[2024-01-24 13:41:25,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg31b17417-8e4a-4ba7-a484-1266a81504a0/dqc_reference
[2024-01-24 13:41:26,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:26,709] [INFO] Task started: Prodigal
[2024-01-24 13:41:26,710] [INFO] Running command: gunzip -c /var/lib/cwl/stgd998aeac-d5f2-4b75-aec5-10e6e4b1169d/GCF_002879875.1_ASM287987v1_genomic.fna.gz | prodigal -d GCF_002879875.1_ASM287987v1_genomic.fna/cds.fna -a GCF_002879875.1_ASM287987v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:48,749] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:48,749] [INFO] Task started: HMMsearch
[2024-01-24 13:41:48,749] [INFO] Running command: hmmsearch --tblout GCF_002879875.1_ASM287987v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31b17417-8e4a-4ba7-a484-1266a81504a0/dqc_reference/reference_markers.hmm GCF_002879875.1_ASM287987v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:49,116] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:49,118] [INFO] Found 6/6 markers.
[2024-01-24 13:41:49,182] [INFO] Query marker FASTA was written to GCF_002879875.1_ASM287987v1_genomic.fna/markers.fasta
[2024-01-24 13:41:49,183] [INFO] Task started: Blastn
[2024-01-24 13:41:49,183] [INFO] Running command: blastn -query GCF_002879875.1_ASM287987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31b17417-8e4a-4ba7-a484-1266a81504a0/dqc_reference/reference_markers.fasta -out GCF_002879875.1_ASM287987v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:50,309] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:50,313] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:50,314] [INFO] Target genome list was writen to GCF_002879875.1_ASM287987v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:50,367] [INFO] Task started: fastANI
[2024-01-24 13:41:50,368] [INFO] Running command: fastANI --query /var/lib/cwl/stgd998aeac-d5f2-4b75-aec5-10e6e4b1169d/GCF_002879875.1_ASM287987v1_genomic.fna.gz --refList GCF_002879875.1_ASM287987v1_genomic.fna/target_genomes.txt --output GCF_002879875.1_ASM287987v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:13,128] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:13,129] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31b17417-8e4a-4ba7-a484-1266a81504a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:13,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31b17417-8e4a-4ba7-a484-1266a81504a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:13,147] [INFO] Found 15 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:42:13,147] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:13,147] [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 caryophylli	strain=Ballard 720	GCA_002879875.1	28094	28094	type	True	100.0	2143	2144	95	conclusive
Trinickia caryophylli	strain=DSM 50341	GCA_007097545.1	28094	28094	type	True	99.9952	2143	2144	95	conclusive
Trinickia caryophylli	strain=LMG 2155	GCA_902833925.1	28094	28094	type	True	99.9934	2135	2144	95	conclusive
Trinickia caryophylli	strain=HAMBI_2159	GCA_003350265.1	28094	28094	type	True	99.9866	2121	2144	95	conclusive
Trinickia symbiotica	strain=JPY-345	GCA_002934455.1	863227	863227	type	True	80.8432	974	2144	95	below_threshold
Burkholderia thailandensis	strain=E264; ATCC 700388	GCA_000012365.1	57975	57975	type	True	80.3108	893	2144	95	below_threshold
Trinickia soli	strain=LMG 24076	GCA_902859815.1	380675	380675	type	True	80.2799	877	2144	95	below_threshold
Burkholderia multivorans	strain=ATCC BAA-247	GCA_000959525.1	87883	87883	type	True	80.2692	886	2144	95	below_threshold
Trinickia dabaoshanensis	strain=GIMN1.004	GCA_002879885.1	564714	564714	type	True	80.2202	909	2144	95	below_threshold
Paraburkholderia acidipaludis	strain=NBRC 101816	GCA_000684975.1	660537	660537	type	True	80.0293	811	2144	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	79.9428	876	2144	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	79.7872	875	2144	95	below_threshold
Paraburkholderia podalyriae	strain=WC7.3b	GCA_014397785.1	1938811	1938811	type	True	79.7269	853	2144	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	79.6525	863	2144	95	below_threshold
Paraburkholderia saeva	strain=LMG 31841	GCA_907164555.1	2777537	2777537	type	True	79.614	729	2144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:13,150] [INFO] DFAST Taxonomy check result was written to GCF_002879875.1_ASM287987v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:13,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:13,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:13,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31b17417-8e4a-4ba7-a484-1266a81504a0/dqc_reference/checkm_data
