[2024-01-24 14:54:49,530] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:49,532] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:49,532] [INFO] DQC Reference Directory: /var/lib/cwl/stga418f658-2acc-44e4-af54-e20347d83c67/dqc_reference
[2024-01-24 14:54:50,792] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:50,793] [INFO] Task started: Prodigal
[2024-01-24 14:54:50,793] [INFO] Running command: gunzip -c /var/lib/cwl/stga190182d-89c2-4ac7-90e8-fae7e56c5b9d/GCF_001698205.1_ASM169820v1_genomic.fna.gz | prodigal -d GCF_001698205.1_ASM169820v1_genomic.fna/cds.fna -a GCF_001698205.1_ASM169820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:54:59,620] [INFO] Task succeeded: Prodigal
[2024-01-24 14:54:59,620] [INFO] Task started: HMMsearch
[2024-01-24 14:54:59,621] [INFO] Running command: hmmsearch --tblout GCF_001698205.1_ASM169820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga418f658-2acc-44e4-af54-e20347d83c67/dqc_reference/reference_markers.hmm GCF_001698205.1_ASM169820v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:54:59,878] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:54:59,879] [INFO] Found 6/6 markers.
[2024-01-24 14:54:59,910] [INFO] Query marker FASTA was written to GCF_001698205.1_ASM169820v1_genomic.fna/markers.fasta
[2024-01-24 14:54:59,911] [INFO] Task started: Blastn
[2024-01-24 14:54:59,911] [INFO] Running command: blastn -query GCF_001698205.1_ASM169820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga418f658-2acc-44e4-af54-e20347d83c67/dqc_reference/reference_markers.fasta -out GCF_001698205.1_ASM169820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:00,916] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:00,919] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:00,919] [INFO] Target genome list was writen to GCF_001698205.1_ASM169820v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:00,946] [INFO] Task started: fastANI
[2024-01-24 14:55:00,946] [INFO] Running command: fastANI --query /var/lib/cwl/stga190182d-89c2-4ac7-90e8-fae7e56c5b9d/GCF_001698205.1_ASM169820v1_genomic.fna.gz --refList GCF_001698205.1_ASM169820v1_genomic.fna/target_genomes.txt --output GCF_001698205.1_ASM169820v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:09,749] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:09,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga418f658-2acc-44e4-af54-e20347d83c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:09,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga418f658-2acc-44e4-af54-e20347d83c67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:09,774] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:09,775] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:09,775] [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
Tsuneonella troitsensis	strain=JCM 17037	GCA_001441535.1	292222	292222	type	True	82.3617	611	1003	95	below_threshold
Tsuneonella troitsensis	strain=KMM 6042	GCA_003730315.1	292222	292222	type	True	82.3555	619	1003	95	below_threshold
Tsuneonella amylolytica	strain=NS1	GCA_003626915.1	2338327	2338327	type	True	82.0262	607	1003	95	below_threshold
Tsuneonella rigui	strain=KCTC 42620	GCA_003958625.1	1708790	1708790	type	True	81.6515	591	1003	95	below_threshold
Tsuneonella deserti	strain=CGMCC 1.15959	GCA_014644315.1	2035528	2035528	type	True	80.5848	504	1003	95	below_threshold
Tsuneonella aeria	strain=100921-2	GCA_009827495.1	1837929	1837929	type	True	80.2547	483	1003	95	below_threshold
Pelagerythrobacter aerophilus	strain=Ery1	GCA_003581645.1	2306995	2306995	type	True	80.1678	450	1003	95	below_threshold
Qipengyuania proteolytica	strain=6B39	GCA_019711565.1	2867239	2867239	type	True	80.028	433	1003	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	79.8921	470	1003	95	below_threshold
Pelagerythrobacter marinus	strain=H32	GCA_009827515.1	538382	538382	type	True	79.7154	488	1003	95	below_threshold
Qipengyuania pelagi	strain=JCM 17468	GCA_009827295.1	994320	994320	type	True	78.9815	360	1003	95	below_threshold
Novosphingobium flavum	strain=NBRC 111647	GCA_014230315.1	1778672	1778672	type	True	78.9411	359	1003	95	below_threshold
Qipengyuania nanhaisediminis	strain=CGMCC 1.7715	GCA_900115585.1	604088	604088	type	True	78.8603	344	1003	95	below_threshold
