[2024-01-24 13:32:25,291] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:25,293] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:25,293] [INFO] DQC Reference Directory: /var/lib/cwl/stgc61bd331-64cc-411a-87aa-90f23ac156c2/dqc_reference
[2024-01-24 13:32:26,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:26,616] [INFO] Task started: Prodigal
[2024-01-24 13:32:26,616] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cf2e671-3503-4c50-8f62-56bbb9d0492f/GCF_021117425.1_ASM2111742v1_genomic.fna.gz | prodigal -d GCF_021117425.1_ASM2111742v1_genomic.fna/cds.fna -a GCF_021117425.1_ASM2111742v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:40,594] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:40,594] [INFO] Task started: HMMsearch
[2024-01-24 13:32:40,594] [INFO] Running command: hmmsearch --tblout GCF_021117425.1_ASM2111742v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc61bd331-64cc-411a-87aa-90f23ac156c2/dqc_reference/reference_markers.hmm GCF_021117425.1_ASM2111742v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:40,932] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:40,933] [INFO] Found 6/6 markers.
[2024-01-24 13:32:40,977] [INFO] Query marker FASTA was written to GCF_021117425.1_ASM2111742v1_genomic.fna/markers.fasta
[2024-01-24 13:32:40,978] [INFO] Task started: Blastn
[2024-01-24 13:32:40,978] [INFO] Running command: blastn -query GCF_021117425.1_ASM2111742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc61bd331-64cc-411a-87aa-90f23ac156c2/dqc_reference/reference_markers.fasta -out GCF_021117425.1_ASM2111742v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:41,891] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:41,898] [INFO] Selected 9 target genomes.
[2024-01-24 13:32:41,899] [INFO] Target genome list was writen to GCF_021117425.1_ASM2111742v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:41,908] [INFO] Task started: fastANI
[2024-01-24 13:32:41,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cf2e671-3503-4c50-8f62-56bbb9d0492f/GCF_021117425.1_ASM2111742v1_genomic.fna.gz --refList GCF_021117425.1_ASM2111742v1_genomic.fna/target_genomes.txt --output GCF_021117425.1_ASM2111742v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:50,978] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:50,979] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc61bd331-64cc-411a-87aa-90f23ac156c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:50,979] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc61bd331-64cc-411a-87aa-90f23ac156c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:50,988] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:50,988] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:50,988] [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
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	100.0	1467	1469	95	conclusive
Brevibacterium aurantiacum	strain=ATCC 9175	GCA_900169065.1	273384	273384	type	True	92.686	1100	1469	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	87.7567	1129	1469	95	below_threshold
Brevibacterium sandarakinum	strain=DSM 22082	GCA_900105045.1	629680	629680	type	True	86.7181	1102	1469	95	below_threshold
Brevibacterium marinum	strain=DSM 18964	GCA_011927955.1	418643	418643	type	True	84.6302	1064	1469	95	below_threshold
Brevibacterium oceani	strain=BBH7	GCA_013623835.1	358099	358099	type	True	81.2932	862	1469	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	78.1877	332	1469	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	77.7753	271	1469	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	76.7658	134	1469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:50,990] [INFO] DFAST Taxonomy check result was written to GCF_021117425.1_ASM2111742v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:50,990] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:50,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:50,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc61bd331-64cc-411a-87aa-90f23ac156c2/dqc_reference/checkm_data
[2024-01-24 13:32:50,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:51,036] [INFO] Task started: CheckM
[2024-01-24 13:32:51,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021117425.1_ASM2111742v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021117425.1_ASM2111742v1_genomic.fna/checkm_input GCF_021117425.1_ASM2111742v1_genomic.fna/checkm_result
[2024-01-24 13:33:39,585] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:39,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:39,612] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:39,613] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:39,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021117425.1_ASM2111742v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:39,613] [INFO] Task started: Blastn
[2024-01-24 13:33:39,614] [INFO] Running command: blastn -query GCF_021117425.1_ASM2111742v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc61bd331-64cc-411a-87aa-90f23ac156c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_021117425.1_ASM2111742v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:40,904] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:40,908] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:40,908] [INFO] Target genome list was writen to GCF_021117425.1_ASM2111742v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:40,921] [INFO] Task started: fastANI
[2024-01-24 13:33:40,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cf2e671-3503-4c50-8f62-56bbb9d0492f/GCF_021117425.1_ASM2111742v1_genomic.fna.gz --refList GCF_021117425.1_ASM2111742v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021117425.1_ASM2111742v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:49,534] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:49,547] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:33:49,548] [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_900169065.1	s__Brevibacterium aurantiacum	92.686	1100	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.70	96.91	0.88	0.85	28	-
GCF_016107655.1	s__Brevibacterium antiquum	87.7567	1129	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016892625.1	s__Brevibacterium sp016892625	87.5512	1195	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007558825.1	s__Brevibacterium aurantiacum_A	87.4708	1187	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169145.1	s__Brevibacterium antiquum_A	86.9802	963	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.98	97.98	0.94	0.91	3	-
GCF_900105045.1	s__Brevibacterium sandarakinum	86.7181	1102	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900169365.1	s__Brevibacterium sp900169365	86.3984	1094	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.94	97.94	0.86	0.85	3	-
GCF_013623835.1	s__Brevibacterium oceani	81.2932	862	1469	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.48	96.48	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:49,549] [INFO] GTDB search result was written to GCF_021117425.1_ASM2111742v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:49,550] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:49,553] [INFO] DFAST_QC result json was written to GCF_021117425.1_ASM2111742v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:49,553] [INFO] DFAST_QC completed!
[2024-01-24 13:33:49,553] [INFO] Total running time: 0h1m24s