[2024-01-25 20:07:35,858] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:35,861] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:35,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg9db8bcab-51be-43bd-9fc5-d19c4fba70eb/dqc_reference
[2024-01-25 20:07:37,001] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:37,002] [INFO] Task started: Prodigal
[2024-01-25 20:07:37,002] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa22ed9c-611e-4127-af26-88209f0f5da1/GCF_902859815.1_LMG_24076_genomic.fna.gz | prodigal -d GCF_902859815.1_LMG_24076_genomic.fna/cds.fna -a GCF_902859815.1_LMG_24076_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:54,011] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:54,011] [INFO] Task started: HMMsearch
[2024-01-25 20:07:54,011] [INFO] Running command: hmmsearch --tblout GCF_902859815.1_LMG_24076_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9db8bcab-51be-43bd-9fc5-d19c4fba70eb/dqc_reference/reference_markers.hmm GCF_902859815.1_LMG_24076_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:54,277] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:54,278] [INFO] Found 6/6 markers.
[2024-01-25 20:07:54,323] [INFO] Query marker FASTA was written to GCF_902859815.1_LMG_24076_genomic.fna/markers.fasta
[2024-01-25 20:07:54,324] [INFO] Task started: Blastn
[2024-01-25 20:07:54,324] [INFO] Running command: blastn -query GCF_902859815.1_LMG_24076_genomic.fna/markers.fasta -db /var/lib/cwl/stg9db8bcab-51be-43bd-9fc5-d19c4fba70eb/dqc_reference/reference_markers.fasta -out GCF_902859815.1_LMG_24076_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:55,133] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:55,136] [INFO] Selected 13 target genomes.
[2024-01-25 20:07:55,136] [INFO] Target genome list was writen to GCF_902859815.1_LMG_24076_genomic.fna/target_genomes.txt
[2024-01-25 20:07:55,147] [INFO] Task started: fastANI
[2024-01-25 20:07:55,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa22ed9c-611e-4127-af26-88209f0f5da1/GCF_902859815.1_LMG_24076_genomic.fna.gz --refList GCF_902859815.1_LMG_24076_genomic.fna/target_genomes.txt --output GCF_902859815.1_LMG_24076_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:15,006] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:15,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9db8bcab-51be-43bd-9fc5-d19c4fba70eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:15,007] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9db8bcab-51be-43bd-9fc5-d19c4fba70eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:15,018] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:08:15,018] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:15,018] [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
Trinickia soli	strain=LMG 24076	GCA_902859815.1	380675	380675	type	True	100.0	1995	2000	95	conclusive
Trinickia soli	strain=GP25-8	GCA_002879855.1	380675	380675	type	True	99.9937	1981	2000	95	conclusive
Trinickia dinghuensis	strain=DHOM06	GCA_003367175.1	2291023	2291023	type	True	82.8176	1216	2000	95	below_threshold
Trinickia dabaoshanensis	strain=GIMN1.004	GCA_002879885.1	564714	564714	type	True	82.0725	1173	2000	95	below_threshold
Trinickia diaoshuihuensis	strain=NEAU-SY24	GCA_003390925.1	2292265	2292265	type	True	82.0033	1082	2000	95	below_threshold
Trinickia symbiotica	strain=JPY-345	GCA_002934455.1	863227	863227	type	True	80.3118	826	2000	95	below_threshold
Burkholderia pseudomultivorans		GCA_902499075.1	1207504	1207504	suspected-type	True	80.0093	758	2000	95	below_threshold
Paraburkholderia flava	strain=LD6	GCA_004359985.1	2547393	2547393	type	True	79.9644	760	2000	95	below_threshold
Paraburkholderia phosphatilytica	strain=7QSK02	GCA_003443895.1	2282883	2282883	type	True	79.8441	815	2000	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	79.7912	791	2000	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	79.7639	665	2000	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	79.7562	776	2000	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	79.6423	753	2000	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:15,021] [INFO] DFAST Taxonomy check result was written to GCF_902859815.1_LMG_24076_genomic.fna/tc_result.tsv
[2024-01-25 20:08:15,021] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:15,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:15,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9db8bcab-51be-43bd-9fc5-d19c4fba70eb/dqc_reference/checkm_data
[2024-01-25 20:08:15,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:15,081] [INFO] Task started: CheckM
[2024-01-25 20:08:15,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902859815.1_LMG_24076_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902859815.1_LMG_24076_genomic.fna/checkm_input GCF_902859815.1_LMG_24076_genomic.fna/checkm_result
[2024-01-25 20:09:03,436] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:03,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:03,459] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:03,459] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:03,460] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902859815.1_LMG_24076_genomic.fna/markers.fasta)
[2024-01-25 20:09:03,460] [INFO] Task started: Blastn
[2024-01-25 20:09:03,460] [INFO] Running command: blastn -query GCF_902859815.1_LMG_24076_genomic.fna/markers.fasta -db /var/lib/cwl/stg9db8bcab-51be-43bd-9fc5-d19c4fba70eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_902859815.1_LMG_24076_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:04,933] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:04,935] [INFO] Selected 9 target genomes.
[2024-01-25 20:09:04,935] [INFO] Target genome list was writen to GCF_902859815.1_LMG_24076_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:04,948] [INFO] Task started: fastANI
[2024-01-25 20:09:04,949] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa22ed9c-611e-4127-af26-88209f0f5da1/GCF_902859815.1_LMG_24076_genomic.fna.gz --refList GCF_902859815.1_LMG_24076_genomic.fna/target_genomes_gtdb.txt --output GCF_902859815.1_LMG_24076_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:09:18,239] [INFO] Task succeeded: fastANI
[2024-01-25 20:09:18,245] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:09:18,246] [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_002879855.1	s__Trinickia soli	99.9937	1981	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	99.68	99.37	0.95	0.90	3	conclusive
GCA_004322045.1	s__Trinickia sp004322045	83.2681	1245	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	96.62	96.62	0.93	0.93	2	-
GCF_017315725.1	s__Trinickia sp017315725	83.0099	1182	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003367175.1	s__Trinickia dinghuensis	82.8267	1215	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879885.1	s__Trinickia dabaoshanensis	82.0705	1173	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390925.1	s__Trinickia diaoshuihuensis	81.9845	1085	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144415.1	s__Trinickia sp005144415	80.6813	870	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499075.1	s__Burkholderia pseudomultivorans	79.9822	761	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.22	95.54	0.83	0.81	13	-
GCF_003443895.1	s__Paraburkholderia phosphatilytica	79.853	814	2000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:09:18,247] [INFO] GTDB search result was written to GCF_902859815.1_LMG_24076_genomic.fna/result_gtdb.tsv
[2024-01-25 20:09:18,247] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:09:18,250] [INFO] DFAST_QC result json was written to GCF_902859815.1_LMG_24076_genomic.fna/dqc_result.json
[2024-01-25 20:09:18,250] [INFO] DFAST_QC completed!
[2024-01-25 20:09:18,250] [INFO] Total running time: 0h1m42s