[2023-03-15 17:24:01,481] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:24:01,481] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:24:01,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg2426d9f3-e311-411c-9282-1584613fc6cf/dqc_reference
[2023-03-15 17:24:02,803] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:24:02,803] [INFO] Task started: Prodigal
[2023-03-15 17:24:02,803] [INFO] Running command: cat /var/lib/cwl/stg10a9a1ba-c6af-4e32-91de-88242189443c/OceanDNA-b30963.fa | prodigal -d OceanDNA-b30963/cds.fna -a OceanDNA-b30963/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:24:21,859] [INFO] Task succeeded: Prodigal
[2023-03-15 17:24:21,859] [INFO] Task started: HMMsearch
[2023-03-15 17:24:21,859] [INFO] Running command: hmmsearch --tblout OceanDNA-b30963/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2426d9f3-e311-411c-9282-1584613fc6cf/dqc_reference/reference_markers.hmm OceanDNA-b30963/protein.faa > /dev/null
[2023-03-15 17:24:22,200] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:24:22,200] [INFO] Found 6/6 markers.
[2023-03-15 17:24:22,225] [INFO] Query marker FASTA was written to OceanDNA-b30963/markers.fasta
[2023-03-15 17:24:22,227] [INFO] Task started: Blastn
[2023-03-15 17:24:22,227] [INFO] Running command: blastn -query OceanDNA-b30963/markers.fasta -db /var/lib/cwl/stg2426d9f3-e311-411c-9282-1584613fc6cf/dqc_reference/reference_markers.fasta -out OceanDNA-b30963/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:24:23,136] [INFO] Task succeeded: Blastn
[2023-03-15 17:24:23,137] [INFO] Selected 42 target genomes.
[2023-03-15 17:24:23,137] [INFO] Target genome list was writen to OceanDNA-b30963/target_genomes.txt
[2023-03-15 17:24:23,172] [INFO] Task started: fastANI
[2023-03-15 17:24:23,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a9a1ba-c6af-4e32-91de-88242189443c/OceanDNA-b30963.fa --refList OceanDNA-b30963/target_genomes.txt --output OceanDNA-b30963/fastani_result.tsv --threads 1
[2023-03-15 17:24:54,864] [INFO] Task succeeded: fastANI
[2023-03-15 17:24:54,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2426d9f3-e311-411c-9282-1584613fc6cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:24:54,865] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2426d9f3-e311-411c-9282-1584613fc6cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:24:54,886] [INFO] Found 42 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:24:54,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 17:24:54,886] [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
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8741	160	953	95	below_threshold
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.8098	142	953	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.7592	156	953	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	76.7334	124	953	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.6964	157	953	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.6821	136	953	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.6788	213	953	95	below_threshold
Caenispirillum salinarum	strain=AK4	GCA_000315795.1	859058	859058	type	True	76.6407	187	953	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.6196	169	953	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.56	157	953	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	76.5274	159	953	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.4484	136	953	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	76.409	183	953	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.363	158	953	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3572	116	953	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3117	210	953	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.282	157	953	95	below_threshold
Varunaivibrio sulfuroxidans	strain=DSM 101688	GCA_004341725.1	1773489	1773489	type	True	76.2438	86	953	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.1659	135	953	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	76.147	84	953	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.0804	151	953	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.0781	107	953	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.0778	111	953	95	below_threshold
Zhengella mangrovi	strain=X9-2-2	GCA_002727065.1	1982044	1982044	type	True	76.0126	111	953	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	76.0045	111	953	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.9061	117	953	95	below_threshold
Novispirillum itersonii subsp. itersonii	strain=ATCC 12639	GCA_000381985.1	180199	189	type	True	75.8985	78	953	95	below_threshold
Paroceanicella profunda	strain=D4M1	GCA_005887635.2	2579971	2579971	type	True	75.8907	105	953	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	75.89	63	953	95	below_threshold
