[2023-06-05 18:53:31,436] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:53:31,438] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:53:31,439] [INFO] DQC Reference Directory: /var/lib/cwl/stga78ed6a3-15a2-447f-8937-9e27780e9401/dqc_reference
[2023-06-05 18:53:33,399] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:53:33,400] [INFO] Task started: Prodigal
[2023-06-05 18:53:33,401] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd410f76-4f7d-43e3-a1a7-14ecc6a6d7aa/GCA_001628085.1_ASM162808v1_genomic.fna.gz | prodigal -d GCA_001628085.1_ASM162808v1_genomic.fna/cds.fna -a GCA_001628085.1_ASM162808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:53:44,161] [INFO] Task succeeded: Prodigal
[2023-06-05 18:53:44,161] [INFO] Task started: HMMsearch
[2023-06-05 18:53:44,161] [INFO] Running command: hmmsearch --tblout GCA_001628085.1_ASM162808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga78ed6a3-15a2-447f-8937-9e27780e9401/dqc_reference/reference_markers.hmm GCA_001628085.1_ASM162808v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:53:44,406] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:53:44,407] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcd410f76-4f7d-43e3-a1a7-14ecc6a6d7aa/GCA_001628085.1_ASM162808v1_genomic.fna.gz]
[2023-06-05 18:53:44,443] [INFO] Query marker FASTA was written to GCA_001628085.1_ASM162808v1_genomic.fna/markers.fasta
[2023-06-05 18:53:44,444] [INFO] Task started: Blastn
[2023-06-05 18:53:44,444] [INFO] Running command: blastn -query GCA_001628085.1_ASM162808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga78ed6a3-15a2-447f-8937-9e27780e9401/dqc_reference/reference_markers.fasta -out GCA_001628085.1_ASM162808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:53:45,096] [INFO] Task succeeded: Blastn
[2023-06-05 18:53:45,100] [INFO] Selected 11 target genomes.
[2023-06-05 18:53:45,101] [INFO] Target genome list was writen to GCA_001628085.1_ASM162808v1_genomic.fna/target_genomes.txt
[2023-06-05 18:53:45,103] [INFO] Task started: fastANI
[2023-06-05 18:53:45,103] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd410f76-4f7d-43e3-a1a7-14ecc6a6d7aa/GCA_001628085.1_ASM162808v1_genomic.fna.gz --refList GCA_001628085.1_ASM162808v1_genomic.fna/target_genomes.txt --output GCA_001628085.1_ASM162808v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:53:57,221] [INFO] Task succeeded: fastANI
[2023-06-05 18:53:57,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga78ed6a3-15a2-447f-8937-9e27780e9401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:53:57,222] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga78ed6a3-15a2-447f-8937-9e27780e9401/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:53:57,233] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-05 18:53:57,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-05 18:53:57,233] [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
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	96.9516	939	1116	95	conclusive
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	96.9445	932	1116	95	conclusive
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	96.8122	950	1116	95	conclusive
Sphingopyxis terrae subsp. terrae	strain=203-1	GCA_001610975.1	2448440	33052	type	True	95.7472	962	1116	95	conclusive
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	84.6686	762	1116	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	84.0618	751	1116	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.0761	358	1116	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	77.765	327	1116	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	77.5043	338	1116	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	77.3924	282	1116	95	below_threshold
Sphingomonas segetis	strain=YJ09	GCA_009720245.1	1104779	1104779	type	True	77.2659	179	1116	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:53:57,235] [INFO] DFAST Taxonomy check result was written to GCA_001628085.1_ASM162808v1_genomic.fna/tc_result.tsv
[2023-06-05 18:53:57,236] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:53:57,236] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:53:57,237] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga78ed6a3-15a2-447f-8937-9e27780e9401/dqc_reference/checkm_data
[2023-06-05 18:53:57,238] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:53:57,279] [INFO] Task started: CheckM
[2023-06-05 18:53:57,279] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001628085.1_ASM162808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001628085.1_ASM162808v1_genomic.fna/checkm_input GCA_001628085.1_ASM162808v1_genomic.fna/checkm_result
[2023-06-05 18:54:36,423] [INFO] Task succeeded: CheckM
[2023-06-05 18:54:36,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:54:36,515] [INFO] ===== Completeness check finished =====
[2023-06-05 18:54:36,516] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:54:36,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001628085.1_ASM162808v1_genomic.fna/markers.fasta)
[2023-06-05 18:54:36,516] [INFO] Task started: Blastn
[2023-06-05 18:54:36,516] [INFO] Running command: blastn -query GCA_001628085.1_ASM162808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga78ed6a3-15a2-447f-8937-9e27780e9401/dqc_reference/reference_markers_gtdb.fasta -out GCA_001628085.1_ASM162808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:54:39,464] [INFO] Task succeeded: Blastn
[2023-06-05 18:54:39,468] [INFO] Selected 11 target genomes.
[2023-06-05 18:54:39,468] [INFO] Target genome list was writen to GCA_001628085.1_ASM162808v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:54:39,484] [INFO] Task started: fastANI
[2023-06-05 18:54:39,484] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd410f76-4f7d-43e3-a1a7-14ecc6a6d7aa/GCA_001628085.1_ASM162808v1_genomic.fna.gz --refList GCA_001628085.1_ASM162808v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001628085.1_ASM162808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:55:00,824] [INFO] Task succeeded: fastANI
[2023-06-05 18:55:00,837] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:55:00,837] [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_001598815.1	s__Sphingopyxis terrae	96.8122	950	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.70	95.58	0.84	0.76	19	conclusive
GCF_000756385.1	s__Sphingopyxis sp000756385	84.747	787	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	84.6931	806	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018682675.1	s__Sphingopyxis soli	84.6821	761	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309275.1	s__Sphingopyxis sp017309275	84.6533	800	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468395.1	s__Sphingopyxis sp001468395	84.5785	797	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.27	97.10	0.97	0.89	9	-
GCF_002277025.1	s__Sphingopyxis sp002277025	84.4613	805	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	84.3484	802	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900188185.1	s__Sphingopyxis indica	84.0574	752	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	83.9749	795	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410105.1	s__Sphingopyxis sp013410105	83.6414	776	1116	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.44	99.44	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:55:00,839] [INFO] GTDB search result was written to GCA_001628085.1_ASM162808v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:55:00,840] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:55:00,844] [INFO] DFAST_QC result json was written to GCA_001628085.1_ASM162808v1_genomic.fna/dqc_result.json
[2023-06-05 18:55:00,844] [INFO] DFAST_QC completed!
[2023-06-05 18:55:00,844] [INFO] Total running time: 0h1m29s