725	80.1937	711	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000454065.1	s__Brevibacillus thermoruber	79.8907	548	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.54	98.43	0.91	0.89	5	-
GCF_003710985.1	s__Brevibacillus panacihumi	78.6714	355	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013096935.1	s__Brevibacillus sp003388715	78.6322	467	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.49	99.45	0.95	0.95	3	-
GCF_004117055.1	s__Brevibacillus agri	78.4401	416	1707	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	78.0763	372	1707	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	78.0558	310	1707	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	77.9052	387	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_003710815.1	s__Brevibacillus centrosporus	77.796	364	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_003710825.1	s__Brevibacillus_D fluminis	77.4937	172	1707	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:28:39,125] [INFO] GTDB search result was written to GCF_003710865.1_ASM371086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:28:39,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:28:39,129] [INFO] DFAST_QC result json was written to GCF_003710865.1_ASM371086v1_genomic.fna/dqc_result.json
[2024-01-24 11:28:39,129] [INFO] DFAST_QC completed!
[2024-01-24 11:28:39,129] [INFO] Total running time: 0h1m34s