[2023-03-18 02:02:52,820] [INFO] DFAST_QC pipeline started.
[2023-03-18 02:02:52,820] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 02:02:52,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg538942b2-94f4-4fcf-82a5-3d62cb9e2543/dqc_reference
[2023-03-18 02:02:53,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 02:02:53,945] [INFO] Task started: Prodigal
[2023-03-18 02:02:53,945] [INFO] Running command: cat /var/lib/cwl/stgdac676b9-8ec9-44f1-b478-48dcebe0748f/OceanDNA-b27524.fa | prodigal -d OceanDNA-b27524/cds.fna -a OceanDNA-b27524/protein.faa -g 11 -q > /dev/null
[2023-03-18 02:03:14,104] [INFO] Task succeeded: Prodigal
[2023-03-18 02:03:14,104] [INFO] Task started: HMMsearch
[2023-03-18 02:03:14,104] [INFO] Running command: hmmsearch --tblout OceanDNA-b27524/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg538942b2-94f4-4fcf-82a5-3d62cb9e2543/dqc_reference/reference_markers.hmm OceanDNA-b27524/protein.faa > /dev/null
[2023-03-18 02:03:14,319] [INFO] Task succeeded: HMMsearch
[2023-03-18 02:03:14,320] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdac676b9-8ec9-44f1-b478-48dcebe0748f/OceanDNA-b27524.fa]
[2023-03-18 02:03:14,347] [INFO] Query marker FASTA was written to OceanDNA-b27524/markers.fasta
[2023-03-18 02:03:14,348] [INFO] Task started: Blastn
[2023-03-18 02:03:14,348] [INFO] Running command: blastn -query OceanDNA-b27524/markers.fasta -db /var/lib/cwl/stg538942b2-94f4-4fcf-82a5-3d62cb9e2543/dqc_reference/reference_markers.fasta -out OceanDNA-b27524/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:03:14,996] [INFO] Task succeeded: Blastn
[2023-03-18 02:03:14,997] [INFO] Selected 28 target genomes.
[2023-03-18 02:03:14,997] [INFO] Target genome list was writen to OceanDNA-b27524/target_genomes.txt
[2023-03-18 02:03:15,067] [INFO] Task started: fastANI
[2023-03-18 02:03:15,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac676b9-8ec9-44f1-b478-48dcebe0748f/OceanDNA-b27524.fa --refList OceanDNA-b27524/target_genomes.txt --output OceanDNA-b27524/fastani_result.tsv --threads 1
[2023-03-18 02:03:32,000] [INFO] Task succeeded: fastANI
[2023-03-18 02:03:32,000] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg538942b2-94f4-4fcf-82a5-3d62cb9e2543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 02:03:32,000] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg538942b2-94f4-4fcf-82a5-3d62cb9e2543/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 02:03:32,013] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 02:03:32,013] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 02:03:32,013] [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
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.0727	82	1047	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	76.0676	73	1047	95	below_threshold
Oceaniglobus trochenteri	strain=G4	GCA_020529025.1	2763260	2763260	type	True	75.9663	69	1047	95	below_threshold
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	75.9338	96	1047	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	75.9206	96	1047	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.8766	104	1047	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	75.8698	75	1047	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	75.8542	73	1047	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	75.7255	74	1047	95	below_threshold
Albimonas donghaensis	strain=DSM 17890	GCA_900106695.1	356660	356660	type	True	75.6945	90	1047	95	below_threshold
Jannaschia rubra	strain=CECT 5088	GCA_001403735.1	282197	282197	type	True	75.6771	61	1047	95	below_threshold
Jannaschia rubra	strain=DSM 16279	GCA_900113265.1	282197	282197	type	True	75.6727	61	1047	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	75.6075	85	1047	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.5874	81	1047	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	75.5761	87	1047	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	75.519	73	1047	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	75.5154	68	1047	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	75.4884	82	1047	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	75.4356	54	1047	95	below_threshold
Jannaschia aquimarina	strain=DSM 28248	GCA_900188045.1	935700	935700	type	True	75.4163	63	1047	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	75.3504	76	1047	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	75.3171	78	1047	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	75.1703	53	1047	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 02:03:32,014] [INFO] DFAST Taxonomy check result was written to OceanDNA-b27524/tc_result.tsv
