[2024-01-24 12:39:39,814] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:39,819] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:39,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg16ce6144-931d-4f39-b4e1-c6b9cf81d619/dqc_reference
[2024-01-24 12:39:41,085] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:41,086] [INFO] Task started: Prodigal
[2024-01-24 12:39:41,086] [INFO] Running command: gunzip -c /var/lib/cwl/stg992e8439-e706-4fbf-b70b-0c169a8f3b97/GCF_006539005.1_ASM653900v1_genomic.fna.gz | prodigal -d GCF_006539005.1_ASM653900v1_genomic.fna/cds.fna -a GCF_006539005.1_ASM653900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:53,401] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:53,401] [INFO] Task started: HMMsearch
[2024-01-24 12:39:53,401] [INFO] Running command: hmmsearch --tblout GCF_006539005.1_ASM653900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16ce6144-931d-4f39-b4e1-c6b9cf81d619/dqc_reference/reference_markers.hmm GCF_006539005.1_ASM653900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:53,660] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:53,662] [INFO] Found 6/6 markers.
[2024-01-24 12:39:53,712] [INFO] Query marker FASTA was written to GCF_006539005.1_ASM653900v1_genomic.fna/markers.fasta
[2024-01-24 12:39:53,712] [INFO] Task started: Blastn
[2024-01-24 12:39:53,712] [INFO] Running command: blastn -query GCF_006539005.1_ASM653900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16ce6144-931d-4f39-b4e1-c6b9cf81d619/dqc_reference/reference_markers.fasta -out GCF_006539005.1_ASM653900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:54,574] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:54,579] [INFO] Selected 8 target genomes.
[2024-01-24 12:39:54,579] [INFO] Target genome list was writen to GCF_006539005.1_ASM653900v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:54,583] [INFO] Task started: fastANI
[2024-01-24 12:39:54,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg992e8439-e706-4fbf-b70b-0c169a8f3b97/GCF_006539005.1_ASM653900v1_genomic.fna.gz --refList GCF_006539005.1_ASM653900v1_genomic.fna/target_genomes.txt --output GCF_006539005.1_ASM653900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:02,179] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:02,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16ce6144-931d-4f39-b4e1-c6b9cf81d619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:02,179] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16ce6144-931d-4f39-b4e1-c6b9cf81d619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:02,188] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:02,188] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:02,188] [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 aurantiacum	strain=ATCC 9175	GCA_900169065.1	273384	273384	type	True	99.9951	1328	1339	95	conclusive
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	92.6329	1101	1339	95	below_threshold
Brevibacterium antiquum	strain=DSM 21545	GCA_016107655.1	234835	234835	type	True	88.0492	1071	1339	95	below_threshold
Brevibacterium sandarakinum	strain=DSM 22082	GCA_900105045.1	629680	629680	type	True	87.3632	1060	1339	95	below_threshold
Brevibacterium marinum	strain=DSM 18964	GCA_011927955.1	418643	418643	type	True	84.7413	1011	1339	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	78.072	343	1339	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	77.5264	280	1339	95	below_threshold
Sediminivirga luteola	strain=CGMCC 1.12785	GCA_021729215.1	1774748	1774748	type	True	76.8298	183	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:02,193] [INFO] DFAST Taxonomy check result was written to GCF_006539005.1_ASM653900v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:02,194] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:02,194] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:02,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16ce6144-931d-4f39-b4e1-c6b9cf81d619/dqc_reference/checkm_data
[2024-01-24 12:40:02,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:02,256] [INFO] Task started: CheckM
[2024-01-24 12:40:02,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539005.1_ASM653900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539005.1_ASM653900v1_genomic.fna/checkm_input GCF_006539005.1_ASM653900v1_genomic.fna/checkm_result
[2024-01-24 12:40:42,672] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:42,674] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:42,697] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:42,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:42,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539005.1_ASM653900v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:42,698] [INFO] Task started: Blastn
[2024-01-24 12:40:42,699] [INFO] Running command: blastn -query GCF_006539005.1_ASM653900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16ce6144-931d-4f39-b4e1-c6b9cf81d619/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539005.1_ASM653900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:43,968] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:43,971] [INFO] Selected 7 target genomes.
[2024-01-24 12:40:43,971] [INFO] Target genome list was writen to GCF_006539005.1_ASM653900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:43,977] [INFO] Task started: fastANI
[2024-01-24 12:40:43,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg992e8439-e706-4fbf-b70b-0c169a8f3b97/GCF_006539005.1_ASM653900v1_genomic.fna.gz --refList GCF_006539005.1_ASM653900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539005.1_ASM653900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:51,023] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:51,036] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:51,036] [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	99.9951	1328	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.70	96.91	0.88	0.85	28	conclusive
GCF_016107655.1	s__Brevibacterium antiquum	88.0543	1070	1339	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	87.9745	987	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.98	97.98	0.94	0.91	3	-
GCF_016892625.1	s__Brevibacterium sp016892625	87.8078	1075	1339	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	87.7632	1072	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105045.1	s__Brevibacterium sandarakinum	87.3509	1061	1339	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	86.5775	1030	1339	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.94	97.94	0.86	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:40:51,038] [INFO] GTDB search result was written to GCF_006539005.1_ASM653900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:51,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:51,042] [INFO] DFAST_QC result json was written to GCF_006539005.1_ASM653900v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:51,042] [INFO] DFAST_QC completed!
[2024-01-24 12:40:51,043] [INFO] Total running time: 0h1m11s