[2023-03-16 23:35:14,557] [INFO] DFAST_QC pipeline started.
[2023-03-16 23:35:14,557] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 23:35:14,557] [INFO] DQC Reference Directory: /var/lib/cwl/stg41b03e43-55dc-411f-90c4-fbbae61c132e/dqc_reference
[2023-03-16 23:35:15,644] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 23:35:15,644] [INFO] Task started: Prodigal
[2023-03-16 23:35:15,644] [INFO] Running command: cat /var/lib/cwl/stge6f6398a-7ec1-4dc1-9efd-d7b7f6fe0280/OceanDNA-b26842.fa | prodigal -d OceanDNA-b26842/cds.fna -a OceanDNA-b26842/protein.faa -g 11 -q > /dev/null
[2023-03-16 23:35:32,480] [INFO] Task succeeded: Prodigal
[2023-03-16 23:35:32,480] [INFO] Task started: HMMsearch
[2023-03-16 23:35:32,480] [INFO] Running command: hmmsearch --tblout OceanDNA-b26842/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41b03e43-55dc-411f-90c4-fbbae61c132e/dqc_reference/reference_markers.hmm OceanDNA-b26842/protein.faa > /dev/null
[2023-03-16 23:35:32,668] [INFO] Task succeeded: HMMsearch
[2023-03-16 23:35:32,668] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge6f6398a-7ec1-4dc1-9efd-d7b7f6fe0280/OceanDNA-b26842.fa]
[2023-03-16 23:35:32,688] [INFO] Query marker FASTA was written to OceanDNA-b26842/markers.fasta
[2023-03-16 23:35:32,688] [INFO] Task started: Blastn
[2023-03-16 23:35:32,688] [INFO] Running command: blastn -query OceanDNA-b26842/markers.fasta -db /var/lib/cwl/stg41b03e43-55dc-411f-90c4-fbbae61c132e/dqc_reference/reference_markers.fasta -out OceanDNA-b26842/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:35:33,462] [INFO] Task succeeded: Blastn
[2023-03-16 23:35:33,462] [INFO] Selected 13 target genomes.
[2023-03-16 23:35:33,463] [INFO] Target genome list was writen to OceanDNA-b26842/target_genomes.txt
[2023-03-16 23:35:33,470] [INFO] Task started: fastANI
[2023-03-16 23:35:33,470] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f6398a-7ec1-4dc1-9efd-d7b7f6fe0280/OceanDNA-b26842.fa --refList OceanDNA-b26842/target_genomes.txt --output OceanDNA-b26842/fastani_result.tsv --threads 1
[2023-03-16 23:35:45,877] [INFO] Task succeeded: fastANI
[2023-03-16 23:35:45,877] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41b03e43-55dc-411f-90c4-fbbae61c132e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 23:35:45,877] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41b03e43-55dc-411f-90c4-fbbae61c132e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 23:35:45,886] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 23:35:45,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 23:35:45,887] [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 halophila	strain=KCTC 23107	GCA_900220985.1	714899	714899	type	True	84.978	746	878	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	82.4089	702	878	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	80.4107	566	878	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.163	497	878	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.141	435	878	95	below_threshold
Rhizobium ruizarguesonis	strain=UPM1133	GCA_012349115.1	2081791	2081791	type	True	77.3471	183	878	95	below_threshold
Shinella curvata	strain=C3	GCA_022899935.1	1817964	1817964	type	True	77.1794	216	878	95	below_threshold
Rhizobium pseudoryzae	strain=DSM 19479	GCA_011046245.1	379684	379684	type	True	77.1076	193	878	95	below_threshold
Rhizobium changzhiense	strain=WYCCWR 11279	GCA_013087625.1	2692317	2692317	type	True	77.0595	197	878	95	below_threshold
Rhizobium ecuadorense	strain=CNPSO 671	GCA_001187535.1	1671795	1671795	type	True	76.9821	199	878	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	76.8954	203	878	95	below_threshold
Rhizobium dioscoreae	strain=S-93	GCA_009176305.1	2653122	2653122	type	True	76.6419	168	878	95	below_threshold
Rhizobium skierniewicense	strain=Ch11	GCA_023757665.1	984260	984260	type	True	76.4862	115	878	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 23:35:45,887] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26842/tc_result.tsv
[2023-03-16 23:35:45,887] [INFO] ===== Taxonomy check completed =====
[2023-03-16 23:35:45,887] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 23:35:45,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41b03e43-55dc-411f-90c4-fbbae61c132e/dqc_reference/checkm_data
[2023-03-16 23:35:45,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 23:35:45,892] [INFO] Task started: CheckM
[2023-03-16 23:35:45,892] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26842/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26842/checkm_input OceanDNA-b26842/checkm_result
[2023-03-16 23:36:30,488] [INFO] Task succeeded: CheckM
[2023-03-16 23:36:30,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 23:36:30,491] [INFO] ===== Completeness check finished =====
[2023-03-16 23:36:30,491] [INFO] ===== Start GTDB Search =====
[2023-03-16 23:36:30,491] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26842/markers.fasta)
[2023-03-16 23:36:30,492] [INFO] Task started: Blastn
[2023-03-16 23:36:30,492] [INFO] Running command: blastn -query OceanDNA-b26842/markers.fasta -db /var/lib/cwl/stg41b03e43-55dc-411f-90c4-fbbae61c132e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26842/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 23:36:31,923] [INFO] Task succeeded: Blastn
[2023-03-16 23:36:31,924] [INFO] Selected 11 target genomes.
[2023-03-16 23:36:31,924] [INFO] Target genome list was writen to OceanDNA-b26842/target_genomes_gtdb.txt
[2023-03-16 23:36:32,118] [INFO] Task started: fastANI
[2023-03-16 23:36:32,118] [INFO] Running command: fastANI --query /var/lib/cwl/stge6f6398a-7ec1-4dc1-9efd-d7b7f6fe0280/OceanDNA-b26842.fa --refList OceanDNA-b26842/target_genomes_gtdb.txt --output OceanDNA-b26842/fastani_result_gtdb.tsv --threads 1
[2023-03-16 23:36:41,675] [INFO] Task succeeded: fastANI
[2023-03-16 23:36:41,682] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 23:36:41,682] [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_002733955.1	s__Hoeflea sp002733955	88.7114	817	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900220985.1	s__Hoeflea halophila	84.978	746	878	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	82.5951	463	878	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	82.4324	687	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCF_000759435.1	s__Hoeflea sp000759435	81.379	598	878	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	81.3055	605	878	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	81.2317	574	878	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	81.2025	402	878	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	81.0851	603	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_001703635.1	s__Hoeflea olei	80.4141	565	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154705.2	s__Hoeflea phototrophica	80.1376	500	878	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 23:36:41,682] [INFO] GTDB search result was written to OceanDNA-b26842/result_gtdb.tsv
[2023-03-16 23:36:41,682] [INFO] ===== GTDB Search completed =====
[2023-03-16 23:36:41,684] [INFO] DFAST_QC result json was written to OceanDNA-b26842/dqc_result.json
[2023-03-16 23:36:41,684] [INFO] DFAST_QC completed!
[2023-03-16 23:36:41,684] [INFO] Total running time: 0h1m27s