[2023-03-19 05:00:56,910] [INFO] DFAST_QC pipeline started.
[2023-03-19 05:00:56,911] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 05:00:56,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg8aa015a7-5d0d-4a34-90df-2973b8a7f770/dqc_reference
[2023-03-19 05:00:58,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 05:00:58,046] [INFO] Task started: Prodigal
[2023-03-19 05:00:58,046] [INFO] Running command: cat /var/lib/cwl/stg291543b4-40f8-4dec-a340-d6e25d127792/OceanDNA-b33288.fa | prodigal -d OceanDNA-b33288/cds.fna -a OceanDNA-b33288/protein.faa -g 11 -q > /dev/null
[2023-03-19 05:01:19,133] [INFO] Task succeeded: Prodigal
[2023-03-19 05:01:19,133] [INFO] Task started: HMMsearch
[2023-03-19 05:01:19,133] [INFO] Running command: hmmsearch --tblout OceanDNA-b33288/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8aa015a7-5d0d-4a34-90df-2973b8a7f770/dqc_reference/reference_markers.hmm OceanDNA-b33288/protein.faa > /dev/null
[2023-03-19 05:01:19,357] [INFO] Task succeeded: HMMsearch
[2023-03-19 05:01:19,357] [INFO] Found 6/6 markers.
[2023-03-19 05:01:19,379] [INFO] Query marker FASTA was written to OceanDNA-b33288/markers.fasta
[2023-03-19 05:01:19,380] [INFO] Task started: Blastn
[2023-03-19 05:01:19,380] [INFO] Running command: blastn -query OceanDNA-b33288/markers.fasta -db /var/lib/cwl/stg8aa015a7-5d0d-4a34-90df-2973b8a7f770/dqc_reference/reference_markers.fasta -out OceanDNA-b33288/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:01:20,255] [INFO] Task succeeded: Blastn
[2023-03-19 05:01:20,256] [INFO] Selected 25 target genomes.
[2023-03-19 05:01:20,256] [INFO] Target genome list was writen to OceanDNA-b33288/target_genomes.txt
[2023-03-19 05:01:20,270] [INFO] Task started: fastANI
[2023-03-19 05:01:20,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg291543b4-40f8-4dec-a340-d6e25d127792/OceanDNA-b33288.fa --refList OceanDNA-b33288/target_genomes.txt --output OceanDNA-b33288/fastani_result.tsv --threads 1
[2023-03-19 05:01:40,419] [INFO] Task succeeded: fastANI
[2023-03-19 05:01:40,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8aa015a7-5d0d-4a34-90df-2973b8a7f770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 05:01:40,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8aa015a7-5d0d-4a34-90df-2973b8a7f770/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 05:01:40,434] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2023-03-19 05:01:40,434] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 05:01:40,434] [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
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	95.7188	943	1036	95	conclusive
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	84.5771	737	1036	95	below_threshold
Aquabacterium olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	82.5338	645	1036	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	82.0598	618	1036	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	82.0266	587	1036	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	81.9499	600	1036	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.8298	464	1036	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	79.7677	440	1036	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	79.6512	447	1036	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.6281	458	1036	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	79.6139	432	1036	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.5968	420	1036	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	79.5665	459	1036	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	79.5575	427	1036	95	below_threshold
Ideonella benzenivorans	strain=B7	GCA_020387415.1	2831643	2831643	type	True	79.4366	431	1036	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	79.372	476	1036	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	79.221	391	1036	95	below_threshold
Hydrogenophaga aromaticivorans	strain=D2P1	GCA_013387465.1	2610898	2610898	type	True	79.131	352	1036	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	79.0523	367	1036	95	below_threshold
Hydrogenophaga pseudoflava	strain=NBRC 102511	GCA_001592285.1	47421	47421	type	True	79.0019	379	1036	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	78.8981	407	1036	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.8268	402	1036	95	below_threshold
Hydrogenophaga taeniospiralis	strain=NBRC 102512	GCA_001592305.1	65656	65656	type	True	78.8076	370	1036	95	below_threshold
Corticibacter populi	strain=DSM 105136	GCA_004217315.1	1550736	1550736	type	True	78.1966	265	1036	95	below_threshold
