[2024-01-25 19:04:05,745] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:04:05,774] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:04:05,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg55f74378-fc73-4c50-ad9f-201f33d1a5d6/dqc_reference
[2024-01-25 19:04:06,883] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:04:06,883] [INFO] Task started: Prodigal
[2024-01-25 19:04:06,884] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb0e5690-4b29-4610-ab40-b221358e3525/GCF_016907735.1_ASM1690773v1_genomic.fna.gz | prodigal -d GCF_016907735.1_ASM1690773v1_genomic.fna/cds.fna -a GCF_016907735.1_ASM1690773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:14,057] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:14,057] [INFO] Task started: HMMsearch
[2024-01-25 19:04:14,057] [INFO] Running command: hmmsearch --tblout GCF_016907735.1_ASM1690773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55f74378-fc73-4c50-ad9f-201f33d1a5d6/dqc_reference/reference_markers.hmm GCF_016907735.1_ASM1690773v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:14,276] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:14,278] [INFO] Found 6/6 markers.
[2024-01-25 19:04:14,300] [INFO] Query marker FASTA was written to GCF_016907735.1_ASM1690773v1_genomic.fna/markers.fasta
[2024-01-25 19:04:14,300] [INFO] Task started: Blastn
[2024-01-25 19:04:14,300] [INFO] Running command: blastn -query GCF_016907735.1_ASM1690773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55f74378-fc73-4c50-ad9f-201f33d1a5d6/dqc_reference/reference_markers.fasta -out GCF_016907735.1_ASM1690773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:14,907] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:14,909] [INFO] Selected 22 target genomes.
[2024-01-25 19:04:14,910] [INFO] Target genome list was writen to GCF_016907735.1_ASM1690773v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:14,923] [INFO] Task started: fastANI
[2024-01-25 19:04:14,923] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb0e5690-4b29-4610-ab40-b221358e3525/GCF_016907735.1_ASM1690773v1_genomic.fna.gz --refList GCF_016907735.1_ASM1690773v1_genomic.fna/target_genomes.txt --output GCF_016907735.1_ASM1690773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:26,165] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:26,165] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55f74378-fc73-4c50-ad9f-201f33d1a5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:26,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55f74378-fc73-4c50-ad9f-201f33d1a5d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:26,176] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:26,176] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:26,176] [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 paucivorans	strain=DSM 13657	GCA_016907735.1	170994	170994	type	True	100.0	803	803	95	conclusive
Brevibacterium mcbrellneri	strain=ATCC 49030	GCA_000178455.1	53363	53363	type	True	88.2925	672	803	95	below_threshold
Brevibacterium ravenspurgense	strain=CCUG56047	GCA_001584615.1	479117	479117	type	True	78.9214	160	803	95	below_threshold
Brevibacterium siliguriense	strain=DSM 23676	GCA_900105315.1	1136497	1136497	type	True	77.9269	80	803	95	below_threshold
Brevibacterium atlanticum	strain=WO024	GCA_011617245.1	2697563	2697563	type	True	77.8383	84	803	95	below_threshold
Brevibacterium marinum	strain=DSM 18964	GCA_011927955.1	418643	418643	type	True	77.6539	78	803	95	below_threshold
Brevibacterium zhoupengii	strain=HY170	GCA_021117425.1	2898795	2898795	type	True	77.4733	85	803	95	below_threshold
Brevibacterium permense	strain=VKM Ac-2280	GCA_013280495.1	234834	234834	type	True	77.3229	83	803	95	below_threshold
Brevibacterium daeguense	strain=DSM 27938	GCA_021729135.1	909936	909936	type	True	77.2394	84	803	95	below_threshold
Brevibacterium casei	strain=FDAARGOS_936	GCA_016026595.1	33889	33889	type	True	77.1932	88	803	95	below_threshold
Brevibacterium aurantiacum	strain=ATCC 9175	GCA_900169065.1	273384	273384	type	True	77.0683	87	803	95	below_threshold
Brevibacterium luteolum	strain=DSM 15022	GCA_016907415.1	199591	199591	type	True	77.04	117	803	95	below_threshold
Brevibacterium gallinarum	strain=Re57	GCA_014836885.1	2762220	2762220	type	True	76.8598	109	803	95	below_threshold
Brevibacterium sediminis	strain=FXJ8.269	GCA_013623905.1	1857024	1857024	type	True	76.8373	80	803	95	below_threshold
Brevibacterium sediminis	strain=CGMCC 1.15472	GCA_014643055.1	1857024	1857024	type	True	76.8152	80	803	95	below_threshold
Brevibacterium luteolum	strain=CCUG 46604	GCA_013004595.1	199591	199591	type	True	76.8046	114	803	95	below_threshold
