[2023-03-19 03:22:59,878] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:22:59,880] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:22:59,880] [INFO] DQC Reference Directory: /var/lib/cwl/stg2332c6f2-c918-48d8-9bfc-da4f3cb5e0fb/dqc_reference
[2023-03-19 03:23:01,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:23:01,024] [INFO] Task started: Prodigal
[2023-03-19 03:23:01,024] [INFO] Running command: cat /var/lib/cwl/stg457659a0-3ce4-41ab-a21d-0a72ca659bc3/OceanDNA-b23489.fa | prodigal -d OceanDNA-b23489/cds.fna -a OceanDNA-b23489/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:23:14,322] [INFO] Task succeeded: Prodigal
[2023-03-19 03:23:14,323] [INFO] Task started: HMMsearch
[2023-03-19 03:23:14,323] [INFO] Running command: hmmsearch --tblout OceanDNA-b23489/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2332c6f2-c918-48d8-9bfc-da4f3cb5e0fb/dqc_reference/reference_markers.hmm OceanDNA-b23489/protein.faa > /dev/null
[2023-03-19 03:23:14,510] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:23:14,510] [INFO] Found 6/6 markers.
[2023-03-19 03:23:14,568] [INFO] Query marker FASTA was written to OceanDNA-b23489/markers.fasta
[2023-03-19 03:23:14,569] [INFO] Task started: Blastn
[2023-03-19 03:23:14,569] [INFO] Running command: blastn -query OceanDNA-b23489/markers.fasta -db /var/lib/cwl/stg2332c6f2-c918-48d8-9bfc-da4f3cb5e0fb/dqc_reference/reference_markers.fasta -out OceanDNA-b23489/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:23:15,342] [INFO] Task succeeded: Blastn
[2023-03-19 03:23:15,356] [INFO] Selected 22 target genomes.
[2023-03-19 03:23:15,357] [INFO] Target genome list was writen to OceanDNA-b23489/target_genomes.txt
[2023-03-19 03:23:15,369] [INFO] Task started: fastANI
[2023-03-19 03:23:15,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg457659a0-3ce4-41ab-a21d-0a72ca659bc3/OceanDNA-b23489.fa --refList OceanDNA-b23489/target_genomes.txt --output OceanDNA-b23489/fastani_result.tsv --threads 1
[2023-03-19 03:23:29,051] [INFO] Task succeeded: fastANI
[2023-03-19 03:23:29,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2332c6f2-c918-48d8-9bfc-da4f3cb5e0fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:23:29,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2332c6f2-c918-48d8-9bfc-da4f3cb5e0fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:23:29,064] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:23:29,064] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:23:29,064] [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
Henriciella mobilis	strain=M65	GCA_003576315.1	2305467	2305467	type	True	77.1973	165	728	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	77.1402	197	728	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.1199	224	728	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	77.0158	165	728	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	76.9889	165	728	95	below_threshold
Hyphomonas polymorpha	strain=PS728	GCA_000685315.1	74319	74319	type	True	76.9851	159	728	95	below_threshold
Henriciella pelagia	strain=CGMCC 1.15928	GCA_014644035.1	1977912	1977912	type	True	76.8684	130	728	95	below_threshold
Henriciella pelagia	strain=LA220	GCA_002088945.1	1977912	1977912	type	True	76.8522	129	728	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.8421	73	728	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.8358	72	728	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	76.7995	184	728	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	76.7236	142	728	95	below_threshold
Henriciella marina	strain=DSM 19595	GCA_000376805.1	453851	453851	type	True	76.6269	136	728	95	below_threshold
Henriciella algicola	strain=CCUG67844	GCA_003576245.1	1608422	1608422	type	True	76.5328	140	728	95	below_threshold
Henriciella barbarensis	strain=CCUG66934	GCA_003576345.1	86342	86342	type	True	76.1226	110	728	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	76.0112	86	728	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	76.0065	114	728	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	75.9661	53	728	95	below_threshold
Pseudaminobacter soli	strain=19-2017	GCA_018310375.1	2831468	2831468	type	True	75.9566	66	728	95	below_threshold
Pseudaminobacter soli	strain=HC19	GCA_014595955.1	2831468	2831468	type	True	75.9565	66	728	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.7625	88	728	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	75.5913	74	728	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:23:29,073] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23489/tc_result.tsv
