[2024-01-24 14:06:06,363] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,365] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,366] [INFO] DQC Reference Directory: /var/lib/cwl/stg32d94001-3207-4de8-a384-ea840a0b2d4d/dqc_reference
[2024-01-24 14:06:07,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:07,605] [INFO] Task started: Prodigal
[2024-01-24 14:06:07,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg179245c6-892e-42fe-a2bb-4da5d15e3b54/GCF_003390925.1_ASM339092v1_genomic.fna.gz | prodigal -d GCF_003390925.1_ASM339092v1_genomic.fna/cds.fna -a GCF_003390925.1_ASM339092v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:29,958] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:29,959] [INFO] Task started: HMMsearch
[2024-01-24 14:06:29,959] [INFO] Running command: hmmsearch --tblout GCF_003390925.1_ASM339092v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32d94001-3207-4de8-a384-ea840a0b2d4d/dqc_reference/reference_markers.hmm GCF_003390925.1_ASM339092v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:30,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:30,387] [INFO] Found 6/6 markers.
[2024-01-24 14:06:30,457] [INFO] Query marker FASTA was written to GCF_003390925.1_ASM339092v1_genomic.fna/markers.fasta
[2024-01-24 14:06:30,457] [INFO] Task started: Blastn
[2024-01-24 14:06:30,457] [INFO] Running command: blastn -query GCF_003390925.1_ASM339092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32d94001-3207-4de8-a384-ea840a0b2d4d/dqc_reference/reference_markers.fasta -out GCF_003390925.1_ASM339092v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:31,379] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:31,382] [INFO] Selected 13 target genomes.
[2024-01-24 14:06:31,383] [INFO] Target genome list was writen to GCF_003390925.1_ASM339092v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:31,396] [INFO] Task started: fastANI
[2024-01-24 14:06:31,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg179245c6-892e-42fe-a2bb-4da5d15e3b54/GCF_003390925.1_ASM339092v1_genomic.fna.gz --refList GCF_003390925.1_ASM339092v1_genomic.fna/target_genomes.txt --output GCF_003390925.1_ASM339092v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:53,995] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:53,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32d94001-3207-4de8-a384-ea840a0b2d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:53,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32d94001-3207-4de8-a384-ea840a0b2d4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:54,010] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:54,011] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:54,011] [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 diaoshuihuensis	strain=NEAU-SY24	GCA_003390925.1	2292265	2292265	type	True	100.0	2182	2192	95	conclusive
Trinickia dabaoshanensis	strain=GIMN1.004	GCA_002879885.1	564714	564714	type	True	85.7761	1596	2192	95	below_threshold
Trinickia dinghuensis	strain=DHOM06	GCA_003367175.1	2291023	2291023	type	True	83.6115	1283	2192	95	below_threshold
Trinickia soli	strain=GP25-8	GCA_002879855.1	380675	380675	type	True	81.983	1097	2192	95	below_threshold
Trinickia soli	strain=LMG 24076	GCA_902859815.1	380675	380675	type	True	81.9478	1098	2192	95	below_threshold
Burkholderia pseudomultivorans		GCA_902499075.1	1207504	1207504	suspected-type	True	79.81	843	2192	95	below_threshold
Paraburkholderia phosphatilytica	strain=7QSK02	GCA_003443895.1	2282883	2282883	type	True	79.6371	840	2192	95	below_threshold
Paraburkholderia azotifigens	strain=NF 2-5-3	GCA_007995085.1	2057004	2057004	type	True	79.6129	827	2192	95	below_threshold
Burkholderia territorii	strain=LMG 28158	GCA_902833055.1	1503055	1503055	type	True	79.6108	829	2192	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	79.6026	792	2192	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	79.5855	814	2192	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	79.5676	784	2192	95	below_threshold
Paraburkholderia gardini	strain=LMG 32171	GCA_907164575.1	2823469	2823469	type	True	79.5322	711	2192	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,013] [INFO] DFAST Taxonomy check result was written to GCF_003390925.1_ASM339092v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:54,014] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:54,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:54,015] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32d94001-3207-4de8-a384-ea840a0b2d4d/dqc_reference/checkm_data
[2024-01-24 14:06:54,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:54,085] [INFO] Task started: CheckM
[2024-01-24 14:06:54,086] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003390925.1_ASM339092v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003390925.1_ASM339092v1_genomic.fna/checkm_input GCF_003390925.1_ASM339092v1_genomic.fna/checkm_result
[2024-01-24 14:07:52,161] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:52,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:52,182] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:52,183] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:52,183] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003390925.1_ASM339092v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:52,184] [INFO] Task started: Blastn
[2024-01-24 14:07:52,184] [INFO] Running command: blastn -query GCF_003390925.1_ASM339092v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32d94001-3207-4de8-a384-ea840a0b2d4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003390925.1_ASM339092v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:53,455] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:53,459] [INFO] Selected 9 target genomes.
[2024-01-24 14:07:53,460] [INFO] Target genome list was writen to GCF_003390925.1_ASM339092v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:53,468] [INFO] Task started: fastANI
[2024-01-24 14:07:53,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg179245c6-892e-42fe-a2bb-4da5d15e3b54/GCF_003390925.1_ASM339092v1_genomic.fna.gz --refList GCF_003390925.1_ASM339092v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003390925.1_ASM339092v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:06,701] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:06,711] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:06,711] [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_003390925.1	s__Trinickia diaoshuihuensis	100.0	2181	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002879885.1	s__Trinickia dabaoshanensis	85.7621	1598	2192	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	83.6076	1284	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315725.1	s__Trinickia sp017315725	83.289	1201	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322045.1	s__Trinickia sp004322045	82.0285	1063	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	96.62	96.62	0.93	0.93	2	-
GCF_002879855.1	s__Trinickia soli	81.9669	1100	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	99.68	99.37	0.95	0.90	3	-
GCF_902499075.1	s__Burkholderia pseudomultivorans	79.8106	842	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	96.22	95.54	0.83	0.81	13	-
GCF_001547525.1	s__Burkholderia anthina_A	79.761	903	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.44	98.20	0.94	0.91	13	-
GCF_003443895.1	s__Paraburkholderia phosphatilytica	79.6066	846	2192	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:06,712] [INFO] GTDB search result was written to GCF_003390925.1_ASM339092v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:06,713] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:06,717] [INFO] DFAST_QC result json was written to GCF_003390925.1_ASM339092v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:06,717] [INFO] DFAST_QC completed!
[2024-01-24 14:08:06,717] [INFO] Total running time: 0h2m0s