[2023-03-15 22:10:43,695] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:10:43,698] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:10:43,698] [INFO] DQC Reference Directory: /var/lib/cwl/stgee29cec6-683d-46e7-81aa-9657a10202bf/dqc_reference
[2023-03-15 22:10:44,792] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:10:44,792] [INFO] Task started: Prodigal
[2023-03-15 22:10:44,792] [INFO] Running command: cat /var/lib/cwl/stg2f09e8e1-4b99-40ca-8c99-72b9a0e2e3df/OceanDNA-b24066.fa | prodigal -d OceanDNA-b24066/cds.fna -a OceanDNA-b24066/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:11:11,652] [INFO] Task succeeded: Prodigal
[2023-03-15 22:11:11,652] [INFO] Task started: HMMsearch
[2023-03-15 22:11:11,652] [INFO] Running command: hmmsearch --tblout OceanDNA-b24066/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee29cec6-683d-46e7-81aa-9657a10202bf/dqc_reference/reference_markers.hmm OceanDNA-b24066/protein.faa > /dev/null
[2023-03-15 22:11:11,862] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:11:11,863] [INFO] Found 6/6 markers.
[2023-03-15 22:11:11,890] [INFO] Query marker FASTA was written to OceanDNA-b24066/markers.fasta
[2023-03-15 22:11:11,891] [INFO] Task started: Blastn
[2023-03-15 22:11:11,891] [INFO] Running command: blastn -query OceanDNA-b24066/markers.fasta -db /var/lib/cwl/stgee29cec6-683d-46e7-81aa-9657a10202bf/dqc_reference/reference_markers.fasta -out OceanDNA-b24066/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:11:12,651] [INFO] Task succeeded: Blastn
[2023-03-15 22:11:12,651] [INFO] Selected 35 target genomes.
[2023-03-15 22:11:12,652] [INFO] Target genome list was writen to OceanDNA-b24066/target_genomes.txt
[2023-03-15 22:11:12,723] [INFO] Task started: fastANI
[2023-03-15 22:11:12,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f09e8e1-4b99-40ca-8c99-72b9a0e2e3df/OceanDNA-b24066.fa --refList OceanDNA-b24066/target_genomes.txt --output OceanDNA-b24066/fastani_result.tsv --threads 1
[2023-03-15 22:11:41,058] [INFO] Task succeeded: fastANI
[2023-03-15 22:11:41,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee29cec6-683d-46e7-81aa-9657a10202bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:11:41,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee29cec6-683d-46e7-81aa-9657a10202bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:11:41,077] [INFO] Found 33 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:11:41,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:11:41,077] [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
Parvibaculum lavamentivorans	strain=DS-1	GCA_000017565.1	256618	256618	type	True	76.2963	96	1477	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.2234	137	1477	95	below_threshold
Parvibaculum sedimenti	strain=HXT-9	GCA_009184905.1	2608632	2608632	type	True	76.158	78	1477	95	below_threshold
Pelagibius litoralis	strain=DSM 21314	GCA_011683915.1	374515	374515	type	True	76.0745	138	1477	95	below_threshold
Oricola indica	strain=JL-62	GCA_019966595.1	2872591	2872591	type	True	76.0456	82	1477	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	76.0401	195	1477	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.022	123	1477	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.9954	112	1477	95	below_threshold
Mesorhizobium temperatum	strain=SDW018	GCA_002284575.1	241416	241416	type	True	75.9604	111	1477	95	below_threshold
Mesorhizobium neociceri	strain=CCANP35	GCA_013520985.1	1307853	1307853	type	True	75.8931	118	1477	95	below_threshold
Nisaea nitritireducens	strain=DSM 19540	GCA_014904795.1	568392	568392	type	True	75.8315	111	1477	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.8289	194	1477	95	below_threshold
Mesorhizobium wenxiniae	strain=WYCCWR 10195	GCA_002284535.1	2014805	2014805	type	True	75.813	109	1477	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	75.7532	194	1477	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	75.7468	195	1477	95	below_threshold
Paracoccus acridae	strain=CGMCC 1.15419	GCA_014642735.1	1795310	1795310	type	True	75.6961	66	1477	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	75.6802	98	1477	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	75.6571	167	1477	95	below_threshold
Nisaea denitrificans	strain=DSM 18348	GCA_000426505.1	390877	390877	type	True	75.6376	97	1477	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	75.5938	148	1477	95	below_threshold
Rhizobium anhuiense	strain=CCBAU 23252	GCA_003985145.1	1184720	1184720	type	True	75.5749	81	1477	95	below_threshold
Bradyrhizobium paxllaeri	strain=LMTR 21	GCA_001693515.2	190148	190148	type	True	75.5727	114	1477	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	75.5511	107	1477	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.5326	143	1477	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	75.5301	74	1477	95	below_threshold
Rhizobium anhuiense	strain=CGMCC 1.12621	GCA_014638185.1	1184720	1184720	type	True	75.522	81	1477	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	75.5082	70	1477	95	below_threshold
Phreatobacter stygius	strain=KCTC 52518	GCA_005144885.1	1940610	1940610	type	True	75.5059	148	1477	95	below_threshold
Sneathiella chungangensis	strain=KCTC 32476	GCA_009882935.1	1418234	1418234	type	True	75.4919	82	1477	95	below_threshold
Rhizobium petrolearium	strain=DSM 26482	GCA_017873175.1	515361	515361	type	True	75.4755	83	1477	95	below_threshold
Sneathiella chungangensis	strain=KCTC32476	GCA_012720125.1	1418234	1418234	type	True	75.41	83	1477	95	below_threshold