[2023-03-18 02:03:32,014] [INFO] ===== Taxonomy check completed =====
[2023-03-18 02:03:32,014] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 02:03:32,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg538942b2-94f4-4fcf-82a5-3d62cb9e2543/dqc_reference/checkm_data
[2023-03-18 02:03:32,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 02:03:32,020] [INFO] Task started: CheckM
[2023-03-18 02:03:32,020] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b27524/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b27524/checkm_input OceanDNA-b27524/checkm_result
[2023-03-18 02:04:22,927] [INFO] Task succeeded: CheckM
[2023-03-18 02:04:22,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.27%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 02:04:22,930] [INFO] ===== Completeness check finished =====
[2023-03-18 02:04:22,930] [INFO] ===== Start GTDB Search =====
[2023-03-18 02:04:22,930] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b27524/markers.fasta)
[2023-03-18 02:04:22,931] [INFO] Task started: Blastn
[2023-03-18 02:04:22,932] [INFO] Running command: blastn -query OceanDNA-b27524/markers.fasta -db /var/lib/cwl/stg538942b2-94f4-4fcf-82a5-3d62cb9e2543/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b27524/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 02:04:23,962] [INFO] Task succeeded: Blastn
[2023-03-18 02:04:23,963] [INFO] Selected 26 target genomes.
[2023-03-18 02:04:23,963] [INFO] Target genome list was writen to OceanDNA-b27524/target_genomes_gtdb.txt
[2023-03-18 02:04:23,992] [INFO] Task started: fastANI
[2023-03-18 02:04:23,992] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac676b9-8ec9-44f1-b478-48dcebe0748f/OceanDNA-b27524.fa --refList OceanDNA-b27524/target_genomes_gtdb.txt --output OceanDNA-b27524/fastani_result_gtdb.tsv --threads 1
[2023-03-18 02:04:39,629] [INFO] Task succeeded: fastANI
[2023-03-18 02:04:39,642] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 02:04:39,642] [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_009649175.1	s__Rhodovulum strictum	76.0676	73	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006227805.1	s__Aestuariivita sp006227805	76.0203	57	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aestuariivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	75.9522	80	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	75.9333	96	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	75.8785	65	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	75.8766	104	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCF_003944755.1	s__Rhodovulum robiginosum	75.8542	73	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	75.7734	52	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	75.7494	76	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016806125.1	s__AWRV01 sp000504185	75.7428	95	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	99.97	99.97	1.00	1.00	2	-
GCA_018240425.1	s__TMP-24 sp018240425	75.7278	68	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCF_003664585.1	s__Paenirhodobacter hankyongi	75.7255	74	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019061145.1	s__ASV31 sp019061145	75.7245	82	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	75.7133	52	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908505.1	s__Salibaculum sp009908505	75.6773	61	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003448965.1	s__Paroceanicella sp003448965	75.583	72	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paroceanicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022215.1	s__Paenirhodobacter populi	75.5821	57	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	75.5761	87	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCA_007131945.1	s__Pararhodobacter sp007131945	75.5728	77	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCF_900101475.1	s__Ruegeria_B marina	75.4884	82	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141735.1	s__Wenxinia saemankumensis	75.3504	76	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016595245.1	s__Azospirillum sp016595245	74.9381	74	1047	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 02:04:39,642] [INFO] GTDB search result was written to OceanDNA-b27524/result_gtdb.tsv
[2023-03-18 02:04:39,642] [INFO] ===== GTDB Search completed =====
[2023-03-18 02:04:39,645] [INFO] DFAST_QC result json was written to OceanDNA-b27524/dqc_result.json
[2023-03-18 02:04:39,645] [INFO] DFAST_QC completed!
[2023-03-18 02:04:39,645] [INFO] Total running time: 0h1m47s