[2023-03-15 06:35:36,162] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:35:36,163] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:35:36,163] [INFO] DQC Reference Directory: /var/lib/cwl/stg0592a0a6-cfb5-4a3f-b48f-0eae5e2ac41a/dqc_reference
[2023-03-15 06:35:37,250] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:35:37,251] [INFO] Task started: Prodigal
[2023-03-15 06:35:37,251] [INFO] Running command: cat /var/lib/cwl/stgffc631b8-3bee-485b-8d1e-a09fe2da860a/OceanDNA-b23848.fa | prodigal -d OceanDNA-b23848/cds.fna -a OceanDNA-b23848/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:35:50,537] [INFO] Task succeeded: Prodigal
[2023-03-15 06:35:50,538] [INFO] Task started: HMMsearch
[2023-03-15 06:35:50,538] [INFO] Running command: hmmsearch --tblout OceanDNA-b23848/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0592a0a6-cfb5-4a3f-b48f-0eae5e2ac41a/dqc_reference/reference_markers.hmm OceanDNA-b23848/protein.faa > /dev/null
[2023-03-15 06:35:50,708] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:35:50,709] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgffc631b8-3bee-485b-8d1e-a09fe2da860a/OceanDNA-b23848.fa]
[2023-03-15 06:35:50,746] [INFO] Query marker FASTA was written to OceanDNA-b23848/markers.fasta
[2023-03-15 06:35:50,747] [INFO] Task started: Blastn
[2023-03-15 06:35:50,747] [INFO] Running command: blastn -query OceanDNA-b23848/markers.fasta -db /var/lib/cwl/stg0592a0a6-cfb5-4a3f-b48f-0eae5e2ac41a/dqc_reference/reference_markers.fasta -out OceanDNA-b23848/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:35:51,404] [INFO] Task succeeded: Blastn
[2023-03-15 06:35:51,411] [INFO] Selected 26 target genomes.
[2023-03-15 06:35:51,411] [INFO] Target genome list was writen to OceanDNA-b23848/target_genomes.txt
[2023-03-15 06:35:51,424] [INFO] Task started: fastANI
[2023-03-15 06:35:51,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgffc631b8-3bee-485b-8d1e-a09fe2da860a/OceanDNA-b23848.fa --refList OceanDNA-b23848/target_genomes.txt --output OceanDNA-b23848/fastani_result.tsv --threads 1
[2023-03-15 06:36:06,038] [INFO] Task succeeded: fastANI
[2023-03-15 06:36:06,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0592a0a6-cfb5-4a3f-b48f-0eae5e2ac41a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:36:06,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0592a0a6-cfb5-4a3f-b48f-0eae5e2ac41a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:36:06,050] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:36:06,050] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:36:06,051] [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
Marinicauda salina	strain=WD6-1	GCA_003122085.1	2135793	2135793	type	True	76.1059	108	708	95	below_threshold
Marinicauda algicola	strain=RMAR8-3	GCA_017161425.1	2029849	2029849	type	True	76.0276	106	708	95	below_threshold
Marinicauda algicola	strain=JCM 31718	GCA_004793685.1	2029849	2029849	type	True	76.0268	107	708	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	76.0165	74	708	95	below_threshold
Phenylobacterium zucineum	strain=HLK1	GCA_000017265.1	284016	284016	type	True	75.9935	82	708	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	75.8838	66	708	95	below_threshold
Pyruvatibacter mobilis	strain=CGMCC 1.15125	GCA_014640905.1	1712261	1712261	type	True	75.829	66	708	95	below_threshold
Pyruvatibacter mobilis	strain=GYP-11	GCA_009910475.1	1712261	1712261	type	True	75.829	66	708	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	75.8097	54	708	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.7902	73	708	95	below_threshold
Microvirga roseola	strain=SM2	GCA_020866965.1	2883126	2883126	type	True	75.7458	60	708	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	75.7451	81	708	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	75.7451	81	708	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	75.715	90	708	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	75.7059	65	708	95	below_threshold
Novosphingobium jiangmenense	strain=1Y9A	GCA_015694345.1	2791981	2791981	type	True	75.6337	54	708	95	below_threshold
Phenylobacterium parvum	strain=HYN0004	GCA_003150835.1	2201350	2201350	type	True	75.63	53	708	95	below_threshold
Methylobacterium aerolatum	strain=DSM 19013	GCA_022179085.1	418708	418708	type	True	75.5761	73	708	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	75.5731	65	708	95	below_threshold
Brevundimonas bacteroides	strain=DSM 4726	GCA_000701445.1	74311	74311	type	True	75.4493	64	708	95	below_threshold
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	75.4073	96	708	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:36:06,055] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23848/tc_result.tsv
