[2023-03-15 15:18:22,009] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:18:22,009] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:18:22,010] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3e94628-9927-4df7-8480-91846a45cb63/dqc_reference
[2023-03-15 15:18:23,175] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:18:23,176] [INFO] Task started: Prodigal
[2023-03-15 15:18:23,176] [INFO] Running command: cat /var/lib/cwl/stgf09bf5f7-d5de-4c5f-8790-252ab7f131a5/OceanDNA-b38551.fa | prodigal -d OceanDNA-b38551/cds.fna -a OceanDNA-b38551/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:18:39,281] [INFO] Task succeeded: Prodigal
[2023-03-15 15:18:39,281] [INFO] Task started: HMMsearch
[2023-03-15 15:18:39,281] [INFO] Running command: hmmsearch --tblout OceanDNA-b38551/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3e94628-9927-4df7-8480-91846a45cb63/dqc_reference/reference_markers.hmm OceanDNA-b38551/protein.faa > /dev/null
[2023-03-15 15:18:39,488] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:18:39,489] [INFO] Found 6/6 markers.
[2023-03-15 15:18:39,515] [INFO] Query marker FASTA was written to OceanDNA-b38551/markers.fasta
[2023-03-15 15:18:39,516] [INFO] Task started: Blastn
[2023-03-15 15:18:39,516] [INFO] Running command: blastn -query OceanDNA-b38551/markers.fasta -db /var/lib/cwl/stgb3e94628-9927-4df7-8480-91846a45cb63/dqc_reference/reference_markers.fasta -out OceanDNA-b38551/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:18:40,165] [INFO] Task succeeded: Blastn
[2023-03-15 15:18:40,167] [INFO] Selected 12 target genomes.
[2023-03-15 15:18:40,167] [INFO] Target genome list was writen to OceanDNA-b38551/target_genomes.txt
[2023-03-15 15:18:40,176] [INFO] Task started: fastANI
[2023-03-15 15:18:40,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgf09bf5f7-d5de-4c5f-8790-252ab7f131a5/OceanDNA-b38551.fa --refList OceanDNA-b38551/target_genomes.txt --output OceanDNA-b38551/fastani_result.tsv --threads 1
[2023-03-15 15:18:49,420] [INFO] Task succeeded: fastANI
[2023-03-15 15:18:49,421] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3e94628-9927-4df7-8480-91846a45cb63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:18:49,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3e94628-9927-4df7-8480-91846a45cb63/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:18:49,429] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-03-15 15:18:49,429] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 15:18:49,429] [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
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	95.9572	842	952	95	conclusive
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	95.9101	873	952	95	conclusive
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	95.9083	871	952	95	conclusive
Acinetobacter johnsonii	strain=CIP 64.6	GCA_000368045.1	40214	40214	suspected-type	True	95.9013	873	952	95	conclusive
Acinetobacter tandoii	strain=CIP 107469	GCA_000400735.1	202954	202954	type	True	81.4363	508	952	95	below_threshold
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	80.8338	537	952	95	below_threshold
Acinetobacter chengduensis	strain=WCHAc060005	GCA_003664645.1	2420890	2420890	type	True	80.374	453	952	95	below_threshold
Acinetobacter defluvii	strain=WCHA30	GCA_001704615.3	1871111	1871111	type	True	79.7691	430	952	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	79.7554	413	952	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	79.2755	318	952	95	below_threshold
Acinetobacter pittii	strain=CIP70.29	GCA_024390955.1	48296	48296	type	True	79.2085	337	952	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 15:18:49,430] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38551/tc_result.tsv
[2023-03-15 15:18:49,432] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:18:49,433] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:18:49,433] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3e94628-9927-4df7-8480-91846a45cb63/dqc_reference/checkm_data
[2023-03-15 15:18:49,434] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:18:49,442] [INFO] Task started: CheckM
[2023-03-15 15:18:49,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38551/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38551/checkm_input OceanDNA-b38551/checkm_result
[2023-03-15 15:19:32,473] [INFO] Task succeeded: CheckM
[2023-03-15 15:19:32,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.86%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 15:19:32,615] [INFO] ===== Completeness check finished =====
[2023-03-15 15:19:32,615] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:19:32,616] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38551/markers.fasta)
[2023-03-15 15:19:32,617] [INFO] Task started: Blastn
[2023-03-15 15:19:32,617] [INFO] Running command: blastn -query OceanDNA-b38551/markers.fasta -db /var/lib/cwl/stgb3e94628-9927-4df7-8480-91846a45cb63/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38551/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:19:33,671] [INFO] Task succeeded: Blastn
[2023-03-15 15:19:33,675] [INFO] Selected 14 target genomes.
[2023-03-15 15:19:33,675] [INFO] Target genome list was writen to OceanDNA-b38551/target_genomes_gtdb.txt
[2023-03-15 15:19:33,686] [INFO] Task started: fastANI
[2023-03-15 15:19:33,686] [INFO] Running command: fastANI --query /var/lib/cwl/stgf09bf5f7-d5de-4c5f-8790-252ab7f131a5/OceanDNA-b38551.fa --refList OceanDNA-b38551/target_genomes_gtdb.txt --output OceanDNA-b38551/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:19:43,431] [INFO] Task succeeded: fastANI
[2023-03-15 15:19:43,439] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 15:19:43,440] [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_000368045.1	s__Acinetobacter johnsonii	95.8851	874	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	conclusive
GCF_002165305.2	s__Acinetobacter sp002165305	93.0692	864	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135205.1	s__Acinetobacter sp002135205	89.6798	848	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.42	98.15	0.90	0.88	5	-
GCF_004331175.1	s__Acinetobacter sp004331175	81.8482	514	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000400735.1	s__Acinetobacter tandoii	81.4344	508	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.61	97.12	0.93	0.84	5	-
GCF_001758345.1	s__Acinetobacter towneri_A	81.0655	460	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.24	97.24	0.85	0.85	2	-
GCF_002018365.1	s__Acinetobacter sp002018365	80.919	485	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.65	95.34	0.86	0.83	71	-
GCF_000367925.1	s__Acinetobacter bohemicus	80.8406	536	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	-
GCF_009939195.1	s__Acinetobacter kanungonis	80.692	507	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.15	96.11	0.90	0.89	4	-
GCF_003711395.1	s__Acinetobacter sp003711395	80.6371	378	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.62	98.61	0.92	0.90	3	-
GCF_900107285.1	s__Acinetobacter kyonggiensis	80.589	533	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.53	95.22	0.88	0.86	3	-
GCA_002365595.1	s__Acinetobacter sp002365595	80.4221	467	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.10	98.08	0.91	0.89	3	-
GCF_003664645.1	s__Acinetobacter chengduensis	80.3687	452	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	99.56	99.34	0.91	0.89	3	-
GCF_001704615.3	s__Acinetobacter defluvii	79.7786	428	952	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	97.60	97.60	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-15 15:19:43,441] [INFO] GTDB search result was written to OceanDNA-b38551/result_gtdb.tsv
[2023-03-15 15:19:43,441] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:19:43,444] [INFO] DFAST_QC result json was written to OceanDNA-b38551/dqc_result.json
[2023-03-15 15:19:43,444] [INFO] DFAST_QC completed!
[2023-03-15 15:19:43,444] [INFO] Total running time: 0h1m21s