[2023-03-15 12:13:55,700] [INFO] DFAST_QC pipeline started.
[2023-03-15 12:13:55,701] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 12:13:55,701] [INFO] DQC Reference Directory: /var/lib/cwl/stg73729586-3a44-456e-b542-cc2c7bf923d9/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/stgab700def-b7ac-40ba-b244-5728b85fb2a6/OceanDNA-b33048.fa | prodigal -d OceanDNA-b33048/cds.fna -a OceanDNA-b33048/protein.faa -g 11 -q > /dev/null
[2023-03-15 12:14:16,313] [INFO] Task succeeded: Prodigal
[2023-03-15 12:14:16,314] [INFO] Task started: HMMsearch
[2023-03-15 12:14:16,314] [INFO] Running command: hmmsearch --tblout OceanDNA-b33048/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg73729586-3a44-456e-b542-cc2c7bf923d9/dqc_reference/reference_markers.hmm OceanDNA-b33048/protein.faa > /dev/null
[2023-03-15 12:14:16,545] [INFO] Task succeeded: HMMsearch
[2023-03-15 12:14:16,545] [INFO] Found 6/6 markers.
[2023-03-15 12:14:16,590] [INFO] Query marker FASTA was written to OceanDNA-b33048/markers.fasta
[2023-03-15 12:14:16,591] [INFO] Task started: Blastn
[2023-03-15 12:14:16,592] [INFO] Running command: blastn -query OceanDNA-b33048/markers.fasta -db /var/lib/cwl/stg73729586-3a44-456e-b542-cc2c7bf923d9/dqc_reference/reference_markers.fasta -out OceanDNA-b33048/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:14:17,214] [INFO] Task succeeded: Blastn
[2023-03-15 12:14:17,218] [INFO] Selected 39 target genomes.
[2023-03-15 12:14:17,218] [INFO] Target genome list was writen to OceanDNA-b33048/target_genomes.txt
[2023-03-15 12:14:17,297] [INFO] Task started: fastANI
[2023-03-15 12:14:17,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgab700def-b7ac-40ba-b244-5728b85fb2a6/OceanDNA-b33048.fa --refList OceanDNA-b33048/target_genomes.txt --output OceanDNA-b33048/fastani_result.tsv --threads 1
[2023-03-15 12:14:47,513] [INFO] Task succeeded: fastANI
[2023-03-15 12:14:47,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg73729586-3a44-456e-b542-cc2c7bf923d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 12:14:47,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg73729586-3a44-456e-b542-cc2c7bf923d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 12:14:47,525] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 12:14:47,525] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 12:14:47,525] [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
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.8244	62	835	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	75.8058	70	835	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	75.7796	55	835	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	75.5898	55	835	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	75.5463	65	835	95	below_threshold
Azospirillum palustre	strain=B2	GCA_002573965.1	2044885	2044885	type	True	75.5378	66	835	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	75.5318	57	835	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.5117	75	835	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	75.5033	55	835	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.4973	76	835	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.496	59	835	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.4641	57	835	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.4566	59	835	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	75.3805	59	835	95	below_threshold
Skermanella aerolata	strain=5416T-32	GCA_000936425.1	393310	393310	type	True	75.2809	57	835	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	75.2723	75	835	95	below_threshold
Oceanibacterium hippocampi	strain=CECT 7691	GCA_900172325.1	745714	745714	type	True	75.2622	73	835	95	below_threshold
Azospirillum doebereinerae	strain=GSF71	GCA_003989665.1	92933	92933	type	True	75.1408	61	835	95	below_threshold
Arenibaculum pallidiluteum	strain=SYSU D00532	GCA_017355985.1	2812559	2812559	type	True	75.1371	53	835	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.098	70	835	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 12:14:47,527] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33048/tc_result.tsv
[2023-03-15 12:14:47,529] [INFO] ===== Taxonomy check completed =====
[2023-03-15 12:14:47,529] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 12:14:47,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg73729586-3a44-456e-b542-cc2c7bf923d9/dqc_reference/checkm_data
[2023-03-15 12:14:47,530] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 12:14:47,537] [INFO] Task started: CheckM
[2023-03-15 12:14:47,537] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33048/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33048/checkm_input OceanDNA-b33048/checkm_result
[2023-03-15 12:15:36,582] [INFO] Task succeeded: CheckM
[2023-03-15 12:15:36,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.29%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 12:15:36,765] [INFO] ===== Completeness check finished =====
[2023-03-15 12:15:36,765] [INFO] ===== Start GTDB Search =====
[2023-03-15 12:15:36,765] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33048/markers.fasta)
[2023-03-15 12:15:36,766] [INFO] Task started: Blastn
[2023-03-15 12:15:36,766] [INFO] Running command: blastn -query OceanDNA-b33048/markers.fasta -db /var/lib/cwl/stg73729586-3a44-456e-b542-cc2c7bf923d9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33048/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 12:15:37,752] [INFO] Task succeeded: Blastn
[2023-03-15 12:15:37,758] [INFO] Selected 35 target genomes.
[2023-03-15 12:15:37,758] [INFO] Target genome list was writen to OceanDNA-b33048/target_genomes_gtdb.txt
[2023-03-15 12:15:38,397] [INFO] Task started: fastANI
[2023-03-15 12:15:38,397] [INFO] Running command: fastANI --query /var/lib/cwl/stgab700def-b7ac-40ba-b244-5728b85fb2a6/OceanDNA-b33048.fa --refList OceanDNA-b33048/target_genomes_gtdb.txt --output OceanDNA-b33048/fastani_result_gtdb.tsv --threads 1
[2023-03-15 12:16:03,865] [INFO] Task succeeded: fastANI
[2023-03-15 12:16:03,876] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 12:16:03,876] [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_002717185.1	s__GCA-2717185 sp002717185	78.35	333	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012103325.1	s__GCA-2717185 sp012103325	77.8951	308	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__GCA-2717185	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937525.1	s__MarineAlpha4-Bin1 sp002937525	76.5955	93	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__GCA-2717185;g__MarineAlpha4-Bin1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_009377445.1	s__WHUA01 sp009377445	76.0679	118	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.671	84	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__SYSU-D60015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006738865.1	s__Stella sp006738865	75.563	77	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016653635.2	s__Skermanella sp016653635	75.5519	70	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001315015.1	s__Azospirillum brasilense	75.5304	57	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0321	99.35	95.17	0.92	0.83	16	-
GCF_016765655.1	s__Skermanella mucosa	75.5061	55	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	75.4132	68	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130795.1	s__Azospirillum thermophilum	75.3865	61	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102465.1	s__Thalassobaculum litoreum	75.3555	70	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCF_003119115.1	s__Azospirillum sp003119115	75.3396	53	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_000936425.1	s__Skermanella aerolata	75.2809	57	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	99.99	99.99	0.98	0.98	2	-
GCF_003349955.1	s__Azospirillum brasilense_B	75.257	54	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_006980715.1	s__Oleiliquidispirillum nitrogeniifigens	75.1691	56	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Oleiliquidispirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576635.1	s__Skermanella stibiiresistens	75.1053	69	835	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 12:16:03,888] [INFO] GTDB search result was written to OceanDNA-b33048/result_gtdb.tsv
[2023-03-15 12:16:03,911] [INFO] ===== GTDB Search completed =====
[2023-03-15 12:16:03,926] [INFO] DFAST_QC result json was written to OceanDNA-b33048/dqc_result.json
[2023-03-15 12:16:03,926] [INFO] DFAST_QC completed!
[2023-03-15 12:16:03,926] [INFO] Total running time: 0h2m8s