Qipengyuania qiaonensis	strain=6D47A	GCA_019711515.1	2867240	2867240	type	True	78.8551	330	1003	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	78.41	271	1003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:09,777] [INFO] DFAST Taxonomy check result was written to GCF_001698205.1_ASM169820v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:09,778] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:09,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:09,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga418f658-2acc-44e4-af54-e20347d83c67/dqc_reference/checkm_data
[2024-01-24 14:55:09,780] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:09,814] [INFO] Task started: CheckM
[2024-01-24 14:55:09,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001698205.1_ASM169820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001698205.1_ASM169820v1_genomic.fna/checkm_input GCF_001698205.1_ASM169820v1_genomic.fna/checkm_result
[2024-01-24 14:55:39,593] [INFO] Task succeeded: CheckM
[2024-01-24 14:55:39,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:55:39,613] [INFO] ===== Completeness check finished =====
[2024-01-24 14:55:39,614] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:55:39,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001698205.1_ASM169820v1_genomic.fna/markers.fasta)
[2024-01-24 14:55:39,615] [INFO] Task started: Blastn
[2024-01-24 14:55:39,615] [INFO] Running command: blastn -query GCF_001698205.1_ASM169820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga418f658-2acc-44e4-af54-e20347d83c67/dqc_reference/reference_markers_gtdb.fasta -out GCF_001698205.1_ASM169820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:41,513] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:41,520] [INFO] Selected 15 target genomes.
[2024-01-24 14:55:41,520] [INFO] Target genome list was writen to GCF_001698205.1_ASM169820v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:55:41,537] [INFO] Task started: fastANI
[2024-01-24 14:55:41,537] [INFO] Running command: fastANI --query /var/lib/cwl/stga190182d-89c2-4ac7-90e8-fae7e56c5b9d/GCF_001698205.1_ASM169820v1_genomic.fna.gz --refList GCF_001698205.1_ASM169820v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001698205.1_ASM169820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:55:51,066] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:51,083] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:55:51,084] [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_001698205.1	s__Tsuneonella dongtanensis	100.0	1003	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001441535.1	s__Tsuneonella troitsensis	82.3617	611	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003626915.1	s__Tsuneonella amylolytica	82.0262	607	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003958625.1	s__Tsuneonella rigui	81.6632	590	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644315.1	s__Tsuneonella deserti	80.5972	503	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007065885.1	s__Tsuneonella sp007065885	80.4738	488	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009827495.1	s__Tsuneonella aeria	80.2674	482	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016803135.1	s__Pelagerythrobacter sp016803135	80.1779	477	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002269345.1	s__Tsuneonella mangrovi	80.1587	469	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Tsuneonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135625.1	s__Pelagerythrobacter rhizovicinus	79.8805	471	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Pelagerythrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763545.1	s__JACXVD01 sp014763545	79.3427	426	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__JACXVD01	95.0	99.92	99.92	0.96	0.96	2	-
GCA_016793865.1	s__Qipengyuania sp016793865	79.1345	379	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828205.1	s__Qipengyuania sp018828205	79.0018	309	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014230315.1	s__Novosphingobium flavum	78.9411	359	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678665.1	s__Qipengyuania sp001678665	78.7448	378	1003	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Qipengyuania	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:55:51,086] [INFO] GTDB search result was written to GCF_001698205.1_ASM169820v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:55:51,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:55:51,090] [INFO] DFAST_QC result json was written to GCF_001698205.1_ASM169820v1_genomic.fna/dqc_result.json
[2024-01-24 14:55:51,090] [INFO] DFAST_QC completed!
[2024-01-24 14:55:51,090] [INFO] Total running time: 0h1m2s