[2023-03-16 06:33:31,999] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:33:31,999] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:33:31,999] [INFO] DQC Reference Directory: /var/lib/cwl/stgb890936d-5acc-4764-96fc-9b1d3968bb27/dqc_reference
[2023-03-16 06:33:33,131] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:33:33,131] [INFO] Task started: Prodigal
[2023-03-16 06:33:33,131] [INFO] Running command: cat /var/lib/cwl/stgbca93e33-f4ac-45e8-87c4-88257f6e2dd7/OceanDNA-b44635.fa | prodigal -d OceanDNA-b44635/cds.fna -a OceanDNA-b44635/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:33:55,028] [INFO] Task succeeded: Prodigal
[2023-03-16 06:33:55,028] [INFO] Task started: HMMsearch
[2023-03-16 06:33:55,028] [INFO] Running command: hmmsearch --tblout OceanDNA-b44635/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb890936d-5acc-4764-96fc-9b1d3968bb27/dqc_reference/reference_markers.hmm OceanDNA-b44635/protein.faa > /dev/null
[2023-03-16 06:33:55,220] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:33:55,220] [INFO] Found 6/6 markers.
[2023-03-16 06:33:55,241] [INFO] Query marker FASTA was written to OceanDNA-b44635/markers.fasta
[2023-03-16 06:33:55,241] [INFO] Task started: Blastn
[2023-03-16 06:33:55,241] [INFO] Running command: blastn -query OceanDNA-b44635/markers.fasta -db /var/lib/cwl/stgb890936d-5acc-4764-96fc-9b1d3968bb27/dqc_reference/reference_markers.fasta -out OceanDNA-b44635/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:33:56,068] [INFO] Task succeeded: Blastn
[2023-03-16 06:33:56,068] [INFO] Selected 24 target genomes.
[2023-03-16 06:33:56,069] [INFO] Target genome list was writen to OceanDNA-b44635/target_genomes.txt
[2023-03-16 06:33:56,100] [INFO] Task started: fastANI
[2023-03-16 06:33:56,100] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca93e33-f4ac-45e8-87c4-88257f6e2dd7/OceanDNA-b44635.fa --refList OceanDNA-b44635/target_genomes.txt --output OceanDNA-b44635/fastani_result.tsv --threads 1
[2023-03-16 06:34:09,851] [INFO] Task succeeded: fastANI
[2023-03-16 06:34:09,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb890936d-5acc-4764-96fc-9b1d3968bb27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:34:09,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb890936d-5acc-4764-96fc-9b1d3968bb27/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:34:09,865] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:34:09,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:34:09,866] [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
Wenzhouxiangella sediminis	strain=XDB06	GCA_003410055.1	1792836	1792836	type	True	78.3317	327	1171	95	below_threshold
Wenzhouxiangella marina	strain=KCTC 42284	GCA_001187785.1	1579979	1579979	type	True	77.7968	276	1171	95	below_threshold
Wenzhouxiangella marina	strain=DSM 103414	GCA_014203035.1	1579979	1579979	type	True	77.7453	278	1171	95	below_threshold
Arenimonas malthae	strain=CC-JY-1	GCA_000747075.1	354197	354197	type	True	76.7695	169	1171	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	76.7421	158	1171	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	76.6567	187	1171	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	76.5685	181	1171	95	below_threshold
Lysobacter spongiae	strain=119BY6-57	GCA_014145325.1	2025720	2025720	type	True	76.5558	147	1171	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	76.5032	139	1171	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	76.4583	180	1171	95	below_threshold
Luteimonas abyssi	strain=XH031	GCA_001482195.1	1247514	1247514	type	True	76.4154	135	1171	95	below_threshold
Methylonatrum kenyense	strain=AMT 1	GCA_023195885.1	455253	455253	type	True	76.4025	50	1171	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	76.3885	148	1171	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	76.3832	145	1171	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	76.3593	147	1171	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	76.3114	140	1171	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	76.3093	96	1171	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	76.2829	185	1171	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	76.2815	184	1171	95	below_threshold
Lysobacter xinjiangensis	strain=KCTC 22558	GCA_014651995.1	546892	546892	type	True	76.2665	124	1171	95	below_threshold
Stenotrophomonas chelatiphaga	strain=DSM 21508	GCA_001431535.1	517011	517011	type	True	76.1174	110	1171	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.0427	97	1171	95	below_threshold
Halochromatium glycolicum	strain=DSM 11080	GCA_016584085.1	85075	85075	type	True	75.7329	81	1171	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	75.665	119	1171	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:34:09,866] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44635/tc_result.tsv
