[2023-03-16 04:38:30,091] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:38:30,091] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:38:30,091] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c9db542-c5a9-45d0-8f74-81d098b3c25b/dqc_reference
[2023-03-16 04:38:31,218] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:38:31,218] [INFO] Task started: Prodigal
[2023-03-16 04:38:31,219] [INFO] Running command: cat /var/lib/cwl/stg96bbd524-7305-4ec5-8b51-3911fe42f28d/OceanDNA-b23301.fa | prodigal -d OceanDNA-b23301/cds.fna -a OceanDNA-b23301/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:38:53,502] [INFO] Task succeeded: Prodigal
[2023-03-16 04:38:53,503] [INFO] Task started: HMMsearch
[2023-03-16 04:38:53,503] [INFO] Running command: hmmsearch --tblout OceanDNA-b23301/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c9db542-c5a9-45d0-8f74-81d098b3c25b/dqc_reference/reference_markers.hmm OceanDNA-b23301/protein.faa > /dev/null
[2023-03-16 04:38:53,706] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:38:53,707] [INFO] Found 6/6 markers.
[2023-03-16 04:38:53,729] [INFO] Query marker FASTA was written to OceanDNA-b23301/markers.fasta
[2023-03-16 04:38:53,730] [INFO] Task started: Blastn
[2023-03-16 04:38:53,730] [INFO] Running command: blastn -query OceanDNA-b23301/markers.fasta -db /var/lib/cwl/stg3c9db542-c5a9-45d0-8f74-81d098b3c25b/dqc_reference/reference_markers.fasta -out OceanDNA-b23301/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:38:54,425] [INFO] Task succeeded: Blastn
[2023-03-16 04:38:54,426] [INFO] Selected 35 target genomes.
[2023-03-16 04:38:54,426] [INFO] Target genome list was writen to OceanDNA-b23301/target_genomes.txt
[2023-03-16 04:38:54,448] [INFO] Task started: fastANI
[2023-03-16 04:38:54,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg96bbd524-7305-4ec5-8b51-3911fe42f28d/OceanDNA-b23301.fa --refList OceanDNA-b23301/target_genomes.txt --output OceanDNA-b23301/fastani_result.tsv --threads 1
[2023-03-16 04:39:22,122] [INFO] Task succeeded: fastANI
[2023-03-16 04:39:22,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c9db542-c5a9-45d0-8f74-81d098b3c25b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:39:22,123] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c9db542-c5a9-45d0-8f74-81d098b3c25b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:39:22,138] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:39:22,138] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:39:22,138] [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 pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	76.6255	137	1154	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	76.5956	156	1154	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.4903	214	1154	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	76.4211	173	1154	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	76.3929	178	1154	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	76.32	114	1154	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	76.2943	183	1154	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	76.2924	162	1154	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	76.2683	182	1154	95	below_threshold
Skermanella pratensis	strain=W17	GCA_008843145.1	2233999	2233999	type	True	76.2476	124	1154	95	below_threshold
Azospirillum agricola	strain=CC-HIH038	GCA_017876095.1	1720247	1720247	type	True	76.2122	201	1154	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	76.2064	204	1154	95	below_threshold
Skermanella rosea	strain=KEMB 2255-458	GCA_016806835.2	1817965	1817965	type	True	76.2041	144	1154	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	76.0709	122	1154	95	below_threshold
Caulobacter vibrioides	strain=DSM 9893	GCA_002858865.1	155892	155892	type	True	76.0316	84	1154	95	below_threshold
Rhodopseudomonas pseudopalustris	strain=DSM 123	GCA_900110435.1	1513892	1513892	type	True	75.9609	103	1154	95	below_threshold
Aurantimonas marina	strain=SW136	GCA_017183135.1	2780508	2780508	type	True	75.9103	87	1154	95	below_threshold
Rhodopseudomonas faecalis	strain=JCM 11668	GCA_003217325.1	99655	99655	type	True	75.8822	95	1154	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	75.8237	73	1154	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	75.7816	84	1154	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.7592	116	1154	95	below_threshold
Bradyrhizobium cosmicum	strain=58S1	GCA_007290395.1	1404864	1404864	type	True	75.7371	125	1154	95	below_threshold
Afipia broomeae	strain=ATCC 49717	GCA_000314675.2	56946	56946	type	True	75.7107	72	1154	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.7094	141	1154	95	below_threshold
Azorhizobium oxalatiphilum	strain=CCM 7897	GCA_014635325.1	980631	980631	type	True	75.6624	103	1154	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	75.6551	110	1154	95	below_threshold
Bradyrhizobium guangxiense	strain=CCBAU 53363	GCA_004114915.1	1325115	1325115	type	True	75.6511	140	1154	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	75.4514	102	1154	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	75.2425	65	1154	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:39:22,138] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23301/tc_result.tsv
[2023-03-16 04:39:22,138] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:39:22,139] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:39:22,139] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c9db542-c5a9-45d0-8f74-81d098b3c25b/dqc_reference/checkm_data
[2023-03-16 04:39:22,139] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:39:22,144] [INFO] Task started: CheckM
[2023-03-16 04:39:22,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23301/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23301/checkm_input OceanDNA-b23301/checkm_result
[2023-03-16 04:40:16,130] [INFO] Task succeeded: CheckM
[2023-03-16 04:40:16,130] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 04:40:16,133] [INFO] ===== Completeness check finished =====
[2023-03-16 04:40:16,133] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:40:16,133] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23301/markers.fasta)
[2023-03-16 04:40:16,133] [INFO] Task started: Blastn
[2023-03-16 04:40:16,133] [INFO] Running command: blastn -query OceanDNA-b23301/markers.fasta -db /var/lib/cwl/stg3c9db542-c5a9-45d0-8f74-81d098b3c25b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23301/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:40:17,462] [INFO] Task succeeded: Blastn
[2023-03-16 04:40:17,494] [INFO] Selected 40 target genomes.
