[2023-06-16 19:02:59,083] [INFO] DFAST_QC pipeline started.
[2023-06-16 19:02:59,090] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 19:02:59,090] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1be01cb-a305-4969-8be6-9d6122819232/dqc_reference
[2023-06-16 19:03:00,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 19:03:00,326] [INFO] Task started: Prodigal
[2023-06-16 19:03:00,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg77a8241c-c4b5-4386-a84c-112e1b80a093/GCA_028820945.1_ASM2882094v1_genomic.fna.gz | prodigal -d GCA_028820945.1_ASM2882094v1_genomic.fna/cds.fna -a GCA_028820945.1_ASM2882094v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 19:03:05,467] [INFO] Task succeeded: Prodigal
[2023-06-16 19:03:05,468] [INFO] Task started: HMMsearch
[2023-06-16 19:03:05,468] [INFO] Running command: hmmsearch --tblout GCA_028820945.1_ASM2882094v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1be01cb-a305-4969-8be6-9d6122819232/dqc_reference/reference_markers.hmm GCA_028820945.1_ASM2882094v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 19:03:05,625] [INFO] Task succeeded: HMMsearch
[2023-06-16 19:03:05,627] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg77a8241c-c4b5-4386-a84c-112e1b80a093/GCA_028820945.1_ASM2882094v1_genomic.fna.gz]
[2023-06-16 19:03:05,650] [INFO] Query marker FASTA was written to GCA_028820945.1_ASM2882094v1_genomic.fna/markers.fasta
[2023-06-16 19:03:05,650] [INFO] Task started: Blastn
[2023-06-16 19:03:05,650] [INFO] Running command: blastn -query GCA_028820945.1_ASM2882094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1be01cb-a305-4969-8be6-9d6122819232/dqc_reference/reference_markers.fasta -out GCA_028820945.1_ASM2882094v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:03:06,174] [INFO] Task succeeded: Blastn
[2023-06-16 19:03:06,177] [INFO] Selected 24 target genomes.
[2023-06-16 19:03:06,178] [INFO] Target genome list was writen to GCA_028820945.1_ASM2882094v1_genomic.fna/target_genomes.txt
[2023-06-16 19:03:06,261] [INFO] Task started: fastANI
[2023-06-16 19:03:06,261] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a8241c-c4b5-4386-a84c-112e1b80a093/GCA_028820945.1_ASM2882094v1_genomic.fna.gz --refList GCA_028820945.1_ASM2882094v1_genomic.fna/target_genomes.txt --output GCA_028820945.1_ASM2882094v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 19:03:26,822] [INFO] Task succeeded: fastANI
[2023-06-16 19:03:26,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1be01cb-a305-4969-8be6-9d6122819232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 19:03:26,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1be01cb-a305-4969-8be6-9d6122819232/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 19:03:26,836] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 19:03:26,836] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 19:03:26,837] [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	76.5023	68	620	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.1979	58	620	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.1895	149	620	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.1844	74	620	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.1773	150	620	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1512	139	620	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.1295	83	620	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.0414	121	620	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.0348	120	620	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	76.0001	104	620	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.9554	51	620	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	75.9542	94	620	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.9541	109	620	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.9405	108	620	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.9361	110	620	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.7957	106	620	95	below_threshold
Oharaeibacter diazotrophicus	strain=DSM 102969	GCA_004362745.1	1920512	1920512	type	True	75.7096	117	620	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	75.6451	81	620	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	75.6061	84	620	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	75.5988	84	620	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	75.4934	128	620	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.4492	117	620	95	below_threshold
Methylobacterium ajmalii	strain=IF7SW-B2	GCA_016613415.1	2738439	2738439	type	True	75.4288	113	620	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	75.3962	79	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 19:03:26,839] [INFO] DFAST Taxonomy check result was written to GCA_028820945.1_ASM2882094v1_genomic.fna/tc_result.tsv