Rhizobium favelukesii	strain=LPU83	GCA_000577275.2	348824	348824	type	True	75.2491	57	1477	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.2046	107	1477	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:11:41,078] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24066/tc_result.tsv
[2023-03-15 22:11:41,078] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:11:41,078] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:11:41,078] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee29cec6-683d-46e7-81aa-9657a10202bf/dqc_reference/checkm_data
[2023-03-15 22:11:41,079] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:11:41,087] [INFO] Task started: CheckM
[2023-03-15 22:11:41,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24066/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24066/checkm_input OceanDNA-b24066/checkm_result
[2023-03-15 22:12:45,382] [INFO] Task succeeded: CheckM
[2023-03-15 22:12:45,382] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:12:45,386] [INFO] ===== Completeness check finished =====
[2023-03-15 22:12:45,386] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:12:45,386] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24066/markers.fasta)
[2023-03-15 22:12:45,387] [INFO] Task started: Blastn
[2023-03-15 22:12:45,387] [INFO] Running command: blastn -query OceanDNA-b24066/markers.fasta -db /var/lib/cwl/stgee29cec6-683d-46e7-81aa-9657a10202bf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24066/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:12:46,838] [INFO] Task succeeded: Blastn
[2023-03-15 22:12:46,839] [INFO] Selected 28 target genomes.
[2023-03-15 22:12:46,839] [INFO] Target genome list was writen to OceanDNA-b24066/target_genomes_gtdb.txt
[2023-03-15 22:12:47,170] [INFO] Task started: fastANI
[2023-03-15 22:12:47,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f09e8e1-4b99-40ca-8c99-72b9a0e2e3df/OceanDNA-b24066.fa --refList OceanDNA-b24066/target_genomes_gtdb.txt --output OceanDNA-b24066/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:13:06,439] [INFO] Task succeeded: fastANI
[2023-03-15 22:13:06,453] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:13:06,453] [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_009377375.1	s__WHUE01 sp009377375	77.6502	428	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WHUE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660305.1	s__JABJKO01 sp018660305	77.2819	339	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__JABJKO01	95.0	99.60	99.60	0.81	0.81	2	-
GCA_002239065.1	s__MPNO01 sp002239065	76.701	228	1477	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	76.3586	201	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__VGEU01;g__VGEU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017565.1	s__Parvibaculum lavamentivorans	76.2963	96	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232485.1	s__JADFZP01 sp015232485	76.2919	122	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	96.70	95.97	0.70	0.69	3	-
GCA_905181725.1	s__UBA830 sp905181725	76.2614	146	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA830;g__UBA830	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	76.2325	187	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184905.1	s__Parvibaculum sedimenti	76.158	78	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__Parvibaculaceae;g__Parvibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006739055.1	s__Stella vacuolata	76.1138	181	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	76.0893	102	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182615.1	s__WLWZ01 sp905182615	76.0264	105	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__MPNO01;f__UBA2964;g__WLWZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002325375.1	s__UBA1479 sp002325375	76.0099	137	1477	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_016794005.1	s__Tagaea sp016794005	75.9066	96	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CACIAM-22H2;f__CACIAM-22H2;g__Tagaea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001305595.1	s__Azospirillum thiophilum	75.7816	194	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000730165.1	s__Nitrospirillum amazonense	75.7085	108	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCA_016869275.1	s__SHVV01 sp016869275	75.7066	93	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVV01;f__SHVV01;g__SHVV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000576635.1	s__Skermanella stibiiresistens	75.6047	149	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Skermanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002088975.1	s__Henriciella aquimarina	75.5082	70	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Henriciella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144885.1	s__Phreatobacter stygius	75.5027	151	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	75.4888	55	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298965.1	s__Pinisolibacter sp002298965	75.4062	90	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000247475.1	s__Allorhizobium sp000247475	75.3672	67	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447385.1	s__Paracoccus sp001447385	75.2838	118	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872815.1	s__SIAN01 sp016872815	74.7336	54	1477	d__Bacteria;p__Planctomycetota;c__B15-G4;o__B15-G4;f__SIAN01;g__SIAN01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:13:06,453] [INFO] GTDB search result was written to OceanDNA-b24066/result_gtdb.tsv
[2023-03-15 22:13:06,454] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:13:06,456] [INFO] DFAST_QC result json was written to OceanDNA-b24066/dqc_result.json
[2023-03-15 22:13:06,457] [INFO] DFAST_QC completed!
[2023-03-15 22:13:06,457] [INFO] Total running time: 0h2m23s