[2024-01-24 13:42:13,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:13,218] [INFO] Task started: CheckM
[2024-01-24 13:42:13,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002879875.1_ASM287987v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002879875.1_ASM287987v1_genomic.fna/checkm_input GCF_002879875.1_ASM287987v1_genomic.fna/checkm_result
[2024-01-24 13:43:14,856] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:14,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:14,877] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:14,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:14,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002879875.1_ASM287987v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:14,879] [INFO] Task started: Blastn
[2024-01-24 13:43:14,879] [INFO] Running command: blastn -query GCF_002879875.1_ASM287987v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31b17417-8e4a-4ba7-a484-1266a81504a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_002879875.1_ASM287987v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:16,908] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:16,913] [INFO] Selected 17 target genomes.
[2024-01-24 13:43:16,913] [INFO] Target genome list was writen to GCF_002879875.1_ASM287987v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:16,933] [INFO] Task started: fastANI
[2024-01-24 13:43:16,934] [INFO] Running command: fastANI --query /var/lib/cwl/stgd998aeac-d5f2-4b75-aec5-10e6e4b1169d/GCF_002879875.1_ASM287987v1_genomic.fna.gz --refList GCF_002879875.1_ASM287987v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002879875.1_ASM287987v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:38,940] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:38,958] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:38,958] [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_007097545.1	s__Trinickia caryophylli	99.9952	2143	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	100.00	100.00	1.00	1.00	5	conclusive
GCF_003628145.1	s__Trinickia fusca	81.2817	884	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934455.1	s__Trinickia symbiotica	80.8604	970	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	98.34	95.03	0.94	0.86	4	-
GCF_013282575.1	s__Trinickia sp013282575	80.782	1016	2144	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	80.7292	925	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315705.1	s__Trinickia sp017315705	80.7139	841	2144	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	80.6507	956	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002870125.1	s__Paraburkholderia sp002870125	80.4632	654	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002879855.1	s__Trinickia soli	80.3344	865	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	99.68	99.37	0.95	0.90	3	-
GCF_000012365.1	s__Burkholderia thailandensis	80.322	890	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.58	98.83	0.96	0.93	53	-
GCF_000959525.1	s__Burkholderia multivorans	80.274	883	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	97.58	96.90	0.90	0.85	326	-
GCF_000959365.1	s__Burkholderia oklahomensis	80.2615	894	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	98.42	95.09	0.95	0.85	15	-
GCF_002879885.1	s__Trinickia dabaoshanensis	80.2312	907	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298475.1	s__Paraburkholderia sp004298475	80.2294	669	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	99.94	99.94	0.88	0.88	2	-
GCF_001524625.2	s__Burkholderia sp001524625	80.1988	907	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.38	99.33	0.93	0.91	11	-
GCF_000684975.1	s__Paraburkholderia acidipaludis	80.0391	810	2144	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Paraburkholderia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685035.1	s__Paraburkholderia ferrariae	80.0279	840	2144	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 13:43:38,960] [INFO] GTDB search result was written to GCF_002879875.1_ASM287987v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:38,960] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:38,964] [INFO] DFAST_QC result json was written to GCF_002879875.1_ASM287987v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:38,964] [INFO] DFAST_QC completed!
[2024-01-24 13:43:38,964] [INFO] Total running time: 0h2m14s