[2023-03-17 02:03:51,369] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:03:51,369] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:03:51,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b7ed1b8-9a71-400a-a7db-199c55910aa9/dqc_reference
[2023-03-17 02:03:52,463] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:03:52,463] [INFO] Task started: Prodigal
[2023-03-17 02:03:52,463] [INFO] Running command: cat /var/lib/cwl/stg7fe6ed16-e4d8-4ec3-b19f-539ff27f4d09/OceanDNA-b33297.fa | prodigal -d OceanDNA-b33297/cds.fna -a OceanDNA-b33297/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:04:01,742] [INFO] Task succeeded: Prodigal
[2023-03-17 02:04:01,743] [INFO] Task started: HMMsearch
[2023-03-17 02:04:01,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b33297/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b7ed1b8-9a71-400a-a7db-199c55910aa9/dqc_reference/reference_markers.hmm OceanDNA-b33297/protein.faa > /dev/null
[2023-03-17 02:04:01,904] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:04:01,905] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7fe6ed16-e4d8-4ec3-b19f-539ff27f4d09/OceanDNA-b33297.fa]
[2023-03-17 02:04:01,919] [INFO] Query marker FASTA was written to OceanDNA-b33297/markers.fasta
[2023-03-17 02:04:01,920] [INFO] Task started: Blastn
[2023-03-17 02:04:01,920] [INFO] Running command: blastn -query OceanDNA-b33297/markers.fasta -db /var/lib/cwl/stg7b7ed1b8-9a71-400a-a7db-199c55910aa9/dqc_reference/reference_markers.fasta -out OceanDNA-b33297/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:02,414] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:02,415] [INFO] Selected 25 target genomes.
[2023-03-17 02:04:02,415] [INFO] Target genome list was writen to OceanDNA-b33297/target_genomes.txt
[2023-03-17 02:04:02,431] [INFO] Task started: fastANI
[2023-03-17 02:04:02,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fe6ed16-e4d8-4ec3-b19f-539ff27f4d09/OceanDNA-b33297.fa --refList OceanDNA-b33297/target_genomes.txt --output OceanDNA-b33297/fastani_result.tsv --threads 1
[2023-03-17 02:04:19,200] [INFO] Task succeeded: fastANI
[2023-03-17 02:04:19,201] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b7ed1b8-9a71-400a-a7db-199c55910aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:04:19,201] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b7ed1b8-9a71-400a-a7db-199c55910aa9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:04:19,213] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:04:19,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:04:19,213] [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
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	79.615	193	419	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	79.6005	204	419	95	below_threshold
Candidimonas nitroreducens	strain=SC-089	GCA_002209565.1	683354	683354	type	True	77.6356	117	419	95	below_threshold
Candidimonas humi	strain=DSM 25336	GCA_019166065.1	683355	683355	type	True	77.412	117	419	95	below_threshold
Parapusillimonas granuli	strain=LMG 24012	GCA_013416525.1	380911	380911	type	True	77.3094	104	419	95	below_threshold
Bordetella pseudohinzii	strain=8-296-03	GCA_000657795.2	1331258	1331258	type	True	77.3044	87	419	95	below_threshold
Bordetella bronchiseptica	strain=NCTC452	GCA_900445725.1	518	518	suspected-type	True	77.2127	85	419	95	below_threshold
Bordetella bronchiseptica	strain=CCUG 219	GCA_021391275.1	518	518	suspected-type	True	77.1822	81	419	95	below_threshold
Bordetella hinzii	strain=NCTC13199	GCA_900637615.1	103855	103855	type	True	77.1636	86	419	95	below_threshold
Bordetella bronchiseptica	strain=NBRC 13691	GCA_001598655.1	518	518	suspected-type	True	77.1366	85	419	95	below_threshold
Bordetella hinzii	strain=LMG 13501	GCA_001548475.1	103855	103855	type	True	77.1315	86	419	95	below_threshold
Bordetella pertussis	strain=FDAARGOS_1543	GCA_020736265.1	520	520	type	True	77.0386	86	419	95	below_threshold
Achromobacter insolitus	strain=NCTC 13520	GCA_024168865.1	217204	217204	type	True	77.029	75	419	95	below_threshold
Bordetella pertussis	strain=18323	GCA_000306945.1	520	520	type	True	77.0096	87	419	95	below_threshold
Achromobacter xylosoxidans	strain=PartM-Axylosoxidans-RM8376	GCA_022870085.1	85698	85698	type	True	76.9684	110	419	95	below_threshold
Achromobacter insuavis	strain=LMG 26845	GCA_902859645.1	1287735	1287735	type	True	76.8298	104	419	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_013416545.1	645616	645616	type	True	76.7223	67	419	95	below_threshold
Eoetvoesia caeni	strain=DSM 25520	GCA_003315175.1	645616	645616	type	True	76.7223	67	419	95	below_threshold
Achromobacter aloeverae	strain=AVA-1	GCA_004121055.1	1750518	1750518	type	True	76.7128	63	419	95	below_threshold
Eoetvoesia caeni	strain=PB3-7B	GCA_022688825.1	645616	645616	type	True	76.6915	68	419	95	below_threshold
Corticimicrobacter populi	strain=3d-2-2	GCA_003123725.1	2175229	2175229	type	True	76.6055	55	419	95	below_threshold
