[2023-03-16 19:17:49,136] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:17:49,136] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:17:49,136] [INFO] DQC Reference Directory: /var/lib/cwl/stg7a7ec759-2c95-420d-b9bf-f9740654dbfd/dqc_reference
[2023-03-16 19:17:50,380] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:17:50,380] [INFO] Task started: Prodigal
[2023-03-16 19:17:50,381] [INFO] Running command: cat /var/lib/cwl/stg5463d8db-6cf4-409c-92c4-2de7ba232fc3/OceanDNA-b33315.fa | prodigal -d OceanDNA-b33315/cds.fna -a OceanDNA-b33315/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:18:33,523] [INFO] Task succeeded: Prodigal
[2023-03-16 19:18:33,523] [INFO] Task started: HMMsearch
[2023-03-16 19:18:33,523] [INFO] Running command: hmmsearch --tblout OceanDNA-b33315/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7a7ec759-2c95-420d-b9bf-f9740654dbfd/dqc_reference/reference_markers.hmm OceanDNA-b33315/protein.faa > /dev/null
[2023-03-16 19:18:33,783] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:18:33,784] [INFO] Found 6/6 markers.
[2023-03-16 19:18:33,818] [INFO] Query marker FASTA was written to OceanDNA-b33315/markers.fasta
[2023-03-16 19:18:33,819] [INFO] Task started: Blastn
[2023-03-16 19:18:33,819] [INFO] Running command: blastn -query OceanDNA-b33315/markers.fasta -db /var/lib/cwl/stg7a7ec759-2c95-420d-b9bf-f9740654dbfd/dqc_reference/reference_markers.fasta -out OceanDNA-b33315/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:18:34,815] [INFO] Task succeeded: Blastn
[2023-03-16 19:18:34,817] [INFO] Selected 17 target genomes.
[2023-03-16 19:18:34,817] [INFO] Target genome list was writen to OceanDNA-b33315/target_genomes.txt
[2023-03-16 19:18:34,823] [INFO] Task started: fastANI
[2023-03-16 19:18:34,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg5463d8db-6cf4-409c-92c4-2de7ba232fc3/OceanDNA-b33315.fa --refList OceanDNA-b33315/target_genomes.txt --output OceanDNA-b33315/fastani_result.tsv --threads 1
[2023-03-16 19:18:52,932] [INFO] Task succeeded: fastANI
[2023-03-16 19:18:52,933] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7a7ec759-2c95-420d-b9bf-f9740654dbfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:18:52,933] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7a7ec759-2c95-420d-b9bf-f9740654dbfd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:18:52,943] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:18:52,943] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 19:18:52,943] [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
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	83.1932	996	1749	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	82.8467	977	1749	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	81.8365	775	1749	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	81.3858	845	1749	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	81.3359	898	1749	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.832	762	1749	95	below_threshold
Hydrogenophaga intermedia	strain=DSM 5680	GCA_005938115.1	65786	65786	type	True	80.7481	757	1749	95	below_threshold
Hydrogenophaga intermedia	strain=S1	GCA_000723405.1	65786	65786	type	True	80.7365	756	1749	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	79.1649	589	1749	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	78.9253	484	1749	95	below_threshold
Acidovorax cattleyae	strain=DSM 17101	GCA_900104515.1	80868	80868	type	True	78.8015	468	1749	95	below_threshold
Limnohabitans radicicola	strain=JUR4	GCA_014837235.1	2771427	2771427	type	True	78.6997	409	1749	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.6832	523	1749	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	78.6303	454	1749	95	below_threshold
Delftia acidovorans	strain=NBRC 14950	GCA_001598795.1	80866	80866	type	True	78.3963	529	1749	95	below_threshold
Delftia acidovorans	strain=FDAARGOS_997	GCA_016127415.1	80866	80866	type	True	78.3146	534	1749	95	below_threshold
Comamonas koreensis	strain=KCTC 12005	GCA_021026195.1	160825	160825	type	True	78.0578	359	1749	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 19:18:52,944] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33315/tc_result.tsv
