[2023-03-15 12:13:55,704] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:13:55,705] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:13:55,705] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a1cbea6-2418-48a1-a131-d5f2d796db47/dqc_reference
[2023-03-15 12:13:57,407] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 12:13:57,410] [INFO] Task started: Prodigal
[2023-03-15 12:13:57,410] [INFO] Running command: cat /var/lib/cwl/stgb2bbfd6c-c0bd-42f3-b03e-5851623a3c3a/OceanDNA-b33557.fa | prodigal -d OceanDNA-b33557/cds.fna -a OceanDNA-b33557/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:14:08,514] [INFO] Task succeeded: Prodigal
[2023-03-15 12:14:08,514] [INFO] Task started: HMMsearch
[2023-03-15 12:14:08,514] [INFO] Running command: hmmsearch --tblout OceanDNA-b33557/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a1cbea6-2418-48a1-a131-d5f2d796db47/dqc_reference/reference_markers.hmm OceanDNA-b33557/protein.faa > /dev/null
[2023-03-15 12:14:08,698] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:14:08,698] [INFO] Found 6/6 markers.
[2023-03-15 12:14:08,733] [INFO] Query marker FASTA was written to OceanDNA-b33557/markers.fasta
[2023-03-15 12:14:08,733] [INFO] Task started: Blastn
[2023-03-15 12:14:08,733] [INFO] Running command: blastn -query OceanDNA-b33557/markers.fasta -db /var/lib/cwl/stg6a1cbea6-2418-48a1-a131-d5f2d796db47/dqc_reference/reference_markers.fasta -out OceanDNA-b33557/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:14:09,417] [INFO] Task succeeded: Blastn
[2023-03-15 12:14:09,420] [INFO] Selected 34 target genomes.
[2023-03-15 12:14:09,420] [INFO] Target genome list was writen to OceanDNA-b33557/target_genomes.txt
[2023-03-15 12:14:09,441] [INFO] Task started: fastANI
[2023-03-15 12:14:09,441] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2bbfd6c-c0bd-42f3-b03e-5851623a3c3a/OceanDNA-b33557.fa --refList OceanDNA-b33557/target_genomes.txt --output OceanDNA-b33557/fastani_result.tsv --threads 1
[2023-03-15 12:14:34,228] [INFO] Task succeeded: fastANI
[2023-03-15 12:14:34,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a1cbea6-2418-48a1-a131-d5f2d796db47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:14:34,229] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a1cbea6-2418-48a1-a131-d5f2d796db47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:14:34,238] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:14:34,238] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:14:34,239] [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
Cupriavidus nantongensis	strain=X1	GCA_001598055.1	1796606	1796606	type	True	76.6611	70	586	95	below_threshold
Castellaniella defragrans	strain=DSM 12141	GCA_014203015.1	75697	75697	type	True	76.4192	53	586	95	below_threshold
Castellaniella defragrans	strain=CCUG 39790	GCA_008801975.1	75697	75697	type	True	76.3918	55	586	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	76.3684	64	586	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	76.3476	60	586	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	76.1353	70	586	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	76.084	56	586	95	below_threshold
Inhella inkyongensis	strain=IMCC1713	GCA_005952805.1	392593	392593	type	True	76.0677	54	586	95	below_threshold
Inhella inkyongensis	strain=DSM 23958	GCA_014202795.1	392593	392593	type	True	76.0455	55	586	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	76.0157	65	586	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	75.9841	50	586	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	75.8888	72	586	95	below_threshold
Thauera humireducens	strain=SgZ-1	GCA_001051995.2	1134435	1134435	type	True	75.8515	51	586	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	75.8401	51	586	95	below_threshold
Roseateles depolymerans	strain=DSM 11813	GCA_003387155.1	76731	76731	type	True	75.8256	58	586	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	75.817	50	586	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:14:34,240] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33557/tc_result.tsv
[2023-03-15 12:14:34,242] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:14:34,242] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:14:34,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a1cbea6-2418-48a1-a131-d5f2d796db47/dqc_reference/checkm_data
[2023-03-15 12:14:34,243] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:14:34,260] [INFO] Task started: CheckM
[2023-03-15 12:14:34,260] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33557/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33557/checkm_input OceanDNA-b33557/checkm_result
[2023-03-15 12:15:05,793] [INFO] Task succeeded: CheckM
[2023-03-15 12:15:05,793] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 12:15:05,851] [INFO] ===== Completeness check finished =====
[2023-03-15 12:15:05,851] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:15:05,851] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33557/markers.fasta)
[2023-03-15 12:15:05,852] [INFO] Task started: Blastn
[2023-03-15 12:15:05,853] [INFO] Running command: blastn -query OceanDNA-b33557/markers.fasta -db /var/lib/cwl/stg6a1cbea6-2418-48a1-a131-d5f2d796db47/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33557/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:15:07,094] [INFO] Task succeeded: Blastn
[2023-03-15 12:15:07,123] [INFO] Selected 28 target genomes.
[2023-03-15 12:15:07,123] [INFO] Target genome list was writen to OceanDNA-b33557/target_genomes_gtdb.txt
[2023-03-15 12:15:07,546] [INFO] Task started: fastANI
[2023-03-15 12:15:07,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2bbfd6c-c0bd-42f3-b03e-5851623a3c3a/OceanDNA-b33557.fa --refList OceanDNA-b33557/target_genomes_gtdb.txt --output OceanDNA-b33557/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:15:26,150] [INFO] Task succeeded: fastANI
[2023-03-15 12:15:26,160] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:15:26,160] [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_009646425.1	s__UBA2463 sp009646425	77.2814	138	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	95.85	95.85	0.97	0.97	2	-
GCA_016868255.1	s__UBA2463 sp016868255	77.2722	93	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342295.1	s__UBA2463 sp002342295	77.0307	106	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	99.64	99.37	0.90	0.83	6	-
GCA_018401615.1	s__UBA2463 sp018401615	76.8731	81	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402635.1	s__UBA2463 sp018402635	76.7308	67	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970865.1	s__CAIZPE01 sp018970865	76.5003	88	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__CAIZPE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001724315.1	s__SCN-69-89 sp001724315	76.4682	66	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCN-69-89	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018882795.1	s__UBA954 sp018882795	76.4562	52	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA954	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219375.1	s__Aquabacterium sp016219375	76.3124	63	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868305.1	s__UBA2463 sp016868305	76.2622	78	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA2463	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003818495.1	s__UBA4615 sp003818495	76.2428	77	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__UBA4615	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007994965.1	s__Piscinibacter aquaticus	76.2333	66	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	76.1973	80	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_017795745.1	s__Piscinibacter sp017795745	76.166	70	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005952805.1	s__Inhella inkyongensis	76.099	53	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Inhella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016706565.1	s__Piscinibacter sp016706565	76.0937	71	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Piscinibacter	95.0	98.34	98.34	0.95	0.95	2	-
GCF_000960995.1	s__Burkholderia glumae	75.9406	53	586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Burkholderia	95.0	99.66	99.30	0.96	0.92	18	-
--------------------------------------------------------------------------------
[2023-03-15 12:15:26,162] [INFO] GTDB search result was written to OceanDNA-b33557/result_gtdb.tsv
[2023-03-15 12:15:26,164] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:15:26,169] [INFO] DFAST_QC result json was written to OceanDNA-b33557/dqc_result.json
[2023-03-15 12:15:26,169] [INFO] DFAST_QC completed!
[2023-03-15 12:15:26,169] [INFO] Total running time: 0h1m30s