[2023-03-19 02:20:30,846] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:20:30,846] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:20:30,846] [INFO] DQC Reference Directory: /var/lib/cwl/stgd34ef28f-faec-4fb7-b2d8-5223533e47a4/dqc_reference
[2023-03-19 02:20:31,941] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:20:31,942] [INFO] Task started: Prodigal
[2023-03-19 02:20:31,942] [INFO] Running command: cat /var/lib/cwl/stg39830db5-f810-4c28-a3ae-dbf76591d61d/OceanDNA-b39118.fa | prodigal -d OceanDNA-b39118/cds.fna -a OceanDNA-b39118/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:20:52,513] [INFO] Task succeeded: Prodigal
[2023-03-19 02:20:52,514] [INFO] Task started: HMMsearch
[2023-03-19 02:20:52,514] [INFO] Running command: hmmsearch --tblout OceanDNA-b39118/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd34ef28f-faec-4fb7-b2d8-5223533e47a4/dqc_reference/reference_markers.hmm OceanDNA-b39118/protein.faa > /dev/null
[2023-03-19 02:20:52,726] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:20:52,727] [INFO] Found 6/6 markers.
[2023-03-19 02:20:52,750] [INFO] Query marker FASTA was written to OceanDNA-b39118/markers.fasta
[2023-03-19 02:20:52,751] [INFO] Task started: Blastn
[2023-03-19 02:20:52,751] [INFO] Running command: blastn -query OceanDNA-b39118/markers.fasta -db /var/lib/cwl/stgd34ef28f-faec-4fb7-b2d8-5223533e47a4/dqc_reference/reference_markers.fasta -out OceanDNA-b39118/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:20:53,520] [INFO] Task succeeded: Blastn
[2023-03-19 02:20:53,522] [INFO] Selected 16 target genomes.
[2023-03-19 02:20:53,522] [INFO] Target genome list was writen to OceanDNA-b39118/target_genomes.txt
[2023-03-19 02:20:53,558] [INFO] Task started: fastANI
[2023-03-19 02:20:53,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg39830db5-f810-4c28-a3ae-dbf76591d61d/OceanDNA-b39118.fa --refList OceanDNA-b39118/target_genomes.txt --output OceanDNA-b39118/fastani_result.tsv --threads 1
[2023-03-19 02:21:05,925] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:05,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd34ef28f-faec-4fb7-b2d8-5223533e47a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:21:05,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd34ef28f-faec-4fb7-b2d8-5223533e47a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:21:05,935] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2023-03-19 02:21:05,935] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-19 02:21:05,935] [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
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	97.2933	990	1096	95	conclusive
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	96.6653	992	1096	95	conclusive
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	83.221	649	1096	95	below_threshold
Marinobacter halophilus	strain=CGMCC 1.12481	GCA_014637865.1	1323740	1323740	type	True	81.9042	714	1096	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	81.7735	742	1096	95	below_threshold
Marinobacter nauticus	strain=DSM 50418	GCA_003634635.1	2743	2743	type	True	81.7129	650	1096	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.3613	543	1096	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	79.9804	532	1096	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	79.7141	524	1096	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.6821	476	1096	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.3735	411	1096	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.3041	453	1096	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.1997	483	1096	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	79.1547	456	1096	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.1243	479	1096	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	78.459	390	1096	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:21:05,936] [INFO] DFAST Taxonomy check result was written to OceanDNA-b39118/tc_result.tsv
[2023-03-19 02:21:05,937] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:21:05,937] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:21:05,937] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd34ef28f-faec-4fb7-b2d8-5223533e47a4/dqc_reference/checkm_data
[2023-03-19 02:21:05,937] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:21:05,957] [INFO] Task started: CheckM
[2023-03-19 02:21:05,957] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b39118/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b39118/checkm_input OceanDNA-b39118/checkm_result
[2023-03-19 02:21:58,000] [INFO] Task succeeded: CheckM
[2023-03-19 02:21:58,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:21:58,004] [INFO] ===== Completeness check finished =====
[2023-03-19 02:21:58,004] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:21:58,004] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b39118/markers.fasta)
[2023-03-19 02:21:58,005] [INFO] Task started: Blastn
[2023-03-19 02:21:58,005] [INFO] Running command: blastn -query OceanDNA-b39118/markers.fasta -db /var/lib/cwl/stgd34ef28f-faec-4fb7-b2d8-5223533e47a4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b39118/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:21:59,316] [INFO] Task succeeded: Blastn
[2023-03-19 02:21:59,317] [INFO] Selected 11 target genomes.
[2023-03-19 02:21:59,317] [INFO] Target genome list was writen to OceanDNA-b39118/target_genomes_gtdb.txt
[2023-03-19 02:21:59,325] [INFO] Task started: fastANI
[2023-03-19 02:21:59,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg39830db5-f810-4c28-a3ae-dbf76591d61d/OceanDNA-b39118.fa --refList OceanDNA-b39118/target_genomes_gtdb.txt --output OceanDNA-b39118/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:22:08,299] [INFO] Task succeeded: fastANI
[2023-03-19 02:22:08,307] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:22:08,307] [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_003007715.1	s__Marinobacter shengliensis	97.2933	990	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.96	95.10	0.86	0.82	7	conclusive
GCF_001447155.2	s__Marinobacter sp001447155	94.6379	959	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	83.2346	648	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_000934705.1	s__Marinobacter excellens	82.4135	713	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018402255.1	s__Marinobacter sp018402255	82.3549	713	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.33	99.33	0.88	0.88	2	-
GCF_003007685.1	s__Marinobacter halophilus	81.7668	743	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284615.1	s__Marinobacter hydrocarbonoclasticus	81.7107	654	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.10	96.48	0.88	0.81	26	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.36	546	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002744735.1	s__Marinobacter guineae	79.7141	524	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643965.1	s__Marinobacter sp017643965	79.6634	410	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	79.2991	453	1096	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:22:08,308] [INFO] GTDB search result was written to OceanDNA-b39118/result_gtdb.tsv
[2023-03-19 02:22:08,308] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:22:08,311] [INFO] DFAST_QC result json was written to OceanDNA-b39118/dqc_result.json
[2023-03-19 02:22:08,311] [INFO] DFAST_QC completed!
[2023-03-19 02:22:08,311] [INFO] Total running time: 0h1m37s