[2023-03-16 19:18:52,944] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:18:52,944] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:18:52,944] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7a7ec759-2c95-420d-b9bf-f9740654dbfd/dqc_reference/checkm_data
[2023-03-16 19:18:52,945] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:18:53,377] [INFO] Task started: CheckM
[2023-03-16 19:18:53,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33315/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33315/checkm_input OceanDNA-b33315/checkm_result
[2023-03-16 19:21:57,278] [INFO] Task succeeded: CheckM
[2023-03-16 19:21:57,279] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:21:57,294] [INFO] ===== Completeness check finished =====
[2023-03-16 19:21:57,294] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:21:57,294] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33315/markers.fasta)
[2023-03-16 19:21:57,295] [INFO] Task started: Blastn
[2023-03-16 19:21:57,296] [INFO] Running command: blastn -query OceanDNA-b33315/markers.fasta -db /var/lib/cwl/stg7a7ec759-2c95-420d-b9bf-f9740654dbfd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33315/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:21:59,038] [INFO] Task succeeded: Blastn
[2023-03-16 19:21:59,042] [INFO] Selected 19 target genomes.
[2023-03-16 19:21:59,042] [INFO] Target genome list was writen to OceanDNA-b33315/target_genomes_gtdb.txt
[2023-03-16 19:21:59,056] [INFO] Task started: fastANI
[2023-03-16 19:21:59,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg5463d8db-6cf4-409c-92c4-2de7ba232fc3/OceanDNA-b33315.fa --refList OceanDNA-b33315/target_genomes_gtdb.txt --output OceanDNA-b33315/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:22:19,614] [INFO] Task succeeded: fastANI
[2023-03-16 19:22:19,626] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:22:19,626] [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_002840835.1	s__Hydrogenophaga sp002840835	96.8192	1413	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_011390855.1	s__Hydrogenophaga sp011390855	84.9021	425	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013387465.1	s__Hydrogenophaga aromaticivorans	83.181	997	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	96.00	95.64	0.87	0.82	12	-
GCA_001770905.1	s__Hydrogenophaga sp001770905	82.9962	933	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.83	99.75	0.90	0.90	3	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	82.9661	923	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592305.1	s__Hydrogenophaga taeniospiralis	82.8643	975	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780385.1	s__Hydrogenophaga sp018780385	82.7805	889	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428625.1	s__Hydrogenophaga sp001428625	82.7706	942	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241965.1	s__Hydrogenophaga sp003241965	82.6922	845	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599455.1	s__Hydrogenophaga sp003599455	82.5636	811	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018903185.1	s__Hydrogenophaga sp018903185	82.2405	412	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	99.34	99.34	0.82	0.82	2	-
GCF_010104355.1	s__Hydrogenophaga sp010104355	82.1429	831	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002127265.1	s__Hydrogenophaga sp002127265	82.1086	875	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780075.1	s__Hydrogenophaga sp018780075	81.9449	870	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571225.1	s__Hydrogenophaga palleronii	81.8276	776	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823505.1	s__Hydrogenophaga sp013823505	81.7332	736	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018993155.1	s__Hydrogenophaga sp018993155	81.6677	783	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503365.1	s__Hydrogenophaga sp005503365	81.3398	782	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127215.1	s__Hydrogenophaga sp002127215	81.23	641	1749	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 19:22:19,627] [INFO] GTDB search result was written to OceanDNA-b33315/result_gtdb.tsv
[2023-03-16 19:22:19,629] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:22:19,633] [INFO] DFAST_QC result json was written to OceanDNA-b33315/dqc_result.json
[2023-03-16 19:22:19,633] [INFO] DFAST_QC completed!
[2023-03-16 19:22:19,633] [INFO] Total running time: 0h4m30s