[2024-01-24 14:31:14,763] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,766] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,767] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b9553bb-481d-4f4b-a3fd-f080f8aeb9ee/dqc_reference
[2024-01-24 14:31:16,198] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,199] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,199] [INFO] Running command: gunzip -c /var/lib/cwl/stgefc89c40-22e7-400e-9602-6045b5ad8521/GCF_007995065.1_ASM799506v1_genomic.fna.gz | prodigal -d GCF_007995065.1_ASM799506v1_genomic.fna/cds.fna -a GCF_007995065.1_ASM799506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:28,722] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:28,723] [INFO] Task started: HMMsearch
[2024-01-24 14:31:28,723] [INFO] Running command: hmmsearch --tblout GCF_007995065.1_ASM799506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b9553bb-481d-4f4b-a3fd-f080f8aeb9ee/dqc_reference/reference_markers.hmm GCF_007995065.1_ASM799506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:29,039] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:29,040] [INFO] Found 6/6 markers.
[2024-01-24 14:31:29,089] [INFO] Query marker FASTA was written to GCF_007995065.1_ASM799506v1_genomic.fna/markers.fasta
[2024-01-24 14:31:29,089] [INFO] Task started: Blastn
[2024-01-24 14:31:29,089] [INFO] Running command: blastn -query GCF_007995065.1_ASM799506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b9553bb-481d-4f4b-a3fd-f080f8aeb9ee/dqc_reference/reference_markers.fasta -out GCF_007995065.1_ASM799506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:30,203] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:30,207] [INFO] Selected 11 target genomes.
[2024-01-24 14:31:30,207] [INFO] Target genome list was writen to GCF_007995065.1_ASM799506v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:30,212] [INFO] Task started: fastANI
[2024-01-24 14:31:30,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc89c40-22e7-400e-9602-6045b5ad8521/GCF_007995065.1_ASM799506v1_genomic.fna.gz --refList GCF_007995065.1_ASM799506v1_genomic.fna/target_genomes.txt --output GCF_007995065.1_ASM799506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:43,309] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:43,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b9553bb-481d-4f4b-a3fd-f080f8aeb9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:43,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b9553bb-481d-4f4b-a3fd-f080f8aeb9ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:43,321] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:31:43,321] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:43,321] [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
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	100.0	1371	1377	95	conclusive
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	84.3553	821	1377	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	84.0952	768	1377	95	below_threshold
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	83.7432	742	1377	95	below_threshold
Sphingomonas faeni	strain=MA-olki	GCA_003053745.1	185950	185950	type	True	83.6705	815	1377	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	81.9557	737	1377	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.9997	639	1377	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.4558	651	1377	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.2106	668	1377	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.8243	557	1377	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.7472	585	1377	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:43,323] [INFO] DFAST Taxonomy check result was written to GCF_007995065.1_ASM799506v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:43,323] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:43,324] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:43,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b9553bb-481d-4f4b-a3fd-f080f8aeb9ee/dqc_reference/checkm_data
[2024-01-24 14:31:43,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:43,374] [INFO] Task started: CheckM
[2024-01-24 14:31:43,374] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007995065.1_ASM799506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007995065.1_ASM799506v1_genomic.fna/checkm_input GCF_007995065.1_ASM799506v1_genomic.fna/checkm_result
[2024-01-24 14:32:22,797] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:22,798] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:22,817] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:22,817] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:22,818] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007995065.1_ASM799506v1_genomic.fna/markers.fasta)
[2024-01-24 14:32:22,818] [INFO] Task started: Blastn
[2024-01-24 14:32:22,819] [INFO] Running command: blastn -query GCF_007995065.1_ASM799506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b9553bb-481d-4f4b-a3fd-f080f8aeb9ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_007995065.1_ASM799506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:24,859] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:24,865] [INFO] Selected 13 target genomes.
[2024-01-24 14:32:24,865] [INFO] Target genome list was writen to GCF_007995065.1_ASM799506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:24,879] [INFO] Task started: fastANI
[2024-01-24 14:32:24,879] [INFO] Running command: fastANI --query /var/lib/cwl/stgefc89c40-22e7-400e-9602-6045b5ad8521/GCF_007995065.1_ASM799506v1_genomic.fna.gz --refList GCF_007995065.1_ASM799506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007995065.1_ASM799506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:39,226] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:39,242] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:39,242] [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_007995065.1	s__Sphingomonas ginsenosidivorax	100.0	1372	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003050705.1	s__Sphingomonas aurantiaca	84.3317	824	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.29	95.02	0.87	0.86	4	-
GCF_001421805.1	s__Sphingomonas sp001421805	84.1678	786	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.24	98.24	0.93	0.93	2	-
GCF_003046295.1	s__Sphingomonas aerolata	84.0953	768	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.52	96.36	0.90	0.73	15	-
GCF_001421535.1	s__Sphingomonas sp001421535	83.9735	780	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013374115.1	s__Sphingomonas sp013374115	83.9144	762	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424005.1	s__Sphingomonas sp001424005	83.8958	785	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688595.1	s__Sphingomonas sp003688595	83.8607	765	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004101245.1	s__Sphingomonas sp004101245	83.8222	795	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421415.1	s__Sphingomonas sp001421415	83.7348	791	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014358075.1	s__Sphingomonas albertensis	83.7224	744	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001422045.1	s__Sphingomonas sp001422045	83.6901	769	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	81.9769	736	1377	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:39,251] [INFO] GTDB search result was written to GCF_007995065.1_ASM799506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:39,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:39,255] [INFO] DFAST_QC result json was written to GCF_007995065.1_ASM799506v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:39,255] [INFO] DFAST_QC completed!
[2024-01-24 14:32:39,255] [INFO] Total running time: 0h1m24s