[2024-01-24 10:57:32,903] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:32,905] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:32,905] [INFO] DQC Reference Directory: /var/lib/cwl/stg7aef7282-878a-4335-bb24-823ac8c0ce0a/dqc_reference
[2024-01-24 10:57:34,068] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:34,073] [INFO] Task started: Prodigal
[2024-01-24 10:57:34,073] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7bc04ad-f879-421c-aba7-3fdddabe6de4/GCF_003710965.1_ASM371096v1_genomic.fna.gz | prodigal -d GCF_003710965.1_ASM371096v1_genomic.fna/cds.fna -a GCF_003710965.1_ASM371096v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:52,490] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:52,491] [INFO] Task started: HMMsearch
[2024-01-24 10:57:52,491] [INFO] Running command: hmmsearch --tblout GCF_003710965.1_ASM371096v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7aef7282-878a-4335-bb24-823ac8c0ce0a/dqc_reference/reference_markers.hmm GCF_003710965.1_ASM371096v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:52,812] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:52,814] [INFO] Found 6/6 markers.
[2024-01-24 10:57:52,865] [INFO] Query marker FASTA was written to GCF_003710965.1_ASM371096v1_genomic.fna/markers.fasta
[2024-01-24 10:57:52,866] [INFO] Task started: Blastn
[2024-01-24 10:57:52,866] [INFO] Running command: blastn -query GCF_003710965.1_ASM371096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aef7282-878a-4335-bb24-823ac8c0ce0a/dqc_reference/reference_markers.fasta -out GCF_003710965.1_ASM371096v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:53,457] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:53,460] [INFO] Selected 19 target genomes.
[2024-01-24 10:57:53,460] [INFO] Target genome list was writen to GCF_003710965.1_ASM371096v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:53,467] [INFO] Task started: fastANI
[2024-01-24 10:57:53,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7bc04ad-f879-421c-aba7-3fdddabe6de4/GCF_003710965.1_ASM371096v1_genomic.fna.gz --refList GCF_003710965.1_ASM371096v1_genomic.fna/target_genomes.txt --output GCF_003710965.1_ASM371096v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:12,618] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:12,619] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7aef7282-878a-4335-bb24-823ac8c0ce0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:12,620] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7aef7282-878a-4335-bb24-823ac8c0ce0a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:12,634] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 10:58:12,634] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 10:58:12,634] [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 nitrificans	strain=JCM 15774	GCA_003710965.1	651560	651560	type	True	100.0	2088	2092	95	inconclusive
Brevibacillus centrosporus	strain=NBRC 15540	GCA_006540045.1	54910	54910	type	True	95.9305	1686	2092	95	inconclusive
Brevibacillus centrosporus	strain=NRRL NRS 664	GCA_003710815.1	54910	54910	type	True	95.9077	1731	2092	95	inconclusive
Brevibacillus choshinensis	strain=DSM 8552	GCA_001420695.1	54911	54911	type	True	82.2863	1248	2092	95	below_threshold
Brevibacillus agri	strain=NBRC 15538	GCA_006540025.1	51101	51101	type	True	79.6989	673	2092	95	below_threshold
Brevibacillus brevis	strain=NCTC2611	GCA_900637055.1	1393	1393	suspected-type	True	79.6481	640	2092	95	below_threshold
Brevibacillus parabrevis	strain=NBRC 12334	GCA_006539065.1	54914	54914	type	True	79.5881	706	2092	95	below_threshold
Brevibacillus reuszeri	strain=DSM 9887	GCA_001187725.1	54915	54915	type	True	79.5605	729	2092	95	below_threshold
Brevibacillus fortis	strain=NRRL NRS-1210	GCA_003013395.1	2126352	2126352	type	True	79.5529	640	2092	95	below_threshold
Brevibacillus marinus	strain=SCSIO 07484	GCA_003963515.1	2496837	2496837	type	True	76.544	106	2092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,636] [INFO] DFAST Taxonomy check result was written to GCF_003710965.1_ASM371096v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:12,637] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:12,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:12,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7aef7282-878a-4335-bb24-823ac8c0ce0a/dqc_reference/checkm_data
[2024-01-24 10:58:12,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:12,702] [INFO] Task started: CheckM
[2024-01-24 10:58:12,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003710965.1_ASM371096v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003710965.1_ASM371096v1_genomic.fna/checkm_input GCF_003710965.1_ASM371096v1_genomic.fna/checkm_result
[2024-01-24 10:59:07,129] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:07,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:07,157] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:07,157] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:07,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003710965.1_ASM371096v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:07,158] [INFO] Task started: Blastn
[2024-01-24 10:59:07,158] [INFO] Running command: blastn -query GCF_003710965.1_ASM371096v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aef7282-878a-4335-bb24-823ac8c0ce0a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003710965.1_ASM371096v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:07,987] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:07,991] [INFO] Selected 17 target genomes.
[2024-01-24 10:59:07,992] [INFO] Target genome list was writen to GCF_003710965.1_ASM371096v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:08,005] [INFO] Task started: fastANI
[2024-01-24 10:59:08,005] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7bc04ad-f879-421c-aba7-3fdddabe6de4/GCF_003710965.1_ASM371096v1_genomic.fna.gz --refList GCF_003710965.1_ASM371096v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003710965.1_ASM371096v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:25,917] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:25,931] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:25,932] [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_003710815.1	s__Brevibacillus centrosporus	95.8987	1732	2092	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	98.44	95.98	0.93	0.89	4	conclusive
GCF_016811915.1	s__Brevibacillus choshinensis_A	82.3996	1242	2092	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	82.2803	1249	2092	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	79.7356	698	2092	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.52	99.18	0.94	0.89	8	-
GCF_002897295.1	s__Brevibacillus reuszeri_A	79.6651	717	2092	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	96.18	96.18	0.89	0.89	2	-
GCF_900637055.1	s__Brevibacillus brevis	79.652	640	2092	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	99.71	98.86	0.99	0.96	5	-
GCF_000010165.1	s__Brevibacillus brevis_D	79.5979	609	2092	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	97.35	96.52	0.92	0.90	11	-
GCF_003710905.1	s__Brevibacillus parabrevis	79.5864	722	2092	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	79.5462	731	2092	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003013395.1	s__Brevibacillus fortis	79.539	640	2092	d__Bacteria;p__Firmicutes;c__Bacilli;o__Brevibacillales;f__Brevibacillaceae;g__Brevibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013284355.1	s__Brevibacillus sp013284355	79.4821	625	2092	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 10:59:25,933] [INFO] GTDB search result was written to GCF_003710965.1_ASM371096v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:25,934] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:25,937] [INFO] DFAST_QC result json was written to GCF_003710965.1_ASM371096v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:25,937] [INFO] DFAST_QC completed!
[2024-01-24 10:59:25,937] [INFO] Total running time: 0h1m53s