[2023-03-14 11:14:12,736] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:14:12,736] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:14:12,736] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e2b025b-b8d7-4067-8b7e-9d365de0a052/dqc_reference
[2023-03-14 11:14:14,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:14:14,212] [INFO] Task started: Prodigal
[2023-03-14 11:14:14,213] [INFO] Running command: cat /var/lib/cwl/stge87c1acf-6ea6-4073-8b71-66a0914396e0/OceanDNA-b26832.fa | prodigal -d OceanDNA-b26832/cds.fna -a OceanDNA-b26832/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:14:44,169] [INFO] Task succeeded: Prodigal
[2023-03-14 11:14:44,169] [INFO] Task started: HMMsearch
[2023-03-14 11:14:44,169] [INFO] Running command: hmmsearch --tblout OceanDNA-b26832/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e2b025b-b8d7-4067-8b7e-9d365de0a052/dqc_reference/reference_markers.hmm OceanDNA-b26832/protein.faa > /dev/null
[2023-03-14 11:14:44,433] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:14:44,434] [INFO] Found 6/6 markers.
[2023-03-14 11:14:44,462] [INFO] Query marker FASTA was written to OceanDNA-b26832/markers.fasta
[2023-03-14 11:14:44,464] [INFO] Task started: Blastn
[2023-03-14 11:14:44,464] [INFO] Running command: blastn -query OceanDNA-b26832/markers.fasta -db /var/lib/cwl/stg1e2b025b-b8d7-4067-8b7e-9d365de0a052/dqc_reference/reference_markers.fasta -out OceanDNA-b26832/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:14:45,396] [INFO] Task succeeded: Blastn
[2023-03-14 11:14:45,396] [INFO] Selected 14 target genomes.
[2023-03-14 11:14:45,397] [INFO] Target genome list was writen to OceanDNA-b26832/target_genomes.txt
[2023-03-14 11:14:45,408] [INFO] Task started: fastANI
[2023-03-14 11:14:45,408] [INFO] Running command: fastANI --query /var/lib/cwl/stge87c1acf-6ea6-4073-8b71-66a0914396e0/OceanDNA-b26832.fa --refList OceanDNA-b26832/target_genomes.txt --output OceanDNA-b26832/fastani_result.tsv --threads 1
[2023-03-14 11:14:59,463] [INFO] Task succeeded: fastANI
[2023-03-14 11:14:59,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e2b025b-b8d7-4067-8b7e-9d365de0a052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:14:59,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e2b025b-b8d7-4067-8b7e-9d365de0a052/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:14:59,472] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:14:59,472] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:14:59,473] [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 alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	81.6945	902	1546	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	81.4971	937	1546	95	below_threshold
Hoeflea halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	81.1225	827	1546	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.4998	723	1546	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.6835	648	1546	95	below_threshold
Ciceribacter selenitireducens	strain=ATCC BAA-1503	GCA_000518785.1	448181	448181	type	True	77.6797	364	1546	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.4613	363	1546	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.4479	374	1546	95	below_threshold
Shinella oryzae	strain=Z-25	GCA_023038235.1	2871820	2871820	type	True	77.431	332	1546	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.3178	336	1546	95	below_threshold
Ciceribacter ferrooxidans	strain=F8825	GCA_004137355.1	2509717	2509717	type	True	77.3016	280	1546	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_019684455.1	1138190	1138190	type	True	77.2772	317	1546	95	below_threshold
Rhizobium populisoli	strain=XQZ8	GCA_019430945.1	2859785	2859785	type	True	77.2691	288	1546	95	below_threshold
Rhizobium binae	strain=BLR195	GCA_017357225.1	1138190	1138190	type	True	77.2332	325	1546	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:14:59,473] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26832/tc_result.tsv
[2023-03-14 11:14:59,473] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:14:59,473] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:14:59,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e2b025b-b8d7-4067-8b7e-9d365de0a052/dqc_reference/checkm_data
[2023-03-14 11:14:59,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:14:59,498] [INFO] Task started: CheckM
[2023-03-14 11:14:59,499] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26832/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26832/checkm_input OceanDNA-b26832/checkm_result
[2023-03-14 11:16:14,073] [INFO] Task succeeded: CheckM
[2023-03-14 11:16:14,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:16:14,076] [INFO] ===== Completeness check finished =====
[2023-03-14 11:16:14,077] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:16:14,077] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26832/markers.fasta)
[2023-03-14 11:16:14,077] [INFO] Task started: Blastn
[2023-03-14 11:16:14,077] [INFO] Running command: blastn -query OceanDNA-b26832/markers.fasta -db /var/lib/cwl/stg1e2b025b-b8d7-4067-8b7e-9d365de0a052/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26832/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:16:15,907] [INFO] Task succeeded: Blastn
[2023-03-14 11:16:15,908] [INFO] Selected 11 target genomes.
[2023-03-14 11:16:15,908] [INFO] Target genome list was writen to OceanDNA-b26832/target_genomes_gtdb.txt
[2023-03-14 11:16:15,918] [INFO] Task started: fastANI
[2023-03-14 11:16:15,918] [INFO] Running command: fastANI --query /var/lib/cwl/stge87c1acf-6ea6-4073-8b71-66a0914396e0/OceanDNA-b26832.fa --refList OceanDNA-b26832/target_genomes_gtdb.txt --output OceanDNA-b26832/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:16:27,120] [INFO] Task succeeded: fastANI
[2023-03-14 11:16:27,128] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:16:27,128] [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_019084245.1	s__Hoeflea sp019084245	83.7336	1053	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCA_014359905.1	s__Hoeflea sp014359905	83.6299	1035	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000759435.1	s__Hoeflea sp000759435	83.1499	1004	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000961635.1	s__Hoeflea sp000961635	82.6841	633	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001011155.1	s__Hoeflea sp001011155	82.6316	994	1546	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	82.0379	589	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733955.1	s__Hoeflea sp002733955	81.9347	927	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498795.1	s__Hoeflea sp902498795	81.5296	914	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_000185905.1	s__Mesorhizobium ciceri	77.5291	366	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Mesorhizobium	95.0	98.42	98.05	0.90	0.85	36	-
GCA_002307905.1	s__Allorhizobium sp002307905	77.3994	255	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Allorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019216885.1	s__Methylobacterium sp019216885	75.9604	160	1546	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:16:27,128] [INFO] GTDB search result was written to OceanDNA-b26832/result_gtdb.tsv
[2023-03-14 11:16:27,128] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:16:27,130] [INFO] DFAST_QC result json was written to OceanDNA-b26832/dqc_result.json
[2023-03-14 11:16:27,130] [INFO] DFAST_QC completed!
[2023-03-14 11:16:27,130] [INFO] Total running time: 0h2m14s