[2023-06-16 19:03:26,839] [INFO] ===== Taxonomy check completed =====
[2023-06-16 19:03:26,839] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 19:03:26,839] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1be01cb-a305-4969-8be6-9d6122819232/dqc_reference/checkm_data
[2023-06-16 19:03:26,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 19:03:26,871] [INFO] Task started: CheckM
[2023-06-16 19:03:26,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028820945.1_ASM2882094v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028820945.1_ASM2882094v1_genomic.fna/checkm_input GCA_028820945.1_ASM2882094v1_genomic.fna/checkm_result
[2023-06-16 19:03:46,222] [INFO] Task succeeded: CheckM
[2023-06-16 19:03:46,223] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 19:03:46,241] [INFO] ===== Completeness check finished =====
[2023-06-16 19:03:46,241] [INFO] ===== Start GTDB Search =====
[2023-06-16 19:03:46,242] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028820945.1_ASM2882094v1_genomic.fna/markers.fasta)
[2023-06-16 19:03:46,242] [INFO] Task started: Blastn
[2023-06-16 19:03:46,242] [INFO] Running command: blastn -query GCA_028820945.1_ASM2882094v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1be01cb-a305-4969-8be6-9d6122819232/dqc_reference/reference_markers_gtdb.fasta -out GCA_028820945.1_ASM2882094v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 19:03:46,892] [INFO] Task succeeded: Blastn
[2023-06-16 19:03:46,896] [INFO] Selected 20 target genomes.
[2023-06-16 19:03:46,896] [INFO] Target genome list was writen to GCA_028820945.1_ASM2882094v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 19:03:46,967] [INFO] Task started: fastANI
[2023-06-16 19:03:46,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg77a8241c-c4b5-4386-a84c-112e1b80a093/GCA_028820945.1_ASM2882094v1_genomic.fna.gz --refList GCA_028820945.1_ASM2882094v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028820945.1_ASM2882094v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 19:04:05,432] [INFO] Task succeeded: fastANI
[2023-06-16 19:04:05,446] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 19:04:05,446] [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_002239065.1	s__MPNO01 sp002239065	84.199	442	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869145.1	s__VGEU01 sp016869145	77.0534	168	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.8074	148	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	76.5023	68	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823745.1	s__Oceanibaculum sp018823745	76.4769	58	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.3331	70	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576685.1	s__SYSU-D60014 sp003576685	76.3095	88	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__SYSU-D60014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	76.2279	104	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	76.1881	149	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.1345	138	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016792605.1	s__JAEULC01 sp016792605	76.1304	93	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__JAEULC01;f__JAEULC01;g__JAEULC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900110395.1	s__Reyranella sp900110395	76.0404	112	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832005.1	s__Reyranella aerosaccus_B	76.0345	75	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.93	99.93	0.97	0.96	3	-
GCF_003349955.1	s__Azospirillum brasilense_B	75.8601	111	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCA_019241915.1	s__AP-15 sp019241915	75.8441	65	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240125.1	s__AP-15 sp019240125	75.7122	59	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__AP-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151805.1	s__Methylobacterium sp006151805	75.5102	126	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004555.2	s__Methylobacterium sp004004555	75.4582	116	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613415.1	s__Methylobacterium ajmalii	75.4295	113	620	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	98.55	96.20	0.90	0.83	5	-
--------------------------------------------------------------------------------
[2023-06-16 19:04:05,449] [INFO] GTDB search result was written to GCA_028820945.1_ASM2882094v1_genomic.fna/result_gtdb.tsv
[2023-06-16 19:04:05,449] [INFO] ===== GTDB Search completed =====
[2023-06-16 19:04:05,453] [INFO] DFAST_QC result json was written to GCA_028820945.1_ASM2882094v1_genomic.fna/dqc_result.json
[2023-06-16 19:04:05,454] [INFO] DFAST_QC completed!
[2023-06-16 19:04:05,454] [INFO] Total running time: 0h1m6s