[2023-03-16 16:04:03,877] [INFO] DFAST_QC pipeline started.
[2023-03-16 16:04:03,878] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 16:04:03,878] [INFO] DQC Reference Directory: /var/lib/cwl/stga645b943-8f88-4eea-ba17-868b89760500/dqc_reference
[2023-03-16 16:04:05,241] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 16:04:05,242] [INFO] Task started: Prodigal
[2023-03-16 16:04:05,242] [INFO] Running command: cat /var/lib/cwl/stga61cb021-b786-4dfc-bdcb-49552e12e158/OceanDNA-b32687.fa | prodigal -d OceanDNA-b32687/cds.fna -a OceanDNA-b32687/protein.faa -g 11 -q > /dev/null
[2023-03-16 16:04:25,987] [INFO] Task succeeded: Prodigal
[2023-03-16 16:04:25,987] [INFO] Task started: HMMsearch
[2023-03-16 16:04:25,987] [INFO] Running command: hmmsearch --tblout OceanDNA-b32687/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga645b943-8f88-4eea-ba17-868b89760500/dqc_reference/reference_markers.hmm OceanDNA-b32687/protein.faa > /dev/null
[2023-03-16 16:04:26,336] [INFO] Task succeeded: HMMsearch
[2023-03-16 16:04:26,336] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga61cb021-b786-4dfc-bdcb-49552e12e158/OceanDNA-b32687.fa]
[2023-03-16 16:04:26,370] [INFO] Query marker FASTA was written to OceanDNA-b32687/markers.fasta
[2023-03-16 16:04:26,371] [INFO] Task started: Blastn
[2023-03-16 16:04:26,371] [INFO] Running command: blastn -query OceanDNA-b32687/markers.fasta -db /var/lib/cwl/stga645b943-8f88-4eea-ba17-868b89760500/dqc_reference/reference_markers.fasta -out OceanDNA-b32687/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:04:26,994] [INFO] Task succeeded: Blastn
[2023-03-16 16:04:26,995] [INFO] Selected 25 target genomes.
[2023-03-16 16:04:26,995] [INFO] Target genome list was writen to OceanDNA-b32687/target_genomes.txt
[2023-03-16 16:04:27,008] [INFO] Task started: fastANI
[2023-03-16 16:04:27,008] [INFO] Running command: fastANI --query /var/lib/cwl/stga61cb021-b786-4dfc-bdcb-49552e12e158/OceanDNA-b32687.fa --refList OceanDNA-b32687/target_genomes.txt --output OceanDNA-b32687/fastani_result.tsv --threads 1
[2023-03-16 16:04:54,942] [INFO] Task succeeded: fastANI
[2023-03-16 16:04:54,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga645b943-8f88-4eea-ba17-868b89760500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 16:04:54,943] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga645b943-8f88-4eea-ba17-868b89760500/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 16:04:54,956] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 16:04:54,956] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 16:04:54,956] [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	75.9986	192	937	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_000237365.1	1064539	1064539	type	True	75.8713	148	937	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.8632	244	937	95	below_threshold
Azospirillum baldaniorum	strain=Sp245	GCA_003119195.2	1064539	1064539	type	True	75.8579	150	937	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.8453	246	937	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.7949	102	937	95	below_threshold
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	75.7112	102	937	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	75.6625	120	937	95	below_threshold
Magnetospirillum magnetotacticum	strain=MS-1	GCA_000829825.1	188	188	type	True	75.6617	94	937	95	below_threshold
Nitrospirillum iridis	strain=DSM 22198	GCA_014205765.1	765888	765888	type	True	75.6285	146	937	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.6243	194	937	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.6104	194	937	95	below_threshold
Oceanicella actignis	strain=DSM 22673	GCA_008124525.1	1189325	1189325	type	True	75.5624	128	937	95	below_threshold
Aliidongia dinghuensis	strain=CGMCC 1.15725	GCA_014643535.1	1867774	1867774	type	True	75.5038	138	937	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.3652	153	937	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	75.3208	96	937	95	below_threshold
Salinarimonas rosea	strain=DSM 21201	GCA_000429045.1	552063	552063	type	True	75.2412	113	937	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	75.2199	152	937	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	75.1584	70	937	95	below_threshold
Sandarakinorhabdus oryzae	strain=NM-18	GCA_009733735.1	2675220	2675220	type	True	75.102	54	937	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.0687	102	937	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	75.068	99	937	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	75.0479	108	937	95	below_threshold
Methylobacterium gregans	strain=NBRC 103626	GCA_022179245.1	374424	374424	type	True	74.9346	94	937	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 16:04:54,956] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32687/tc_result.tsv
[2023-03-16 16:04:54,956] [INFO] ===== Taxonomy check completed =====
[2023-03-16 16:04:54,957] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 16:04:54,957] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga645b943-8f88-4eea-ba17-868b89760500/dqc_reference/checkm_data
[2023-03-16 16:04:54,957] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 16:04:54,963] [INFO] Task started: CheckM
[2023-03-16 16:04:54,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32687/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32687/checkm_input OceanDNA-b32687/checkm_result
[2023-03-16 16:05:48,724] [INFO] Task succeeded: CheckM
[2023-03-16 16:05:48,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.73%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 16:05:48,727] [INFO] ===== Completeness check finished =====
[2023-03-16 16:05:48,727] [INFO] ===== Start GTDB Search =====
[2023-03-16 16:05:48,728] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32687/markers.fasta)
[2023-03-16 16:05:48,729] [INFO] Task started: Blastn
[2023-03-16 16:05:48,729] [INFO] Running command: blastn -query OceanDNA-b32687/markers.fasta -db /var/lib/cwl/stga645b943-8f88-4eea-ba17-868b89760500/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32687/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 16:05:49,690] [INFO] Task succeeded: Blastn
[2023-03-16 16:05:49,691] [INFO] Selected 21 target genomes.
