[2023-03-15 23:15:05,776] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:15:05,777] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:15:05,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg911fa1ed-2bbf-4918-bdbf-62a66837ca3a/dqc_reference
[2023-03-15 23:15:07,540] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:15:07,541] [INFO] Task started: Prodigal
[2023-03-15 23:15:07,541] [INFO] Running command: cat /var/lib/cwl/stgdbd7b916-5990-4e52-b362-a7734a7bb446/OceanDNA-b26845.fa | prodigal -d OceanDNA-b26845/cds.fna -a OceanDNA-b26845/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:15:27,337] [INFO] Task succeeded: Prodigal
[2023-03-15 23:15:27,338] [INFO] Task started: HMMsearch
[2023-03-15 23:15:27,338] [INFO] Running command: hmmsearch --tblout OceanDNA-b26845/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg911fa1ed-2bbf-4918-bdbf-62a66837ca3a/dqc_reference/reference_markers.hmm OceanDNA-b26845/protein.faa > /dev/null
[2023-03-15 23:15:27,536] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:15:27,537] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdbd7b916-5990-4e52-b362-a7734a7bb446/OceanDNA-b26845.fa]
[2023-03-15 23:15:27,566] [INFO] Query marker FASTA was written to OceanDNA-b26845/markers.fasta
[2023-03-15 23:15:27,568] [INFO] Task started: Blastn
[2023-03-15 23:15:27,568] [INFO] Running command: blastn -query OceanDNA-b26845/markers.fasta -db /var/lib/cwl/stg911fa1ed-2bbf-4918-bdbf-62a66837ca3a/dqc_reference/reference_markers.fasta -out OceanDNA-b26845/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:15:28,378] [INFO] Task succeeded: Blastn
[2023-03-15 23:15:28,380] [INFO] Selected 16 target genomes.
[2023-03-15 23:15:28,380] [INFO] Target genome list was writen to OceanDNA-b26845/target_genomes.txt
[2023-03-15 23:15:28,392] [INFO] Task started: fastANI
[2023-03-15 23:15:28,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd7b916-5990-4e52-b362-a7734a7bb446/OceanDNA-b26845.fa --refList OceanDNA-b26845/target_genomes.txt --output OceanDNA-b26845/fastani_result.tsv --threads 1
[2023-03-15 23:15:43,276] [INFO] Task succeeded: fastANI
[2023-03-15 23:15:43,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg911fa1ed-2bbf-4918-bdbf-62a66837ca3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:15:43,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg911fa1ed-2bbf-4918-bdbf-62a66837ca3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:15:43,287] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:15:43,287] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:15:43,287] [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
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	80.7494	581	1078	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	80.5889	597	1078	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	80.228	526	1078	95	below_threshold
Shinella fusca	strain=DSM 21319	GCA_014203155.1	544480	544480	type	True	79.8503	500	1078	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	79.5802	551	1078	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	79.5529	466	1078	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	79.3703	442	1078	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	79.3388	485	1078	95	below_threshold
Mesorhizobium atlanticum	strain=CNPSo 3140	GCA_003289965.1	2233532	2233532	type	True	79.1358	462	1078	95	below_threshold
Nitratireductor pacificus	strain=pht-3B	GCA_000300335.1	1231180	1231180	type	True	79.1091	417	1078	95	below_threshold
Mesorhizobium silamurunense	strain=CCBAU 01550	GCA_014843825.1	499528	499528	type	True	78.984	438	1078	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	78.9546	434	1078	95	below_threshold
Mesorhizobium opportunistum	strain=WSM2075	GCA_000176035.2	593909	593909	type	True	78.9225	449	1078	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	78.6725	383	1078	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	78.5413	387	1078	95	below_threshold
Chelativorans intermedius	strain=LMG 28482	GCA_025398255.1	515947	515947	type	True	78.1497	333	1078	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:15:43,288] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26845/tc_result.tsv
[2023-03-15 23:15:43,289] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:15:43,289] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:15:43,289] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg911fa1ed-2bbf-4918-bdbf-62a66837ca3a/dqc_reference/checkm_data
[2023-03-15 23:15:43,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:15:43,296] [INFO] Task started: CheckM
[2023-03-15 23:15:43,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26845/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26845/checkm_input OceanDNA-b26845/checkm_result
[2023-03-15 23:16:33,566] [INFO] Task succeeded: CheckM
[2023-03-15 23:16:33,566] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.94%
Contamintation: 5.59%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-15 23:16:33,635] [INFO] ===== Completeness check finished =====
[2023-03-15 23:16:33,635] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:16:33,635] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26845/markers.fasta)
[2023-03-15 23:16:33,636] [INFO] Task started: Blastn
[2023-03-15 23:16:33,636] [INFO] Running command: blastn -query OceanDNA-b26845/markers.fasta -db /var/lib/cwl/stg911fa1ed-2bbf-4918-bdbf-62a66837ca3a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26845/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:16:35,155] [INFO] Task succeeded: Blastn
[2023-03-15 23:16:35,176] [INFO] Selected 17 target genomes.
[2023-03-15 23:16:35,176] [INFO] Target genome list was writen to OceanDNA-b26845/target_genomes_gtdb.txt
[2023-03-15 23:16:35,216] [INFO] Task started: fastANI
[2023-03-15 23:16:35,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbd7b916-5990-4e52-b362-a7734a7bb446/OceanDNA-b26845.fa --refList OceanDNA-b26845/target_genomes_gtdb.txt --output OceanDNA-b26845/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:16:50,536] [INFO] Task succeeded: fastANI
[2023-03-15 23:16:50,546] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 23:16:50,546] [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_000759435.1	s__Hoeflea sp000759435	81.0864	591	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001703635.1	s__Hoeflea olei	80.7525	581	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182275.1	s__Hoeflea marina	80.5585	600	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018829385.1	s__Hoeflea sp018829385	79.9177	340	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	79.8956	516	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019084245.1	s__Hoeflea sp019084245	79.8821	534	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_004354915.1	s__Pseudohoeflea suaedae	79.8211	491	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002709005.1	s__Pseudohoeflea sp002709005	79.7801	454	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudohoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518785.1	s__Allorhizobium selenitireducens	79.3703	442	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	79.3533	494	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_019091085.1	s__Mesorhizobium sp019091085	79.2319	477	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952385.1	s__Mesorhizobium sp003952385	79.2168	464	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.01	97.50	0.89	0.87	7	-
GCF_900220985.1	s__Hoeflea halophila	78.9443	435	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590645.1	s__Pseudaminobacter sp900116595	78.8399	395	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Pseudaminobacter	95.0	98.40	97.54	0.93	0.88	4	-
GCF_003148805.1	s__Aminobacter sp003148805	78.7277	405	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aminobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001011155.1	s__Hoeflea sp001011155	78.5993	411	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008180155.1	s__Aquamicrobium_A microcysteis	78.2965	378	1078	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Aquamicrobium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:16:50,554] [INFO] GTDB search result was written to OceanDNA-b26845/result_gtdb.tsv
[2023-03-15 23:16:50,570] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:16:50,578] [INFO] DFAST_QC result json was written to OceanDNA-b26845/dqc_result.json
[2023-03-15 23:16:50,578] [INFO] DFAST_QC completed!
[2023-03-15 23:16:50,579] [INFO] Total running time: 0h1m45s