[2023-03-16 06:54:59,056] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:54:59,060] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:54:59,060] [INFO] DQC Reference Directory: /var/lib/cwl/stga718755c-022a-47e6-8da0-aae37fe2df34/dqc_reference
[2023-03-16 06:55:00,261] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:55:00,261] [INFO] Task started: Prodigal
[2023-03-16 06:55:00,261] [INFO] Running command: cat /var/lib/cwl/stgb41aad69-cb98-4fa7-9ecb-1280ea69c29f/OceanDNA-b32892.fa | prodigal -d OceanDNA-b32892/cds.fna -a OceanDNA-b32892/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:55:15,812] [INFO] Task succeeded: Prodigal
[2023-03-16 06:55:15,813] [INFO] Task started: HMMsearch
[2023-03-16 06:55:15,813] [INFO] Running command: hmmsearch --tblout OceanDNA-b32892/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga718755c-022a-47e6-8da0-aae37fe2df34/dqc_reference/reference_markers.hmm OceanDNA-b32892/protein.faa > /dev/null
[2023-03-16 06:55:16,019] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:55:16,019] [INFO] Found 6/6 markers.
[2023-03-16 06:55:16,074] [INFO] Query marker FASTA was written to OceanDNA-b32892/markers.fasta
[2023-03-16 06:55:16,075] [INFO] Task started: Blastn
[2023-03-16 06:55:16,075] [INFO] Running command: blastn -query OceanDNA-b32892/markers.fasta -db /var/lib/cwl/stga718755c-022a-47e6-8da0-aae37fe2df34/dqc_reference/reference_markers.fasta -out OceanDNA-b32892/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:55:16,808] [INFO] Task succeeded: Blastn
[2023-03-16 06:55:16,821] [INFO] Selected 32 target genomes.
[2023-03-16 06:55:16,821] [INFO] Target genome list was writen to OceanDNA-b32892/target_genomes.txt
[2023-03-16 06:55:16,844] [INFO] Task started: fastANI
[2023-03-16 06:55:16,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgb41aad69-cb98-4fa7-9ecb-1280ea69c29f/OceanDNA-b32892.fa --refList OceanDNA-b32892/target_genomes.txt --output OceanDNA-b32892/fastani_result.tsv --threads 1
[2023-03-16 06:55:39,490] [INFO] Task succeeded: fastANI
[2023-03-16 06:55:39,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga718755c-022a-47e6-8da0-aae37fe2df34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:55:39,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga718755c-022a-47e6-8da0-aae37fe2df34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:55:39,506] [INFO] Found 30 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:55:39,506] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:55:39,506] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.3918	150	840	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.3379	117	840	95	below_threshold
Rhodospirillum rubrum	strain=ATCC 11170	GCA_000013085.1	1085	1085	type	True	76.3004	95	840	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	76.2805	96	840	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.2352	96	840	95	below_threshold
Blastochloris tepida	strain=GI	GCA_003966715.1	2233851	2233851	type	True	76.2326	80	840	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.2157	97	840	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.1766	86	840	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.1477	119	840	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.123	142	840	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.055	98	840	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.0212	59	840	95	below_threshold
Nisaea sediminum	strain=NBU1469	GCA_014904705.1	2775867	2775867	type	True	76.0038	95	840	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.9856	171	840	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.9843	169	840	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.9712	88	840	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	75.9067	128	840	95	below_threshold
Telmatospirillum siberiense	strain=26-4b1	GCA_002845745.1	382514	382514	type	True	75.8929	81	840	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	75.7592	104	840	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.7393	111	840	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.7345	106	840	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.7307	59	840	95	below_threshold
Pararhodospirillum oryzae	strain=NBRC 107573	GCA_007992075.1	478448	478448	type	True	75.7266	62	840	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.7082	108	840	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.5978	88	840	95	below_threshold
Azospirillum griseum	strain=L-25-5 w-1	GCA_003966125.1	2496639	2496639	type	True	75.553	97	840	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.5006	58	840	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.4297	56	840	95	below_threshold
Falsiroseomonas frigidaquae	strain=JCM 15073	GCA_012163145.1	487318	487318	type	True	75.4026	69	840	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	75.2229	66	840	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:55:39,511] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32892/tc_result.tsv
[2023-03-16 06:55:39,519] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:55:39,519] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:55:39,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga718755c-022a-47e6-8da0-aae37fe2df34/dqc_reference/checkm_data
[2023-03-16 06:55:39,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:55:39,528] [INFO] Task started: CheckM
[2023-03-16 06:55:39,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32892/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32892/checkm_input OceanDNA-b32892/checkm_result
[2023-03-16 06:56:20,816] [INFO] Task succeeded: CheckM
[2023-03-16 06:56:20,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:56:20,878] [INFO] ===== Completeness check finished =====
[2023-03-16 06:56:20,879] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:56:20,879] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32892/markers.fasta)
[2023-03-16 06:56:20,880] [INFO] Task started: Blastn
[2023-03-16 06:56:20,880] [INFO] Running command: blastn -query OceanDNA-b32892/markers.fasta -db /var/lib/cwl/stga718755c-022a-47e6-8da0-aae37fe2df34/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32892/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:56:22,299] [INFO] Task succeeded: Blastn
[2023-03-16 06:56:22,305] [INFO] Selected 33 target genomes.