[2023-03-19 03:23:29,086] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:23:29,087] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:23:29,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2332c6f2-c918-48d8-9bfc-da4f3cb5e0fb/dqc_reference/checkm_data
[2023-03-19 03:23:29,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:23:29,108] [INFO] Task started: CheckM
[2023-03-19 03:23:29,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23489/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23489/checkm_input OceanDNA-b23489/checkm_result
[2023-03-19 03:24:05,189] [INFO] Task succeeded: CheckM
[2023-03-19 03:24:05,190] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.44%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:24:05,354] [INFO] ===== Completeness check finished =====
[2023-03-19 03:24:05,354] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:24:05,354] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23489/markers.fasta)
[2023-03-19 03:24:05,356] [INFO] Task started: Blastn
[2023-03-19 03:24:05,356] [INFO] Running command: blastn -query OceanDNA-b23489/markers.fasta -db /var/lib/cwl/stg2332c6f2-c918-48d8-9bfc-da4f3cb5e0fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23489/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:24:06,850] [INFO] Task succeeded: Blastn
[2023-03-19 03:24:06,857] [INFO] Selected 19 target genomes.
[2023-03-19 03:24:06,857] [INFO] Target genome list was writen to OceanDNA-b23489/target_genomes_gtdb.txt
[2023-03-19 03:24:06,990] [INFO] Task started: fastANI
[2023-03-19 03:24:06,990] [INFO] Running command: fastANI --query /var/lib/cwl/stg457659a0-3ce4-41ab-a21d-0a72ca659bc3/OceanDNA-b23489.fa --refList OceanDNA-b23489/target_genomes_gtdb.txt --output OceanDNA-b23489/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:24:18,681] [INFO] Task succeeded: fastANI
[2023-03-19 03:24:18,692] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 03:24:18,693] [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_003576285.1	s__Henriciella sp003576285	77.3366	167	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	97.82	97.80	0.89	0.89	3	-
GCA_002408125.1	s__UBA5336 sp002408125	77.2359	205	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA5336	95.0	99.93	99.87	0.96	0.95	4	-
GCF_002088975.1	s__Henriciella aquimarina	77.1419	222	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685275.1	s__Hyphomonas johnsonii	77.1418	196	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961795.1	s__Hyphomonas sp000961795	77.0014	179	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763715.1	s__Hyphomonas sp014763715	76.999	174	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000685215.1	s__Hyphomonas jannaschiana	76.9889	165	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125515.1	s__Hyphomonas sp016125515	76.9522	167	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682735.1	s__Hyphomonas sp000682735	76.927	169	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
GCA_018830285.1	s__Hyphomonas sp018830285	76.9164	185	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823385.1	s__Hyphomonas sp013823385	76.8932	185	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402285.1	s__Hyphomonas sp018402285	76.8683	141	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682695.1	s__Hyphomonas chukchiensis	76.7995	184	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792385.1	s__Hyphomonas sp017792385	76.7088	161	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009909065.1	s__UBA5336 sp009909065	76.6862	131	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA5336	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576245.1	s__Henriciella algicola	76.5443	144	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714495.1	s__UBA7672 sp016714495	76.3674	73	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__UBA7672	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854405.1	s__Henriciella sp001854405	75.9227	95	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001767925.1	s__CV81 sp001767925	75.7362	60	728	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:24:18,702] [INFO] GTDB search result was written to OceanDNA-b23489/result_gtdb.tsv
[2023-03-19 03:24:18,721] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:24:18,735] [INFO] DFAST_QC result json was written to OceanDNA-b23489/dqc_result.json
[2023-03-19 03:24:18,736] [INFO] DFAST_QC completed!
[2023-03-19 03:24:18,736] [INFO] Total running time: 0h1m19s