Caulobacter hibisci	strain=KACC 18849	GCA_016135805.1	2035993	2035993	type	True	75.8347	110	953	95	below_threshold
Brevundimonas alba	strain=DSM 4736	GCA_011927945.1	74314	74314	type	True	75.8025	71	953	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	75.8011	134	953	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	75.7637	134	953	95	below_threshold
Elioraea thermophila	strain=YIM 72297	GCA_003336755.1	2185104	2185104	type	True	75.7285	88	953	95	below_threshold
Methylobacterium cerastii	strain=DSM 23679	GCA_022179125.1	932741	932741	type	True	75.7114	88	953	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	75.6921	68	953	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	75.6636	100	953	95	below_threshold
Brevundimonas variabilis	strain=DSM 4737	GCA_014199945.1	74312	74312	type	True	75.6297	53	953	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	75.623	81	953	95	below_threshold
Defluviicoccus vanus	strain=Ben 114	GCA_014672695.1	111831	111831	type	True	75.6186	66	953	95	below_threshold
Brevundimonas basaltis	strain=DSM 25335	GCA_014202075.1	472166	472166	type	True	75.431	70	953	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	75.369	53	953	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 17:24:54,886] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30963/tc_result.tsv
[2023-03-15 17:24:54,886] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:24:54,887] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:24:54,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2426d9f3-e311-411c-9282-1584613fc6cf/dqc_reference/checkm_data
[2023-03-15 17:24:54,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:24:54,893] [INFO] Task started: CheckM
[2023-03-15 17:24:54,893] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30963/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30963/checkm_input OceanDNA-b30963/checkm_result
[2023-03-15 17:25:40,610] [INFO] Task succeeded: CheckM
[2023-03-15 17:25:40,611] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 17:25:40,613] [INFO] ===== Completeness check finished =====
[2023-03-15 17:25:40,613] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:25:40,613] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30963/markers.fasta)
[2023-03-15 17:25:40,614] [INFO] Task started: Blastn
[2023-03-15 17:25:40,614] [INFO] Running command: blastn -query OceanDNA-b30963/markers.fasta -db /var/lib/cwl/stg2426d9f3-e311-411c-9282-1584613fc6cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30963/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:25:42,293] [INFO] Task succeeded: Blastn
[2023-03-15 17:25:42,294] [INFO] Selected 10 target genomes.
[2023-03-15 17:25:42,294] [INFO] Target genome list was writen to OceanDNA-b30963/target_genomes_gtdb.txt
[2023-03-15 17:25:42,303] [INFO] Task started: fastANI
[2023-03-15 17:25:42,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg10a9a1ba-c6af-4e32-91de-88242189443c/OceanDNA-b30963.fa --refList OceanDNA-b30963/target_genomes_gtdb.txt --output OceanDNA-b30963/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:25:49,913] [INFO] Task succeeded: fastANI
[2023-03-15 17:25:49,919] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:25:49,919] [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_002325375.1	s__UBA1479 sp002325375	94.1814	905	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.20	96.43	0.95	0.85	6	-
GCA_002706405.1	s__UBA1479 sp002706405	88.7603	787	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_002781745.1	s__UBA1479 sp002781745	84.1699	703	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696205.1	s__UBA1479 sp002696205	82.4693	654	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002433335.1	s__UBA1479 sp002433335	81.3861	635	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.4991	186	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_017640505.1	s__UBA4479 sp017640505	77.013	190	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCF_000342045.1	s__Phaeospirillum caucaseum	76.8446	162	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003284725.1	s__Phaeospirillum kuznetsovii	76.667	138	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002504165.1	s__Pacificitalea manganoxidans	75.369	53	953	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pacificitalea	95.0	98.03	97.97	0.89	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-15 17:25:49,919] [INFO] GTDB search result was written to OceanDNA-b30963/result_gtdb.tsv
[2023-03-15 17:25:49,919] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:25:49,922] [INFO] DFAST_QC result json was written to OceanDNA-b30963/dqc_result.json
[2023-03-15 17:25:49,922] [INFO] DFAST_QC completed!
[2023-03-15 17:25:49,922] [INFO] Total running time: 0h1m48s