[2023-03-19 02:20:31,370] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:20:31,370] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:20:31,370] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c551dc6-d7cc-4c0a-a428-bd246820f361/dqc_reference
[2023-03-19 02:20:32,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:20:32,469] [INFO] Task started: Prodigal
[2023-03-19 02:20:32,469] [INFO] Running command: cat /var/lib/cwl/stg762f2828-59d4-4db5-bb16-c6cd19198e50/OceanDNA-b24039.fa | prodigal -d OceanDNA-b24039/cds.fna -a OceanDNA-b24039/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:20:47,322] [INFO] Task succeeded: Prodigal
[2023-03-19 02:20:47,322] [INFO] Task started: HMMsearch
[2023-03-19 02:20:47,322] [INFO] Running command: hmmsearch --tblout OceanDNA-b24039/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c551dc6-d7cc-4c0a-a428-bd246820f361/dqc_reference/reference_markers.hmm OceanDNA-b24039/protein.faa > /dev/null
[2023-03-19 02:20:47,508] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:20:47,509] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg762f2828-59d4-4db5-bb16-c6cd19198e50/OceanDNA-b24039.fa]
[2023-03-19 02:20:47,527] [INFO] Query marker FASTA was written to OceanDNA-b24039/markers.fasta
[2023-03-19 02:20:47,527] [INFO] Task started: Blastn
[2023-03-19 02:20:47,527] [INFO] Running command: blastn -query OceanDNA-b24039/markers.fasta -db /var/lib/cwl/stg2c551dc6-d7cc-4c0a-a428-bd246820f361/dqc_reference/reference_markers.fasta -out OceanDNA-b24039/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:20:48,253] [INFO] Task succeeded: Blastn
[2023-03-19 02:20:48,254] [INFO] Selected 20 target genomes.
[2023-03-19 02:20:48,254] [INFO] Target genome list was writen to OceanDNA-b24039/target_genomes.txt
[2023-03-19 02:20:48,264] [INFO] Task started: fastANI
[2023-03-19 02:20:48,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg762f2828-59d4-4db5-bb16-c6cd19198e50/OceanDNA-b24039.fa --refList OceanDNA-b24039/target_genomes.txt --output OceanDNA-b24039/fastani_result.tsv --threads 1
[2023-03-19 02:21:00,061] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:00,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c551dc6-d7cc-4c0a-a428-bd246820f361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:21:00,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c551dc6-d7cc-4c0a-a428-bd246820f361/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:21:00,073] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:21:00,073] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 02:21:00,073] [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
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	78.6406	391	858	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	78.0345	355	858	95	below_threshold
Parvularcula mediterranea	strain=ZS-1/3	GCA_013085255.1	2732508	2732508	type	True	76.5117	137	858	95	below_threshold
Parvularcula lutaonensis	strain=KCTC 22245	GCA_014651915.1	491923	491923	type	True	76.4165	130	858	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.3044	87	858	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	76.2764	91	858	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.249	90	858	95	below_threshold
Amphiplicatus metriothermophilus	strain=DSM 105738	GCA_014199495.1	1519374	1519374	type	True	75.7223	139	858	95	below_threshold
Caulobacter flavus	strain=CGMCC1 15093	GCA_002858845.1	1679497	1679497	type	True	75.6991	155	858	95	below_threshold
Amphiplicatus metriothermophilus	strain=CGMCC 1.12710	GCA_900199215.1	1519374	1519374	type	True	75.6783	142	858	95	below_threshold
Phenylobacterium aquaticum	strain=KACC 18306	GCA_022695515.1	1763816	1763816	type	True	75.6514	128	858	95	below_threshold
Methylobacterium hispanicum	strain=DSM 16372	GCA_022179285.1	270350	270350	type	True	75.5469	176	858	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	75.4903	118	858	95	below_threshold
Frigidibacter albus	strain=CGMCC 1.13995	GCA_014640395.1	1465486	1465486	type	True	75.1582	94	858	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	75.1153	92	858	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	75.109	92	858	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_010993795.1	1465486	1465486	type	True	75.1069	93	858	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	75.0277	127	858	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	74.9746	132	858	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 02:21:00,073] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24039/tc_result.tsv
[2023-03-19 02:21:00,073] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:21:00,073] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:21:00,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c551dc6-d7cc-4c0a-a428-bd246820f361/dqc_reference/checkm_data