[2023-03-16 06:34:09,866] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:34:09,866] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:34:09,866] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb890936d-5acc-4764-96fc-9b1d3968bb27/dqc_reference/checkm_data
[2023-03-16 06:34:09,867] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:34:09,970] [INFO] Task started: CheckM
[2023-03-16 06:34:09,970] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44635/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44635/checkm_input OceanDNA-b44635/checkm_result
[2023-03-16 06:35:03,241] [INFO] Task succeeded: CheckM
[2023-03-16 06:35:03,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:35:03,244] [INFO] ===== Completeness check finished =====
[2023-03-16 06:35:03,244] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:35:03,244] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44635/markers.fasta)
[2023-03-16 06:35:03,245] [INFO] Task started: Blastn
[2023-03-16 06:35:03,245] [INFO] Running command: blastn -query OceanDNA-b44635/markers.fasta -db /var/lib/cwl/stgb890936d-5acc-4764-96fc-9b1d3968bb27/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44635/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:35:04,860] [INFO] Task succeeded: Blastn
[2023-03-16 06:35:04,861] [INFO] Selected 17 target genomes.
[2023-03-16 06:35:04,861] [INFO] Target genome list was writen to OceanDNA-b44635/target_genomes_gtdb.txt
[2023-03-16 06:35:04,874] [INFO] Task started: fastANI
[2023-03-16 06:35:04,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgbca93e33-f4ac-45e8-87c4-88257f6e2dd7/OceanDNA-b44635.fa --refList OceanDNA-b44635/target_genomes_gtdb.txt --output OceanDNA-b44635/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:35:15,546] [INFO] Task succeeded: fastANI
[2023-03-16 06:35:15,556] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:35:15,556] [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_002722315.1	s__GCA-2722315 sp002722315	99.7664	1037	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	99.66	99.66	0.81	0.81	2	conclusive
GCA_018334995.1	s__GCA-2722315 sp018334995	81.6962	630	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	99.60	99.60	0.94	0.94	3	-
GCF_012272825.1	s__GCA-2722315 sp012272825	79.4489	509	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__GCA-2722315	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003410055.1	s__Wenzhouxiangella sediminis	78.3311	327	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908385.1	s__Wenzhouxiangella sp009908385	77.8835	249	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499265.1	s__Wenzhouxiangella sp010499265	77.8377	270	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001187785.1	s__Wenzhouxiangella marina	77.8004	275	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003417465.1	s__Wenzhouxiangella sp003417465	77.6835	274	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003560975.1	s__Wenzhouxiangella sp003560975	77.5588	233	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011008905.1	s__Wenzhouxiangella sp011008905	77.5275	280	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007694885.1	s__Wenzhouxiangella sp007694885	77.3099	201	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007116585.1	s__Wenzhouxiangella sp007116585	77.1035	97	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	98.00	98.00	0.65	0.65	2	-
GCA_003565625.1	s__Wenzhouxiangella sp003565625	77.0444	206	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Wenzhouxiangellaceae;g__Wenzhouxiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009996615.1	s__Dokdonella_A sp009996615	76.518	183	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431535.1	s__Stenotrophomonas chelatiphaga	76.1246	111	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	99.00	99.00	0.96	0.96	2	-
GCA_017744955.1	s__Dokdonella_A sp017744955	76.0169	184	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000802365.1	s__Xanthomonas cannabis	75.9508	107	1171	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
--------------------------------------------------------------------------------
[2023-03-16 06:35:15,556] [INFO] GTDB search result was written to OceanDNA-b44635/result_gtdb.tsv
[2023-03-16 06:35:15,556] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:35:15,559] [INFO] DFAST_QC result json was written to OceanDNA-b44635/dqc_result.json
[2023-03-16 06:35:15,559] [INFO] DFAST_QC completed!
[2023-03-16 06:35:15,559] [INFO] Total running time: 0h1m44s