[2023-03-16 06:56:22,305] [INFO] Target genome list was writen to OceanDNA-b32892/target_genomes_gtdb.txt
[2023-03-16 06:56:22,359] [INFO] Task started: fastANI
[2023-03-16 06:56:22,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgb41aad69-cb98-4fa7-9ecb-1280ea69c29f/OceanDNA-b32892.fa --refList OceanDNA-b32892/target_genomes_gtdb.txt --output OceanDNA-b32892/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:56:43,171] [INFO] Task succeeded: fastANI
[2023-03-16 06:56:43,188] [INFO] Found 31 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:56:43,188] [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_009693995.1	s__SHWA01 sp009693995	76.5904	77	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHWA01;f__SHWA01;g__SHWA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377375.1	s__WHUE01 sp009377375	76.3378	93	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.3307	114	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377535.1	s__WHTV01 sp009377535	76.3209	125	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356985.1	s__SMXQ01 sp004356985	76.3206	84	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SMXQ01;f__SMXQ01;g__SMXQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013085.1	s__Rhodospirillum rubrum	76.2805	96	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospirillum	95.0	98.74	96.31	0.98	0.96	7	-
GCF_003966715.1	s__Blastochloris tepida	76.2326	80	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377525.1	s__Reyranella sp009377525	76.2024	91	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	76.1766	86	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002239065.1	s__MPNO01 sp002239065	76.1647	104	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__MPNO01;g__MPNO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	76.1419	92	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008728835.1	s__Hypericibacter adhaerens	76.1107	143	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Dongiales;f__Dongiaceae;g__Hypericibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002937525.1	s__MarineAlpha4-Bin1 sp002937525	76.0987	57	840	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_016195125.1	s__Phaeospirillum sp016195125	76.068	77	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650635.1	s__Magnetospirillum moscoviense	76.055	98	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	96.81	95.25	0.84	0.84	3	-
GCF_001511835.1	s__Phaeospirillum sp001511835	76.0414	112	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017640745.1	s__Nisaea sp017640745	76.0281	94	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904705.1	s__Nisaea sp014904705	76.0038	95	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016861165.1	s__BOKV01 sp016861165	76.0001	86	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__BOKV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.9856	171	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_900110395.1	s__Reyranella sp900110395	75.9684	106	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576705.1	s__SYSU-D60015 sp003576705	75.8903	145	840	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_016869415.1	s__VGEI01 sp016869415	75.8898	77	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__VGEI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101965.1	s__Rhodospira trueperi	75.852	68	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Rhodospira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903832005.1	s__Reyranella aerosaccus_B	75.8274	78	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	99.93	99.93	0.97	0.96	3	-
GCF_007992075.1	s__Pararhodospirillum oryzae	75.7266	62	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Rhodospirillaceae;g__Pararhodospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009377445.1	s__WHUA01 sp009377445	75.6397	80	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA8366;f__UBA8366;g__WHUA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	75.604	61	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCA_902826885.1	s__CADEGL01 sp902826885	75.5432	80	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CADEGL01;f__CADEGL01;g__CADEGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195115.1	s__JACQAI01 sp016195115	75.489	79	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Elsterales;f__Elsteraceae;g__JACQAI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426505.1	s__Nisaea denitrificans	75.4297	56	840	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Nisaea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:56:43,195] [INFO] GTDB search result was written to OceanDNA-b32892/result_gtdb.tsv
[2023-03-16 06:56:43,209] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:56:43,218] [INFO] DFAST_QC result json was written to OceanDNA-b32892/dqc_result.json
[2023-03-16 06:56:43,218] [INFO] DFAST_QC completed!
[2023-03-16 06:56:43,218] [INFO] Total running time: 0h1m44s