[2023-03-16 16:05:49,691] [INFO] Target genome list was writen to OceanDNA-b32687/target_genomes_gtdb.txt
[2023-03-16 16:05:50,386] [INFO] Task started: fastANI
[2023-03-16 16:05:50,386] [INFO] Running command: fastANI --query /var/lib/cwl/stga61cb021-b786-4dfc-bdcb-49552e12e158/OceanDNA-b32687.fa --refList OceanDNA-b32687/target_genomes_gtdb.txt --output OceanDNA-b32687/fastani_result_gtdb.tsv --threads 1
[2023-03-16 16:06:04,176] [INFO] Task succeeded: fastANI
[2023-03-16 16:06:04,188] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 16:06:04,188] [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_002690215.1	s__GCA-2690215 sp002690215	85.8705	679	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA2966;f__UBA2966;g__GCA-2690215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869515.1	s__VGDZ01 sp016869515	76.3375	192	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__VGDZ01;f__VGDZ01;g__VGDZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002781745.1	s__UBA1479 sp002781745	76.0495	132	937	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_016869235.1	s__CAIVPW01 sp016869235	76.0199	87	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__CAIVPW01;f__CAIVPW01;g__CAIVPW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902729435.1	s__Magnetospirillum sp902729435	76.0085	197	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Magnetospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105535.1	s__Phaeospirillum sp002105535	76.0022	150	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900184795.1	s__Phaeospirillum sp900184795	75.9667	140	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001511835.1	s__Phaeospirillum sp001511835	75.9319	159	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Magnetospirillaceae;g__Phaeospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869335.1	s__VGEJ01 sp016869335	75.8636	74	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVV01;f__SHVV01;g__VGEJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869415.1	s__VGEI01 sp016869415	75.6628	110	937	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	-
GCA_016869765.1	s__SHVP01 sp016869765	75.5974	65	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVP01;f__SHVP01;g__SHVP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124525.1	s__Oceanicella actignis	75.5618	128	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicella	95.0	98.87	98.87	0.96	0.96	3	-
GCA_016869175.1	s__VGEV01 sp016869175	75.5219	154	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2731375;f__GCA-2731375;g__VGEV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018971215.1	s__REEB95 sp018971215	75.4565	72	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__REEB95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016185145.1	s__Reyranella sp016185145	75.4513	156	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242505.1	s__Reyranella sp018242505	75.4021	78	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010525.1	s__Azorhizobium caulinodans	75.308	98	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Azorhizobium	95.0	97.54	97.54	0.94	0.94	2	-
GCA_014138645.1	s__Methylobacterium thiocyanatum	75.2439	88	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	97.87	97.76	0.88	0.86	7	-
GCF_008040085.1	s__Methylobacterium sp008040085	75.1018	96	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	74.7846	81	937	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
--------------------------------------------------------------------------------
[2023-03-16 16:06:04,188] [INFO] GTDB search result was written to OceanDNA-b32687/result_gtdb.tsv
[2023-03-16 16:06:04,188] [INFO] ===== GTDB Search completed =====
[2023-03-16 16:06:04,191] [INFO] DFAST_QC result json was written to OceanDNA-b32687/dqc_result.json
[2023-03-16 16:06:04,191] [INFO] DFAST_QC completed!
[2023-03-16 16:06:04,191] [INFO] Total running time: 0h2m0s