Pusillimonas ginsengisoli	strain=KCTC 22046	GCA_004153455.1	453575	453575	type	True	76.0328	52	419	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:04:19,213] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33297/tc_result.tsv
[2023-03-17 02:04:19,214] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:04:19,214] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:04:19,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b7ed1b8-9a71-400a-a7db-199c55910aa9/dqc_reference/checkm_data
[2023-03-17 02:04:19,214] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:04:19,217] [INFO] Task started: CheckM
[2023-03-17 02:04:19,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33297/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33297/checkm_input OceanDNA-b33297/checkm_result
[2023-03-17 02:04:46,760] [INFO] Task succeeded: CheckM
[2023-03-17 02:04:46,760] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.94%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:04:46,763] [INFO] ===== Completeness check finished =====
[2023-03-17 02:04:46,763] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:04:46,763] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33297/markers.fasta)
[2023-03-17 02:04:46,763] [INFO] Task started: Blastn
[2023-03-17 02:04:46,763] [INFO] Running command: blastn -query OceanDNA-b33297/markers.fasta -db /var/lib/cwl/stg7b7ed1b8-9a71-400a-a7db-199c55910aa9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33297/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:04:47,343] [INFO] Task succeeded: Blastn
[2023-03-17 02:04:47,344] [INFO] Selected 19 target genomes.
[2023-03-17 02:04:47,344] [INFO] Target genome list was writen to OceanDNA-b33297/target_genomes_gtdb.txt
[2023-03-17 02:04:47,663] [INFO] Task started: fastANI
[2023-03-17 02:04:47,663] [INFO] Running command: fastANI --query /var/lib/cwl/stg7fe6ed16-e4d8-4ec3-b19f-539ff27f4d09/OceanDNA-b33297.fa --refList OceanDNA-b33297/target_genomes_gtdb.txt --output OceanDNA-b33297/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:05:00,982] [INFO] Task succeeded: fastANI
[2023-03-17 02:05:00,992] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 02:05:00,993] [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
GCA_004321985.1	s__Castellaniella sp004321985	79.6733	208	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203015.1	s__Castellaniella defragrans	79.6005	204	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.06	98.49	0.94	0.90	4	-
GCF_001592225.1	s__Castellaniella caeni	79.394	194	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	99.69	99.69	0.95	0.95	2	-
GCA_019104865.1	s__Castellaniella sp019104865	78.5795	165	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002421865.1	s__Castellaniella sp002421865	78.3959	137	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Castellaniella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019166065.1	s__Candidimonas humi	77.412	117	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Candidimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000657795.2	s__Bordetella pseudohinzii	77.3703	85	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.97	99.86	0.99	0.98	8	-
GCF_001270295.1	s__Achromobacter sp001270295	77.3216	89	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261345.1	s__Bordetella_A sp002261345	77.1936	90	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	99.26	99.26	0.94	0.94	2	-
GCF_900078315.1	s__Bordetella_B ansorpii	77.1799	102	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001548475.1	s__Bordetella hinzii	77.1315	86	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.54	99.31	0.93	0.91	26	-
GCF_000306945.1	s__Bordetella pertussis	77.0096	87	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella	95.0	99.42	95.13	0.93	0.83	983	-
GCF_002119665.1	s__Bordetella_B sp002119665	76.984	86	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356245.1	s__Bordetella_A petrii_D	76.9676	97	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156745.1	s__Achromobacter sp900156745	76.8221	86	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Achromobacter	95.0	97.81	97.81	0.91	0.91	2	-
GCF_007679965.1	s__Bordetella_B sp007679965	76.7019	102	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002261225.1	s__Bordetella_C sp002261225	76.6777	88	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Bordetella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003123725.1	s__Corticimicrobacter populi	76.6055	55	419	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Corticimicrobacter	95.0	96.49	96.49	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-17 02:05:00,993] [INFO] GTDB search result was written to OceanDNA-b33297/result_gtdb.tsv
[2023-03-17 02:05:00,993] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:05:00,995] [INFO] DFAST_QC result json was written to OceanDNA-b33297/dqc_result.json
[2023-03-17 02:05:00,995] [INFO] DFAST_QC completed!
[2023-03-17 02:05:00,995] [INFO] Total running time: 0h1m10s