[2023-03-19 02:21:00,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:21:00,078] [INFO] Task started: CheckM
[2023-03-19 02:21:00,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24039/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24039/checkm_input OceanDNA-b24039/checkm_result
[2023-03-19 02:21:38,722] [INFO] Task succeeded: CheckM
[2023-03-19 02:21:38,722] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.19%
Contamintation: 12.50%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-19 02:21:38,726] [INFO] ===== Completeness check finished =====
[2023-03-19 02:21:38,726] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:21:38,727] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24039/markers.fasta)
[2023-03-19 02:21:38,727] [INFO] Task started: Blastn
[2023-03-19 02:21:38,727] [INFO] Running command: blastn -query OceanDNA-b24039/markers.fasta -db /var/lib/cwl/stg2c551dc6-d7cc-4c0a-a428-bd246820f361/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24039/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:21:40,069] [INFO] Task succeeded: Blastn
[2023-03-19 02:21:40,070] [INFO] Selected 22 target genomes.
[2023-03-19 02:21:40,071] [INFO] Target genome list was writen to OceanDNA-b24039/target_genomes_gtdb.txt
[2023-03-19 02:21:40,103] [INFO] Task started: fastANI
[2023-03-19 02:21:40,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg762f2828-59d4-4db5-bb16-c6cd19198e50/OceanDNA-b24039.fa --refList OceanDNA-b24039/target_genomes_gtdb.txt --output OceanDNA-b24039/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:21:54,087] [INFO] Task succeeded: fastANI
[2023-03-19 02:21:54,099] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:21:54,099] [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_014199615.1	s__Parvularcula dongshanensis	78.6306	391	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	78.0897	353	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013085255.1	s__Parvularcula mediterranea	76.4962	138	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651915.1	s__Parvularcula lutaonensis	76.4165	130	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640095.1	s__Aquisalinus flavus	76.249	90	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017307205.1	s__Caulobacter sp001896875	76.1261	72	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.25	99.25	0.75	0.75	2	-
GCF_003399445.1	s__Parvularcula sp003399445	75.9933	62	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003722335.1	s__Caulobacter flavus	75.7378	151	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900199215.1	s__Amphiplicatus metriothermophilus	75.6651	143	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Amphiplicatus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001657385.1	s__Marinicaulis sp001657385	75.6622	154	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004004555.2	s__Methylobacterium sp004004555	75.616	187	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	75.5654	127	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899075.1	s__Devosia_A sp001899075	75.4949	98	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_001314805.1	s__Roseicyclus sp001314805	75.4789	74	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745235.1	s__Caulobacter sp017745235	75.4749	125	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Caulobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177295.1	s__Tistlia consotensis	75.4164	192	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001720135.1	s__Methylobrevis pamukkalensis	75.3685	132	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Methylobrevis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011046725.1	s__DSPG01 sp011046725	75.3063	144	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DSPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003506635.1	s__CV81 sp003506635	75.2026	75	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__CV81	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009908165.1	s__Frigidibacter albus	75.109	92	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCF_016106005.1	s__Roseomonas_B sp016106005	74.9939	141	858	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:21:54,100] [INFO] GTDB search result was written to OceanDNA-b24039/result_gtdb.tsv
[2023-03-19 02:21:54,101] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:21:54,104] [INFO] DFAST_QC result json was written to OceanDNA-b24039/dqc_result.json
[2023-03-19 02:21:54,104] [INFO] DFAST_QC completed!
[2023-03-19 02:21:54,104] [INFO] Total running time: 0h1m23s