Corticibacter populi	strain=DSM 105136	GCA_003703815.1	1550736	1550736	type	True	78.1319	268	1036	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 05:01:40,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33288/tc_result.tsv
[2023-03-19 05:01:40,434] [INFO] ===== Taxonomy check completed =====
[2023-03-19 05:01:40,434] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 05:01:40,434] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8aa015a7-5d0d-4a34-90df-2973b8a7f770/dqc_reference/checkm_data
[2023-03-19 05:01:40,435] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 05:01:40,440] [INFO] Task started: CheckM
[2023-03-19 05:01:40,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33288/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33288/checkm_input OceanDNA-b33288/checkm_result
[2023-03-19 05:03:37,906] [INFO] Task succeeded: CheckM
[2023-03-19 05:03:37,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.67%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 05:03:37,909] [INFO] ===== Completeness check finished =====
[2023-03-19 05:03:37,909] [INFO] ===== Start GTDB Search =====
[2023-03-19 05:03:37,909] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33288/markers.fasta)
[2023-03-19 05:03:37,911] [INFO] Task started: Blastn
[2023-03-19 05:03:37,911] [INFO] Running command: blastn -query OceanDNA-b33288/markers.fasta -db /var/lib/cwl/stg8aa015a7-5d0d-4a34-90df-2973b8a7f770/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33288/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 05:03:39,757] [INFO] Task succeeded: Blastn
[2023-03-19 05:03:39,757] [INFO] Selected 16 target genomes.
[2023-03-19 05:03:39,757] [INFO] Target genome list was writen to OceanDNA-b33288/target_genomes_gtdb.txt
[2023-03-19 05:03:39,767] [INFO] Task started: fastANI
[2023-03-19 05:03:39,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg291543b4-40f8-4dec-a340-d6e25d127792/OceanDNA-b33288.fa --refList OceanDNA-b33288/target_genomes_gtdb.txt --output OceanDNA-b33288/fastani_result_gtdb.tsv --threads 1
[2023-03-19 05:03:52,779] [INFO] Task succeeded: fastANI
[2023-03-19 05:03:52,789] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 05:03:52,789] [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_004362855.1	s__Aquabacterium commune	95.7188	943	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	95.44	95.44	0.90	0.90	2	conclusive
GCA_903894125.1	s__Aquabacterium sp903894125	92.4042	638	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.35	99.35	0.82	0.82	2	-
GCA_903871865.1	s__Aquabacterium sp903871865	91.8122	536	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000265.1	s__Aquabacterium sp016000265	85.7175	748	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_001770725.1	s__Aquabacterium sp001770725	84.5731	764	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447195.1	s__Aquabacterium parvum	84.5705	737	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	97.32	96.21	0.91	0.89	4	-
GCA_005502875.1	s__Aquabacterium sp005502875	84.5059	723	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195855.1	s__Aquabacterium sp016195855	82.6279	657	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003963115.1	s__Aquabacterium sp003963115	82.3163	651	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013294065.1	s__Sphaerotilus sp013294065	79.6285	449	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Sphaerotilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571225.1	s__Hydrogenophaga palleronii	79.1742	395	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017992055.1	s__Aquabacterium_A sp017992055	79.1509	497	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713375.1	s__Hydrogenophaga sp001713375	78.9796	356	1036	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	78.8268	398	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010104355.1	s__Hydrogenophaga sp010104355	78.7972	364	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011391495.1	s__Hydrogenophaga sp011391495	78.7705	294	1036	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Hydrogenophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 05:03:52,789] [INFO] GTDB search result was written to OceanDNA-b33288/result_gtdb.tsv
[2023-03-19 05:03:52,789] [INFO] ===== GTDB Search completed =====
[2023-03-19 05:03:52,791] [INFO] DFAST_QC result json was written to OceanDNA-b33288/dqc_result.json
[2023-03-19 05:03:52,791] [INFO] DFAST_QC completed!
[2023-03-19 05:03:52,791] [INFO] Total running time: 0h2m56s