[2023-03-15 23:47:20,277] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:47:20,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:47:20,278] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc0ed8ec-317f-45e4-92d5-9502099d6631/dqc_reference
[2023-03-15 23:47:21,355] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:47:21,356] [INFO] Task started: Prodigal
[2023-03-15 23:47:21,356] [INFO] Running command: cat /var/lib/cwl/stg3ff02cd6-1c47-4ec8-8171-b9351204c8ac/OceanDNA-b33290.fa | prodigal -d OceanDNA-b33290/cds.fna -a OceanDNA-b33290/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:47:36,149] [INFO] Task succeeded: Prodigal
[2023-03-15 23:47:36,150] [INFO] Task started: HMMsearch
[2023-03-15 23:47:36,150] [INFO] Running command: hmmsearch --tblout OceanDNA-b33290/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc0ed8ec-317f-45e4-92d5-9502099d6631/dqc_reference/reference_markers.hmm OceanDNA-b33290/protein.faa > /dev/null
[2023-03-15 23:47:36,365] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:47:36,366] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3ff02cd6-1c47-4ec8-8171-b9351204c8ac/OceanDNA-b33290.fa]
[2023-03-15 23:47:36,391] [INFO] Query marker FASTA was written to OceanDNA-b33290/markers.fasta
[2023-03-15 23:47:36,393] [INFO] Task started: Blastn
[2023-03-15 23:47:36,393] [INFO] Running command: blastn -query OceanDNA-b33290/markers.fasta -db /var/lib/cwl/stgfc0ed8ec-317f-45e4-92d5-9502099d6631/dqc_reference/reference_markers.fasta -out OceanDNA-b33290/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:47:37,397] [INFO] Task succeeded: Blastn
[2023-03-15 23:47:37,405] [INFO] Selected 14 target genomes.
[2023-03-15 23:47:37,405] [INFO] Target genome list was writen to OceanDNA-b33290/target_genomes.txt
[2023-03-15 23:47:37,413] [INFO] Task started: fastANI
[2023-03-15 23:47:37,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff02cd6-1c47-4ec8-8171-b9351204c8ac/OceanDNA-b33290.fa --refList OceanDNA-b33290/target_genomes.txt --output OceanDNA-b33290/fastani_result.tsv --threads 1
[2023-03-15 23:47:48,121] [INFO] Task succeeded: fastANI
[2023-03-15 23:47:48,121] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc0ed8ec-317f-45e4-92d5-9502099d6631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:47:48,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc0ed8ec-317f-45e4-92d5-9502099d6631/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:47:48,191] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:47:48,191] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:47:48,191] [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 olei	strain=NBRC 110486	GCA_003100395.1	1296669	1296669	type	True	86.8526	575	692	95	below_threshold
Aquabacterium parvum	strain=B6	GCA_001447195.1	70584	70584	type	True	82.1658	403	692	95	below_threshold
Aquabacterium commune	strain=DSM 11901	GCA_004362855.1	70586	70586	type	True	82.0782	382	692	95	below_threshold
Aquabacterium fontiphilum	strain=CS-6	GCA_009909205.1	450365	450365	type	True	81.613	353	692	95	below_threshold
Aquabacterium lacunae	strain=KMB7	GCA_004310865.1	2528630	2528630	type	True	81.4905	361	692	95	below_threshold
Aquabacterium soli	strain=SJQ9	GCA_003933735.1	2493092	2493092	type	True	81.3568	365	692	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.9905	291	692	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	79.3716	282	692	95	below_threshold
Pelomonas puraquae	strain=CCUG 52769	GCA_002205845.1	431059	431059	type	True	79.1478	254	692	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	78.9039	225	692	95	below_threshold
Schlegelella brevitalea	strain=DSM 7029	GCA_001017435.1	413882	413882	type	True	78.838	257	692	95	below_threshold
Mitsuaria chitinivorans	strain=HWN-4	GCA_002761755.1	2917965	2917965	type	True	78.8322	252	692	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	78.4609	230	692	95	below_threshold
Ottowia testudinis	strain=27C	GCA_017498525.1	2816950	2816950	type	True	77.7689	179	692	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:47:48,192] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33290/tc_result.tsv
[2023-03-15 23:47:48,197] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:47:48,197] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:47:48,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc0ed8ec-317f-45e4-92d5-9502099d6631/dqc_reference/checkm_data
[2023-03-15 23:47:48,198] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:47:48,206] [INFO] Task started: CheckM
[2023-03-15 23:47:48,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33290/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33290/checkm_input OceanDNA-b33290/checkm_result
[2023-03-15 23:48:32,205] [INFO] Task succeeded: CheckM
[2023-03-15 23:48:32,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.81%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:48:32,215] [INFO] ===== Completeness check finished =====
[2023-03-15 23:48:32,215] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:48:32,215] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33290/markers.fasta)
[2023-03-15 23:48:32,216] [INFO] Task started: Blastn
[2023-03-15 23:48:32,216] [INFO] Running command: blastn -query OceanDNA-b33290/markers.fasta -db /var/lib/cwl/stgfc0ed8ec-317f-45e4-92d5-9502099d6631/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33290/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:48:34,397] [INFO] Task succeeded: Blastn
[2023-03-15 23:48:34,411] [INFO] Selected 14 target genomes.
[2023-03-15 23:48:34,411] [INFO] Target genome list was writen to OceanDNA-b33290/target_genomes_gtdb.txt
[2023-03-15 23:48:34,689] [INFO] Task started: fastANI
[2023-03-15 23:48:34,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ff02cd6-1c47-4ec8-8171-b9351204c8ac/OceanDNA-b33290.fa --refList OceanDNA-b33290/target_genomes_gtdb.txt --output OceanDNA-b33290/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:48:44,756] [INFO] Task succeeded: fastANI
[2023-03-15 23:48:44,764] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:48:44,765] [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_003100395.1	s__Aquabacterium olei	86.8526	575	692	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	82.1658	403	692	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	82.1241	387	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001770725.1	s__Aquabacterium sp001770725	82.0545	412	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768065.1	s__Aquabacterium sp000768065	81.7162	402	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009909205.1	s__Aquabacterium fontiphilum	81.6205	353	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017989885.1	s__Aquabacterium sp017989885	81.6135	210	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	98.47	98.47	0.69	0.69	2	-
GCF_004310865.1	s__Aquabacterium lacunae	81.5164	360	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112875.1	s__Aquabacterium excrementipullorum	81.4447	388	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185075.1	s__Aquabacterium sp016185075	81.4395	302	692	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	81.3777	381	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003933735.1	s__Aquabacterium sp003933735	81.3241	368	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234775.1	s__Aquabacterium sp016234775	80.8994	331	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598255.1	s__Mitsuaria chitosanitabida	79.0805	255	692	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Mitsuaria	95.0	99.05	99.05	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2023-03-15 23:48:44,768] [INFO] GTDB search result was written to OceanDNA-b33290/result_gtdb.tsv
[2023-03-15 23:48:44,771] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:48:44,773] [INFO] DFAST_QC result json was written to OceanDNA-b33290/dqc_result.json
[2023-03-15 23:48:44,773] [INFO] DFAST_QC completed!
[2023-03-15 23:48:44,773] [INFO] Total running time: 0h1m24s