[2024-01-24 11:06:04,661] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:06:04,663] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:06:04,663] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d336188-7f43-42d8-94b4-4dcfb8affb3f/dqc_reference
[2024-01-24 11:06:07,010] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:06:07,011] [INFO] Task started: Prodigal
[2024-01-24 11:06:07,012] [INFO] Running command: gunzip -c /var/lib/cwl/stgf96b3914-8620-415b-8e3a-00b8594b876a/GCF_002706795.1_ASM270679v1_genomic.fna.gz | prodigal -d GCF_002706795.1_ASM270679v1_genomic.fna/cds.fna -a GCF_002706795.1_ASM270679v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:29,040] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:29,041] [INFO] Task started: HMMsearch
[2024-01-24 11:06:29,041] [INFO] Running command: hmmsearch --tblout GCF_002706795.1_ASM270679v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d336188-7f43-42d8-94b4-4dcfb8affb3f/dqc_reference/reference_markers.hmm GCF_002706795.1_ASM270679v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:29,356] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:29,357] [INFO] Found 6/6 markers.
[2024-01-24 11:06:29,399] [INFO] Query marker FASTA was written to GCF_002706795.1_ASM270679v1_genomic.fna/markers.fasta
[2024-01-24 11:06:29,399] [INFO] Task started: Blastn
[2024-01-24 11:06:29,400] [INFO] Running command: blastn -query GCF_002706795.1_ASM270679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d336188-7f43-42d8-94b4-4dcfb8affb3f/dqc_reference/reference_markers.fasta -out GCF_002706795.1_ASM270679v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:29,971] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:29,976] [INFO] Selected 20 target genomes.
[2024-01-24 11:06:29,976] [INFO] Target genome list was writen to GCF_002706795.1_ASM270679v1_genomic.fna/target_genomes.txt
[2024-01-24 11:06:29,985] [INFO] Task started: fastANI
[2024-01-24 11:06:29,985] [INFO] Running command: fastANI --query /var/lib/cwl/stgf96b3914-8620-415b-8e3a-00b8594b876a/GCF_002706795.1_ASM270679v1_genomic.fna.gz --refList GCF_002706795.1_ASM270679v1_genomic.fna/target_genomes.txt --output GCF_002706795.1_ASM270679v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:46,721] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:46,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d336188-7f43-42d8-94b4-4dcfb8affb3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:46,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d336188-7f43-42d8-94b4-4dcfb8affb3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:46,732] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:46,732] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:46,732] [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 laterosporus	strain=DSM 25	GCA_002706795.1	1465	1465	suspected-type	True	100.0	1796	1800	95	conclusive
Brevibacillus laterosporus	strain=DSM 25	GCA_000374385.1	1465	1465	suspected-type	True	99.9505	1722	1800	95	conclusive
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	79.9385	94	1800	95	below_threshold
Brevibacillus fluminis	strain=JCM 15716	GCA_003710825.1	511487	511487	type	True	78.2016	74	1800	95	below_threshold
Brevibacillus nitrificans	strain=JCM 15774	GCA_003710965.1	651560	651560	type	True	77.4312	65	1800	95	below_threshold
Brevibacillus porteri	strain=NRRL B-41110	GCA_003013475.1	2126350	2126350	type	True	77.3937	92	1800	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:46,734] [INFO] DFAST Taxonomy check result was written to GCF_002706795.1_ASM270679v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:46,735] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:46,735] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:46,735] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d336188-7f43-42d8-94b4-4dcfb8affb3f/dqc_reference/checkm_data
[2024-01-24 11:06:46,736] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:46,786] [INFO] Task started: CheckM
[2024-01-24 11:06:46,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002706795.1_ASM270679v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002706795.1_ASM270679v1_genomic.fna/checkm_input GCF_002706795.1_ASM270679v1_genomic.fna/checkm_result
[2024-01-24 11:07:57,221] [INFO] Task succeeded: CheckM
[2024-01-24 11:07:57,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:07:57,243] [INFO] ===== Completeness check finished =====
[2024-01-24 11:07:57,243] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:07:57,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002706795.1_ASM270679v1_genomic.fna/markers.fasta)
[2024-01-24 11:07:57,244] [INFO] Task started: Blastn
[2024-01-24 11:07:57,244] [INFO] Running command: blastn -query GCF_002706795.1_ASM270679v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d336188-7f43-42d8-94b4-4dcfb8affb3f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002706795.1_ASM270679v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:07:58,018] [INFO] Task succeeded: Blastn
[2024-01-24 11:07:58,022] [INFO] Selected 16 target genomes.
[2024-01-24 11:07:58,022] [INFO] Target genome list was writen to GCF_002706795.1_ASM270679v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:07:58,074] [INFO] Task started: fastANI
[2024-01-24 11:07:58,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgf96b3914-8620-415b-8e3a-00b8594b876a/GCF_002706795.1_ASM270679v1_genomic.fna.gz --refList GCF_002706795.1_ASM270679v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002706795.1_ASM270679v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:12,805] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:12,819] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:12,820] [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_002706795.1	s__Brevibacillus_B laterosporus	100.0	1798	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_B	95.0	98.75	97.98	0.92	0.88	16	conclusive
GCF_000219535.2	s__Brevibacillus_B halotolerans	89.3375	1482	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_B	95.0	98.52	96.28	0.94	0.91	14	-
GCF_007833815.1	s__Brevibacillus_B laterosporus_D	87.3471	1425	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_B	95.0	98.56	97.15	0.92	0.89	5	-
GCF_000503775.1	s__Brevibacillus panacihumi_A	80.3922	65	1800	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	79.4125	94	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003710825.1	s__Brevibacillus_D fluminis	78.2082	74	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003013475.1	s__Brevibacillus porteri	77.3004	91	1800	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.63	95.52	0.90	0.88	7	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:12,821] [INFO] GTDB search result was written to GCF_002706795.1_ASM270679v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:12,822] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:12,840] [INFO] DFAST_QC result json was written to GCF_002706795.1_ASM270679v1_genomic.fna/dqc_result.json
[2024-01-24 11:08:12,840] [INFO] DFAST_QC completed!
[2024-01-24 11:08:12,840] [INFO] Total running time: 0h2m8s