[2024-01-24 12:47:05,541] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:05,543] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:05,543] [INFO] DQC Reference Directory: /var/lib/cwl/stgad3aae40-9930-4ab2-b2ed-6bbc1eec6823/dqc_reference
[2024-01-24 12:47:06,732] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:06,733] [INFO] Task started: Prodigal
[2024-01-24 12:47:06,733] [INFO] Running command: gunzip -c /var/lib/cwl/stgf80daed0-1cdf-4322-822c-b8426e0adaa2/GCF_002879885.1_ASM287988v1_genomic.fna.gz | prodigal -d GCF_002879885.1_ASM287988v1_genomic.fna/cds.fna -a GCF_002879885.1_ASM287988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:31,082] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:31,082] [INFO] Task started: HMMsearch
[2024-01-24 12:47:31,082] [INFO] Running command: hmmsearch --tblout GCF_002879885.1_ASM287988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad3aae40-9930-4ab2-b2ed-6bbc1eec6823/dqc_reference/reference_markers.hmm GCF_002879885.1_ASM287988v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:31,404] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:31,405] [INFO] Found 6/6 markers.
[2024-01-24 12:47:31,463] [INFO] Query marker FASTA was written to GCF_002879885.1_ASM287988v1_genomic.fna/markers.fasta
[2024-01-24 12:47:31,463] [INFO] Task started: Blastn
[2024-01-24 12:47:31,463] [INFO] Running command: blastn -query GCF_002879885.1_ASM287988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad3aae40-9930-4ab2-b2ed-6bbc1eec6823/dqc_reference/reference_markers.fasta -out GCF_002879885.1_ASM287988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:32,425] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:32,430] [INFO] Selected 14 target genomes.
[2024-01-24 12:47:32,430] [INFO] Target genome list was writen to GCF_002879885.1_ASM287988v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:32,439] [INFO] Task started: fastANI
[2024-01-24 12:47:32,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80daed0-1cdf-4322-822c-b8426e0adaa2/GCF_002879885.1_ASM287988v1_genomic.fna.gz --refList GCF_002879885.1_ASM287988v1_genomic.fna/target_genomes.txt --output GCF_002879885.1_ASM287988v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:52,849] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:52,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad3aae40-9930-4ab2-b2ed-6bbc1eec6823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:52,850] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad3aae40-9930-4ab2-b2ed-6bbc1eec6823/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:52,861] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:52,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:52,861] [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 dabaoshanensis	strain=GIMN1.004	GCA_002879885.1	564714	564714	type	True	100.0	2316	2321	95	conclusive
Trinickia diaoshuihuensis	strain=NEAU-SY24	GCA_003390925.1	2292265	2292265	type	True	85.7105	1589	2321	95	below_threshold
Trinickia dinghuensis	strain=DHOM06	GCA_003367175.1	2291023	2291023	type	True	83.9698	1339	2321	95	below_threshold
Trinickia soli	strain=LMG 24076	GCA_902859815.1	380675	380675	type	True	82.087	1198	2321	95	below_threshold
Trinickia soli	strain=GP25-8	GCA_002879855.1	380675	380675	type	True	82.0266	1191	2321	95	below_threshold
Burkholderia oklahomensis	strain=C6786	GCA_000170375.1	342113	342113	type	True	80.1248	771	2321	95	below_threshold
Burkholderia oklahomensis	strain=LMG 23618	GCA_900608545.1	342113	342113	type	True	79.9638	860	2321	95	below_threshold
Burkholderia ubonensis		GCA_902499185.1	101571	101571	type	True	79.9552	885	2321	95	below_threshold
Burkholderia ubonensis	strain=LMG 20358	GCA_902833085.1	101571	101571	type	True	79.9499	895	2321	95	below_threshold
Paraburkholderia acidisoli	strain=DHF22	GCA_009789675.1	2571748	2571748	type	True	79.5699	831	2321	95	below_threshold
Paraburkholderia silviterrae	strain=4M-K11	GCA_004353915.1	2528715	2528715	type	True	79.5631	808	2321	95	below_threshold
Paraburkholderia pallida	strain=7MH5	GCA_004524855.1	2547399	2547399	type	True	79.4885	864	2321	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	79.3995	845	2321	95	below_threshold
Paraburkholderia nodosa	strain=DSM 21604	GCA_000519185.1	392320	392320	type	True	79.3867	855	2321	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:52,863] [INFO] DFAST Taxonomy check result was written to GCF_002879885.1_ASM287988v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:52,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:52,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:52,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad3aae40-9930-4ab2-b2ed-6bbc1eec6823/dqc_reference/checkm_data
[2024-01-24 12:47:52,865] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:52,927] [INFO] Task started: CheckM
[2024-01-24 12:47:52,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002879885.1_ASM287988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002879885.1_ASM287988v1_genomic.fna/checkm_input GCF_002879885.1_ASM287988v1_genomic.fna/checkm_result
[2024-01-24 12:48:55,443] [INFO] Task succeeded: CheckM
[2024-01-24 12:48:55,444] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:48:55,465] [INFO] ===== Completeness check finished =====
[2024-01-24 12:48:55,466] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:48:55,466] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002879885.1_ASM287988v1_genomic.fna/markers.fasta)
[2024-01-24 12:48:55,466] [INFO] Task started: Blastn
[2024-01-24 12:48:55,466] [INFO] Running command: blastn -query GCF_002879885.1_ASM287988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgad3aae40-9930-4ab2-b2ed-6bbc1eec6823/dqc_reference/reference_markers_gtdb.fasta -out GCF_002879885.1_ASM287988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:57,094] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:57,097] [INFO] Selected 9 target genomes.
[2024-01-24 12:48:57,097] [INFO] Target genome list was writen to GCF_002879885.1_ASM287988v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:48:57,140] [INFO] Task started: fastANI
[2024-01-24 12:48:57,140] [INFO] Running command: fastANI --query /var/lib/cwl/stgf80daed0-1cdf-4322-822c-b8426e0adaa2/GCF_002879885.1_ASM287988v1_genomic.fna.gz --refList GCF_002879885.1_ASM287988v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002879885.1_ASM287988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:10,188] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:10,197] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:10,197] [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_002879885.1	s__Trinickia dabaoshanensis	100.0	2316	2321	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_003390925.1	s__Trinickia diaoshuihuensis	85.7179	1587	2321	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	83.9279	1346	2321	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	83.4518	1264	2321	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	83.0098	1180	2321	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	82.0324	1190	2321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	99.68	99.37	0.95	0.90	3	-
GCF_003628145.1	s__Trinickia fusca	81.1153	967	2321	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	80.4917	928	2321	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Trinickia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519185.1	s__Paraburkholderia nodosa	79.3526	861	2321	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 12:49:10,198] [INFO] GTDB search result was written to GCF_002879885.1_ASM287988v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:10,199] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:10,202] [INFO] DFAST_QC result json was written to GCF_002879885.1_ASM287988v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:10,202] [INFO] DFAST_QC completed!
[2024-01-24 12:49:10,202] [INFO] Total running time: 0h2m5s