[2023-03-16 04:40:17,494] [INFO] Target genome list was writen to OceanDNA-b23301/target_genomes_gtdb.txt
[2023-03-16 04:40:17,533] [INFO] Task started: fastANI
[2023-03-16 04:40:17,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg96bbd524-7305-4ec5-8b51-3911fe42f28d/OceanDNA-b23301.fa --refList OceanDNA-b23301/target_genomes_gtdb.txt --output OceanDNA-b23301/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:40:46,753] [INFO] Task succeeded: fastANI
[2023-03-16 04:40:46,772] [INFO] Found 36 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:40:46,773] [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
GCF_900102465.1	s__Thalassobaculum litoreum	76.6536	175	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum	95.0	98.83	98.83	0.96	0.96	2	-
GCA_018401495.1	s__Thalassobaculum_A sp018401495	76.5293	188	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	76.4927	216	1154	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_011523655.1	s__Bin65 sp011523655	76.4429	118	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Bin65;f__Bin65;g__Bin65	95.0	95.25	95.16	0.87	0.83	5	-
GCF_001305595.1	s__Azospirillum thiophilum	76.4118	174	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	100.00	100.00	1.00	1.00	2	-
GCA_006739055.1	s__Stella vacuolata	76.3891	197	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014925385.1	s__WHTV01 sp014925385	76.3159	160	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__Kiloniellaceae;g__WHTV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116035.1	s__Azospirillum sp003116035	76.3152	189	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000730165.1	s__Nitrospirillum amazonense	76.2636	110	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	97.38	95.62	0.93	0.89	4	-
GCF_003336875.1	s__Oleisolibacter albus	76.2371	119	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Oleisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.2148	126	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013414705.1	s__SSA4 sp013414705	76.1699	61	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007828035.1	s__Nitrospirillum amazonense_A	76.1231	120	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000333275.1	s__Nitrospirillum sp000333275	76.1033	112	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197805.1	s__Rhodospirillum_A centenum	76.0828	134	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Rhodospirillum_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003116135.1	s__Roseomonas aestuarii	76.0563	158	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793875.1	s__SSA4 sp016793875	76.0155	86	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__UXAT02;g__SSA4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694135.1	s__SHVS01 sp009694135	76.009	50	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__SHVS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016215605.1	s__Rhodopseudomonas palustris_L	76.0028	139	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232025.1	s__JADFZP01 sp015232025	75.9976	90	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__JADFZP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000164635.1	s__Roseomonas cervicalis	75.9923	149	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504425.1	s__Rhodopseudomonas palustris_C	75.9854	93	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	95.77	95.77	0.90	0.90	2	-
GCF_007828045.1	s__Nitrospirillum amazonense_C	75.9268	121	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Nitrospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713455.1	s__Bosea sp001713455	75.901	127	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	97.00	96.54	0.90	0.82	3	-
GCF_010907035.1	s__Rhodopseudomonas sp010907035	75.9005	114	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829925.1	s__Roseomonas coralli	75.8863	147	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002937115.1	s__Rhodopila globiformis	75.8839	174	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240635.1	s__JAFEFJ01 sp018240635	75.8832	136	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFEFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017308575.1	s__Afipia sp001897905	75.873	81	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Afipia	95.0	99.90	99.90	0.96	0.96	2	-
GCF_003217325.1	s__Rhodopseudomonas faecalis	75.856	97	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Rhodopseudomonas	95.0	98.30	98.30	0.93	0.93	2	-
GCA_016780745.1	s__JADHLJ01 sp016780745	75.8278	93	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__JADHLJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903899885.1	s__CAIULK01 sp903899885	75.7635	52	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__CAIULK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000518365.1	s__URHD0088 sp000518365	75.7318	164	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__URHD0088	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019061185.1	s__Paracoccus sp019061185	75.6953	77	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018241625.1	s__Phenylobacterium sp018241625	75.6194	79	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490485.1	s__Roseomonas aerophila	75.6014	123	1154	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:40:46,773] [INFO] GTDB search result was written to OceanDNA-b23301/result_gtdb.tsv
[2023-03-16 04:40:46,773] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:40:46,776] [INFO] DFAST_QC result json was written to OceanDNA-b23301/dqc_result.json
[2023-03-16 04:40:46,776] [INFO] DFAST_QC completed!
[2023-03-16 04:40:46,776] [INFO] Total running time: 0h2m17s