[2023-03-15 06:36:06,060] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:36:06,061] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:36:06,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0592a0a6-cfb5-4a3f-b48f-0eae5e2ac41a/dqc_reference/checkm_data
[2023-03-15 06:36:06,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:36:06,108] [INFO] Task started: CheckM
[2023-03-15 06:36:06,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23848/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23848/checkm_input OceanDNA-b23848/checkm_result
[2023-03-15 06:36:41,578] [INFO] Task succeeded: CheckM
[2023-03-15 06:36:41,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:36:41,590] [INFO] ===== Completeness check finished =====
[2023-03-15 06:36:41,590] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:36:41,591] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23848/markers.fasta)
[2023-03-15 06:36:41,592] [INFO] Task started: Blastn
[2023-03-15 06:36:41,592] [INFO] Running command: blastn -query OceanDNA-b23848/markers.fasta -db /var/lib/cwl/stg0592a0a6-cfb5-4a3f-b48f-0eae5e2ac41a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23848/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:36:42,777] [INFO] Task succeeded: Blastn
[2023-03-15 06:36:42,785] [INFO] Selected 26 target genomes.
[2023-03-15 06:36:42,785] [INFO] Target genome list was writen to OceanDNA-b23848/target_genomes_gtdb.txt
[2023-03-15 06:36:42,870] [INFO] Task started: fastANI
[2023-03-15 06:36:42,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgffc631b8-3bee-485b-8d1e-a09fe2da860a/OceanDNA-b23848.fa --refList OceanDNA-b23848/target_genomes_gtdb.txt --output OceanDNA-b23848/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:36:57,114] [INFO] Task succeeded: fastANI
[2023-03-15 06:36:57,125] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:36:57,125] [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_003122085.1	s__WD6-1 sp003122085	76.1059	108	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017161425.1	s__Marinicauda algicola	76.0276	106	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Marinicauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009363855.1	s__Microvirga thermotolerans	76.0165	74	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823285.1	s__Brevundimonas sp013823285	76.009	71	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	75.924	67	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012848855.1	s__Pyruvatibacter mobilis	75.9158	62	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Parvibaculales;f__CGMCC-115125;g__Pyruvatibacter	95.0	100.00	100.00	1.00	1.00	3	-
GCA_016124675.1	s__Oceanicaulis sp016124675	75.8915	87	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004458765.1	s__Microvirga pakistanensis	75.883	54	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Microvirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630495.1	s__Oceanicaulis satelles	75.8657	90	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Oceanicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744255.1	s__Brevundimonas sp017744255	75.8274	67	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012842935.1	s__DUSC01 sp012842935	75.8133	51	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__DUSC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466985.1	s__Brevundimonas abyssalis	75.7586	73	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	99.78	99.71	0.94	0.89	3	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	75.7451	81	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001824475.1	s__Phenylobacterium sp001824475	75.7112	73	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	96.46	96.46	0.87	0.87	2	-
GCF_009765365.1	s__VTOM01 sp009765365	75.6767	102	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__VTOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003150835.1	s__Phenylobacterium parvum	75.6478	52	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Phenylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382705.1	s__Aureimonas ureilytica	75.6062	79	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aureimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_016411865.1	s__Acuticoccus sp016411865	75.4073	96	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	75.3929	76	708	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:36:57,127] [INFO] GTDB search result was written to OceanDNA-b23848/result_gtdb.tsv
[2023-03-15 06:36:57,127] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:36:57,131] [INFO] DFAST_QC result json was written to OceanDNA-b23848/dqc_result.json
[2023-03-15 06:36:57,131] [INFO] DFAST_QC completed!
[2023-03-15 06:36:57,131] [INFO] Total running time: 0h1m21s