[2023-03-15 10:21:46,236] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:21:46,236] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:21:46,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg809b93e1-ffc4-479a-95ec-77478c35e0f9/dqc_reference
[2023-03-15 10:21:47,928] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:21:47,933] [INFO] Task started: Prodigal
[2023-03-15 10:21:47,933] [INFO] Running command: cat /var/lib/cwl/stgf1d2ff83-bf25-449e-9156-c71d606b053c/OceanDNA-b30966.fa | prodigal -d OceanDNA-b30966/cds.fna -a OceanDNA-b30966/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:22:09,220] [INFO] Task succeeded: Prodigal
[2023-03-15 10:22:09,220] [INFO] Task started: HMMsearch
[2023-03-15 10:22:09,220] [INFO] Running command: hmmsearch --tblout OceanDNA-b30966/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg809b93e1-ffc4-479a-95ec-77478c35e0f9/dqc_reference/reference_markers.hmm OceanDNA-b30966/protein.faa > /dev/null
[2023-03-15 10:22:09,457] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:22:09,457] [INFO] Found 6/6 markers.
[2023-03-15 10:22:09,479] [INFO] Query marker FASTA was written to OceanDNA-b30966/markers.fasta
[2023-03-15 10:22:09,479] [INFO] Task started: Blastn
[2023-03-15 10:22:09,479] [INFO] Running command: blastn -query OceanDNA-b30966/markers.fasta -db /var/lib/cwl/stg809b93e1-ffc4-479a-95ec-77478c35e0f9/dqc_reference/reference_markers.fasta -out OceanDNA-b30966/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:22:10,389] [INFO] Task succeeded: Blastn
[2023-03-15 10:22:10,390] [INFO] Selected 26 target genomes.
[2023-03-15 10:22:10,391] [INFO] Target genome list was writen to OceanDNA-b30966/target_genomes.txt
[2023-03-15 10:22:10,464] [INFO] Task started: fastANI
[2023-03-15 10:22:10,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d2ff83-bf25-449e-9156-c71d606b053c/OceanDNA-b30966.fa --refList OceanDNA-b30966/target_genomes.txt --output OceanDNA-b30966/fastani_result.tsv --threads 1
[2023-03-15 10:22:34,548] [INFO] Task succeeded: fastANI
[2023-03-15 10:22:34,548] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg809b93e1-ffc4-479a-95ec-77478c35e0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:22:34,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg809b93e1-ffc4-479a-95ec-77478c35e0f9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:22:34,563] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:22:34,563] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:22:34,563] [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	76.9899	250	1140	95	below_threshold
Magnetospirillum caucaseum	strain=SO-1	GCA_000342045.1	1244869	1244869	type	True	76.8032	219	1140	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	76.7932	174	1140	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	76.7863	200	1140	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.6827	198	1140	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	76.6165	177	1140	95	below_threshold
Magnetospirillum marisnigri	strain=SP-1	GCA_001650715.1	1285242	1285242	type	True	76.5421	194	1140	95	below_threshold
Roseospirillum parvum	strain=930I	GCA_900100455.1	83401	83401	type	True	76.531	213	1140	95	below_threshold
Skermanella mucosa	strain=KEMB 2255-438	GCA_016765655.2	1789672	1789672	type	True	76.5015	234	1140	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	76.4514	239	1140	95	below_threshold
Skermanella stibiiresistens	strain=SB22	GCA_000576635.1	913326	913326	type	True	76.4112	193	1140	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.3752	201	1140	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	76.3315	241	1140	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.3234	143	1140	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	76.3109	295	1140	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	76.305	291	1140	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.297	263	1140	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.1185	208	1140	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	76.109	192	1140	95	below_threshold
Rhodovibrio sodomensis	strain=DSM 9895	GCA_016583645.1	1088	1088	type	True	76.0774	188	1140	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.0211	152	1140	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.9395	166	1140	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.918	227	1140	95	below_threshold
Mesorhizobium sanjuanii	strain=BSA136	GCA_002529485.1	2037900	2037900	type	True	75.8296	106	1140	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	75.5937	82	1140	95	below_threshold
Polymorphobacter glacialis	strain=CGMCC 1.15519	GCA_014643455.1	1614636	1614636	type	True	75.4328	62	1140	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:22:34,563] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30966/tc_result.tsv
[2023-03-15 10:22:34,563] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:22:34,563] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:22:34,563] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg809b93e1-ffc4-479a-95ec-77478c35e0f9/dqc_reference/checkm_data
[2023-03-15 10:22:34,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:22:34,570] [INFO] Task started: CheckM
[2023-03-15 10:22:34,570] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30966/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30966/checkm_input OceanDNA-b30966/checkm_result
[2023-03-15 10:23:26,983] [INFO] Task succeeded: CheckM
[2023-03-15 10:23:26,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:23:26,986] [INFO] ===== Completeness check finished =====
[2023-03-15 10:23:26,986] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:23:26,986] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30966/markers.fasta)
[2023-03-15 10:23:26,987] [INFO] Task started: Blastn
[2023-03-15 10:23:26,987] [INFO] Running command: blastn -query OceanDNA-b30966/markers.fasta -db /var/lib/cwl/stg809b93e1-ffc4-479a-95ec-77478c35e0f9/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30966/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:23:28,769] [INFO] Task succeeded: Blastn
[2023-03-15 10:23:28,770] [INFO] Selected 10 target genomes.
[2023-03-15 10:23:28,770] [INFO] Target genome list was writen to OceanDNA-b30966/target_genomes_gtdb.txt
[2023-03-15 10:23:29,161] [INFO] Task started: fastANI
[2023-03-15 10:23:29,162] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1d2ff83-bf25-449e-9156-c71d606b053c/OceanDNA-b30966.fa --refList OceanDNA-b30966/target_genomes_gtdb.txt --output OceanDNA-b30966/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:23:36,664] [INFO] Task succeeded: fastANI
[2023-03-15 10:23:36,671] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:23:36,671] [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	91.0378	1024	1140	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	88.0174	885	1140	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	85.0687	825	1140	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	82.8319	726	1140	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	81.6666	712	1140	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	77.0596	245	1140	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	76.9008	256	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	99.97	99.97	1.00	1.00	2	-
GCA_017644185.1	s__UBA4479 sp017644185	76.6165	211	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA4479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	76.437	131	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845145.1	s__TMED8 sp016845145	76.3335	151	1140	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__TMED8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 10:23:36,671] [INFO] GTDB search result was written to OceanDNA-b30966/result_gtdb.tsv
[2023-03-15 10:23:36,671] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:23:36,673] [INFO] DFAST_QC result json was written to OceanDNA-b30966/dqc_result.json
[2023-03-15 10:23:36,674] [INFO] DFAST_QC completed!
[2023-03-15 10:23:36,674] [INFO] Total running time: 0h1m50s