Brevibacterium renqingii	strain=REN4	GCA_017808105.1	2776916	2776916	type	True	76.711	77	803	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:26,178] [INFO] DFAST Taxonomy check result was written to GCF_016907735.1_ASM1690773v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:26,178] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:26,178] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:26,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55f74378-fc73-4c50-ad9f-201f33d1a5d6/dqc_reference/checkm_data
[2024-01-25 19:04:26,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:26,205] [INFO] Task started: CheckM
[2024-01-25 19:04:26,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907735.1_ASM1690773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907735.1_ASM1690773v1_genomic.fna/checkm_input GCF_016907735.1_ASM1690773v1_genomic.fna/checkm_result
[2024-01-25 19:04:50,995] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:50,996] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:51,012] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:51,013] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:51,013] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907735.1_ASM1690773v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:51,013] [INFO] Task started: Blastn
[2024-01-25 19:04:51,013] [INFO] Running command: blastn -query GCF_016907735.1_ASM1690773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55f74378-fc73-4c50-ad9f-201f33d1a5d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907735.1_ASM1690773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:51,893] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:51,897] [INFO] Selected 19 target genomes.
[2024-01-25 19:04:51,897] [INFO] Target genome list was writen to GCF_016907735.1_ASM1690773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:51,912] [INFO] Task started: fastANI
[2024-01-25 19:04:51,913] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb0e5690-4b29-4610-ab40-b221358e3525/GCF_016907735.1_ASM1690773v1_genomic.fna.gz --refList GCF_016907735.1_ASM1690773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907735.1_ASM1690773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:02,937] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:02,949] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:02,950] [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_016907735.1	s__Brevibacterium paucivorans	100.0	803	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000178455.1	s__Brevibacterium mcbrellneri	88.2925	672	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001584615.1	s__Brevibacterium ravenspurgense	78.9074	159	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	96.93	96.42	0.92	0.90	8	-
GCF_001815905.1	s__Brevibacterium sp001815905	78.1232	124	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.85	98.78	0.94	0.92	3	-
GCF_900105315.1	s__Brevibacterium siliguriense	77.9269	80	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927955.1	s__Brevibacterium marinum	77.8455	79	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011617245.1	s__Brevibacterium sp011617245	77.7448	84	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280295.1	s__Brevibacterium sp005280295	77.6032	101	803	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	76.9838	76	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013623905.1	s__Brevibacterium sediminis	76.8373	80	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.24	97.49	0.93	0.90	5	-
GCA_019117325.1	s__Brevibacterium intestinigallinarum	76.8205	51	803	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	76.8183	81	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.94	97.94	0.86	0.85	3	-
GCF_013004595.1	s__Brevibacterium luteolum	76.8046	114	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	97.16	95.46	0.92	0.89	7	-
GCF_004745485.1	s__Brevibacterium sp004745485	76.7942	71	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745075.1	s__Brevibacterium sp004745075	76.7853	73	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006489205.1	s__Brevibacterium sp006489205	76.7658	87	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.50	98.50	0.93	0.93	2	-
GCF_017808105.1	s__Brevibacterium renqingii	76.711	77	803	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Brevibacteriaceae;g__Brevibacterium	95.0	98.54	98.54	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:02,951] [INFO] GTDB search result was written to GCF_016907735.1_ASM1690773v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:02,952] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:02,956] [INFO] DFAST_QC result json was written to GCF_016907735.1_ASM1690773v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:02,956] [INFO] DFAST_QC completed!
[2024-01-25 19:05:02,956] [INFO] Total running time: 0h0m57s