[2023-03-18 00:02:09,193] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:02:09,193] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:02:09,193] [INFO] DQC Reference Directory: /var/lib/cwl/stg200c65c5-bdde-4413-b420-62008363a186/dqc_reference
[2023-03-18 00:02:10,347] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:02:10,347] [INFO] Task started: Prodigal
[2023-03-18 00:02:10,348] [INFO] Running command: cat /var/lib/cwl/stg4533eed5-3113-433f-819e-db21778f4cf8/OceanDNA-b26844.fa | prodigal -d OceanDNA-b26844/cds.fna -a OceanDNA-b26844/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:02:41,159] [INFO] Task succeeded: Prodigal
[2023-03-18 00:02:41,159] [INFO] Task started: HMMsearch
[2023-03-18 00:02:41,160] [INFO] Running command: hmmsearch --tblout OceanDNA-b26844/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg200c65c5-bdde-4413-b420-62008363a186/dqc_reference/reference_markers.hmm OceanDNA-b26844/protein.faa > /dev/null
[2023-03-18 00:02:41,379] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:02:41,380] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4533eed5-3113-433f-819e-db21778f4cf8/OceanDNA-b26844.fa]
[2023-03-18 00:02:41,407] [INFO] Query marker FASTA was written to OceanDNA-b26844/markers.fasta
[2023-03-18 00:02:41,408] [INFO] Task started: Blastn
[2023-03-18 00:02:41,408] [INFO] Running command: blastn -query OceanDNA-b26844/markers.fasta -db /var/lib/cwl/stg200c65c5-bdde-4413-b420-62008363a186/dqc_reference/reference_markers.fasta -out OceanDNA-b26844/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:02:42,196] [INFO] Task succeeded: Blastn
[2023-03-18 00:02:42,197] [INFO] Selected 13 target genomes.
[2023-03-18 00:02:42,197] [INFO] Target genome list was writen to OceanDNA-b26844/target_genomes.txt
[2023-03-18 00:02:42,206] [INFO] Task started: fastANI
[2023-03-18 00:02:42,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg4533eed5-3113-433f-819e-db21778f4cf8/OceanDNA-b26844.fa --refList OceanDNA-b26844/target_genomes.txt --output OceanDNA-b26844/fastani_result.tsv --threads 1
[2023-03-18 00:02:54,775] [INFO] Task succeeded: fastANI
[2023-03-18 00:02:54,775] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg200c65c5-bdde-4413-b420-62008363a186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:02:54,776] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg200c65c5-bdde-4413-b420-62008363a186/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:02:54,784] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:02:54,784] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:02:54,784] [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	82.9391	967	1563	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	81.987	974	1563	95	below_threshold
Hoeflea olei	strain=JC234	GCA_001703635.1	1480615	1480615	type	True	80.659	812	1563	95	below_threshold
Hoeflea phototrophica	strain=DFL-43	GCA_000154705.2	244596	244596	type	True	80.1192	720	1563	95	below_threshold
Hoeflea marina	strain=DSM 16791	GCA_003182275.1	274592	274592	type	True	79.2169	621	1563	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.5057	324	1563	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	77.4143	342	1563	95	below_threshold
Shinella yambaruensis	strain=DSM 18801	GCA_022899355.1	415996	415996	type	True	77.3315	370	1563	95	below_threshold
Shinella sumterensis	strain=MEC087	GCA_004514425.2	1967501	1967501	type	True	77.3305	337	1563	95	below_threshold
Neorhizobium vignae	strain=CCBAU 05176	GCA_000732195.1	690585	690585	type	True	77.1671	320	1563	95	below_threshold
Rhizobium rhizophilum	strain=7209-2	GCA_004912145.1	1850373	1850373	type	True	77.0259	291	1563	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	76.2293	141	1563	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.8206	155	1563	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:02:54,785] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26844/tc_result.tsv
[2023-03-18 00:02:54,785] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:02:54,785] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:02:54,785] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg200c65c5-bdde-4413-b420-62008363a186/dqc_reference/checkm_data
[2023-03-18 00:02:54,786] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:02:54,811] [INFO] Task started: CheckM
[2023-03-18 00:02:54,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26844/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26844/checkm_input OceanDNA-b26844/checkm_result
[2023-03-18 00:04:11,910] [INFO] Task succeeded: CheckM
[2023-03-18 00:04:11,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:04:11,913] [INFO] ===== Completeness check finished =====
[2023-03-18 00:04:11,913] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:04:11,913] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26844/markers.fasta)
[2023-03-18 00:04:11,915] [INFO] Task started: Blastn
[2023-03-18 00:04:11,915] [INFO] Running command: blastn -query OceanDNA-b26844/markers.fasta -db /var/lib/cwl/stg200c65c5-bdde-4413-b420-62008363a186/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26844/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:04:13,488] [INFO] Task succeeded: Blastn
[2023-03-18 00:04:13,489] [INFO] Selected 12 target genomes.
[2023-03-18 00:04:13,489] [INFO] Target genome list was writen to OceanDNA-b26844/target_genomes_gtdb.txt
[2023-03-18 00:04:13,527] [INFO] Task started: fastANI
[2023-03-18 00:04:13,527] [INFO] Running command: fastANI --query /var/lib/cwl/stg4533eed5-3113-433f-819e-db21778f4cf8/OceanDNA-b26844.fa --refList OceanDNA-b26844/target_genomes_gtdb.txt --output OceanDNA-b26844/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:04:25,619] [INFO] Task succeeded: fastANI
[2023-03-18 00:04:25,627] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:04:25,627] [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	84.6487	1087	1563	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	82.9369	967	1563	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	82.4297	595	1563	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	82.1756	953	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	97.67	97.67	0.92	0.92	2	-
GCA_014359905.1	s__Hoeflea sp014359905	81.34	878	1563	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	81.3379	866	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	100.00	100.00	0.99	0.99	6	-
GCF_000759435.1	s__Hoeflea sp000759435	81.3154	844	1563	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	81.3058	575	1563	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	81.2887	895	1563	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	80.1147	721	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017877055.1	s__Neorhizobium galegae_D	77.1375	301	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Neorhizobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630065.1	s__Blastochloris sulfoviridis	76.2293	141	1563	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Blastochloris	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:04:25,628] [INFO] GTDB search result was written to OceanDNA-b26844/result_gtdb.tsv
[2023-03-18 00:04:25,628] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:04:25,629] [INFO] DFAST_QC result json was written to OceanDNA-b26844/dqc_result.json
[2023-03-18 00:04:25,630] [INFO] DFAST_QC completed!
[2023-03-18 00:04:25,630] [INFO] Total running time: 0h2m16s