[2024-01-24 15:27:12,623] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:12,625] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:12,626] [INFO] DQC Reference Directory: /var/lib/cwl/stg2479bad9-0f98-4a29-8224-fdafe274819f/dqc_reference
[2024-01-24 15:27:13,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:13,992] [INFO] Task started: Prodigal
[2024-01-24 15:27:13,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f70eb0f-a258-461b-85ed-aaa1cba4ee56/GCF_003710935.1_ASM371093v1_genomic.fna.gz | prodigal -d GCF_003710935.1_ASM371093v1_genomic.fna/cds.fna -a GCF_003710935.1_ASM371093v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:28,577] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:28,578] [INFO] Task started: HMMsearch
[2024-01-24 15:27:28,578] [INFO] Running command: hmmsearch --tblout GCF_003710935.1_ASM371093v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2479bad9-0f98-4a29-8224-fdafe274819f/dqc_reference/reference_markers.hmm GCF_003710935.1_ASM371093v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:28,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:28,913] [INFO] Found 6/6 markers.
[2024-01-24 15:27:28,958] [INFO] Query marker FASTA was written to GCF_003710935.1_ASM371093v1_genomic.fna/markers.fasta
[2024-01-24 15:27:28,959] [INFO] Task started: Blastn
[2024-01-24 15:27:28,959] [INFO] Running command: blastn -query GCF_003710935.1_ASM371093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2479bad9-0f98-4a29-8224-fdafe274819f/dqc_reference/reference_markers.fasta -out GCF_003710935.1_ASM371093v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:29,608] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:29,612] [INFO] Selected 8 target genomes.
[2024-01-24 15:27:29,613] [INFO] Target genome list was writen to GCF_003710935.1_ASM371093v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:29,619] [INFO] Task started: fastANI
[2024-01-24 15:27:29,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f70eb0f-a258-461b-85ed-aaa1cba4ee56/GCF_003710935.1_ASM371093v1_genomic.fna.gz --refList GCF_003710935.1_ASM371093v1_genomic.fna/target_genomes.txt --output GCF_003710935.1_ASM371093v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:37,775] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:37,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2479bad9-0f98-4a29-8224-fdafe274819f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:37,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2479bad9-0f98-4a29-8224-fdafe274819f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:37,782] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:37,782] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:37,782] [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 gelatini	strain=DSM 100115	GCA_003710935.1	1655277	1655277	type	True	100.0	1497	1497	95	conclusive
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	90.8524	1166	1497	95	below_threshold
Brevibacillus agri	strain=NRRL NRS 1219	GCA_003710885.1	51101	51101	type	True	90.809	1192	1497	95	below_threshold
Brevibacillus agri	strain=DSM 6348	GCA_004117055.1	51101	51101	type	True	90.7671	1218	1497	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	84.1724	1141	1497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,784] [INFO] DFAST Taxonomy check result was written to GCF_003710935.1_ASM371093v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:37,785] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:37,785] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:37,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2479bad9-0f98-4a29-8224-fdafe274819f/dqc_reference/checkm_data
[2024-01-24 15:27:37,787] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:37,837] [INFO] Task started: CheckM
[2024-01-24 15:27:37,838] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710935.1_ASM371093v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710935.1_ASM371093v1_genomic.fna/checkm_input GCF_003710935.1_ASM371093v1_genomic.fna/checkm_result
[2024-01-24 15:28:23,169] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:23,170] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:23,197] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:23,198] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:23,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710935.1_ASM371093v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:23,199] [INFO] Task started: Blastn
[2024-01-24 15:28:23,199] [INFO] Running command: blastn -query GCF_003710935.1_ASM371093v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2479bad9-0f98-4a29-8224-fdafe274819f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710935.1_ASM371093v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:23,969] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:23,973] [INFO] Selected 12 target genomes.
[2024-01-24 15:28:23,974] [INFO] Target genome list was writen to GCF_003710935.1_ASM371093v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:23,987] [INFO] Task started: fastANI
[2024-01-24 15:28:23,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f70eb0f-a258-461b-85ed-aaa1cba4ee56/GCF_003710935.1_ASM371093v1_genomic.fna.gz --refList GCF_003710935.1_ASM371093v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710935.1_ASM371093v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:39,397] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:39,415] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:39,415] [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_003710935.1	s__Brevibacillus gelatini	100.0	1497	1497	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_004117055.1	s__Brevibacillus agri	90.7644	1219	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_003710905.1	s__Brevibacillus parabrevis	84.2065	1159	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.83	96.13	0.96	0.94	7	-
GCF_003013405.1	s__Brevibacillus formosus	80.2698	698	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.07	95.45	0.94	0.90	6	-
GCF_900637055.1	s__Brevibacillus brevis	80.2264	729	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_003013395.1	s__Brevibacillus fortis	80.1342	699	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010165.1	s__Brevibacillus brevis_D	80.1085	721	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_013284355.1	s__Brevibacillus sp013284355	80.0912	708	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811915.1	s__Brevibacillus choshinensis_A	79.85	609	1497	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	79.7484	562	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	-
GCF_001187725.1	s__Brevibacillus reuszeri	79.7376	608	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001420695.1	s__Brevibacillus choshinensis	79.7343	548	1497	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:39,417] [INFO] GTDB search result was written to GCF_003710935.1_ASM371093v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:39,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:39,421] [INFO] DFAST_QC result json was written to GCF_003710935.1_ASM371093v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:39,421] [INFO] DFAST_QC completed!
[2024-01-24 15:28:39,421] [INFO] Total running time: 0h1m27s