[2024-01-25 20:07:20,251] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:20,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:20,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg71608fca-eb66-4cfe-aaaf-bd1593f49e70/dqc_reference
[2024-01-25 20:07:21,388] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:21,389] [INFO] Task started: Prodigal
[2024-01-25 20:07:21,389] [INFO] Running command: gunzip -c /var/lib/cwl/stg4f9dd28e-7b60-480e-be16-5ed4df2b9949/GCF_003053745.1_ASM305374v1_genomic.fna.gz | prodigal -d GCF_003053745.1_ASM305374v1_genomic.fna/cds.fna -a GCF_003053745.1_ASM305374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:32,389] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:32,390] [INFO] Task started: HMMsearch
[2024-01-25 20:07:32,390] [INFO] Running command: hmmsearch --tblout GCF_003053745.1_ASM305374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71608fca-eb66-4cfe-aaaf-bd1593f49e70/dqc_reference/reference_markers.hmm GCF_003053745.1_ASM305374v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:32,606] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:32,608] [INFO] Found 6/6 markers.
[2024-01-25 20:07:32,644] [INFO] Query marker FASTA was written to GCF_003053745.1_ASM305374v1_genomic.fna/markers.fasta
[2024-01-25 20:07:32,645] [INFO] Task started: Blastn
[2024-01-25 20:07:32,645] [INFO] Running command: blastn -query GCF_003053745.1_ASM305374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71608fca-eb66-4cfe-aaaf-bd1593f49e70/dqc_reference/reference_markers.fasta -out GCF_003053745.1_ASM305374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:33,582] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:33,587] [INFO] Selected 11 target genomes.
[2024-01-25 20:07:33,588] [INFO] Target genome list was writen to GCF_003053745.1_ASM305374v1_genomic.fna/target_genomes.txt
[2024-01-25 20:07:33,600] [INFO] Task started: fastANI
[2024-01-25 20:07:33,600] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f9dd28e-7b60-480e-be16-5ed4df2b9949/GCF_003053745.1_ASM305374v1_genomic.fna.gz --refList GCF_003053745.1_ASM305374v1_genomic.fna/target_genomes.txt --output GCF_003053745.1_ASM305374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:45,288] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:45,288] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71608fca-eb66-4cfe-aaaf-bd1593f49e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:45,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71608fca-eb66-4cfe-aaaf-bd1593f49e70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:45,296] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:45,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:45,297] [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 faeni	strain=MA-olki	GCA_003053745.1	185950	185950	type	True	100.0	1441	1441	95	conclusive
Sphingomonas albertensis	strain=DOAB 1063	GCA_014358075.1	2762591	2762591	type	True	88.9658	912	1441	95	below_threshold
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	87.4092	998	1441	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	84.3016	840	1441	95	below_threshold
Sphingomonas ginsenosidivorax	strain=KHI67	GCA_007995065.1	862135	862135	type	True	83.4836	814	1441	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	80.739	726	1441	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.3573	634	1441	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.2674	624	1441	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.2384	644	1441	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.1789	542	1441	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.8992	512	1441	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:45,298] [INFO] DFAST Taxonomy check result was written to GCF_003053745.1_ASM305374v1_genomic.fna/tc_result.tsv
[2024-01-25 20:07:45,298] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:45,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:45,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71608fca-eb66-4cfe-aaaf-bd1593f49e70/dqc_reference/checkm_data
[2024-01-25 20:07:45,299] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:45,341] [INFO] Task started: CheckM
[2024-01-25 20:07:45,342] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003053745.1_ASM305374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003053745.1_ASM305374v1_genomic.fna/checkm_input GCF_003053745.1_ASM305374v1_genomic.fna/checkm_result
[2024-01-25 20:08:18,516] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:18,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:18,538] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:18,538] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:18,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003053745.1_ASM305374v1_genomic.fna/markers.fasta)
[2024-01-25 20:08:18,540] [INFO] Task started: Blastn
[2024-01-25 20:08:18,540] [INFO] Running command: blastn -query GCF_003053745.1_ASM305374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg71608fca-eb66-4cfe-aaaf-bd1593f49e70/dqc_reference/reference_markers_gtdb.fasta -out GCF_003053745.1_ASM305374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:20,430] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:20,433] [INFO] Selected 15 target genomes.
[2024-01-25 20:08:20,433] [INFO] Target genome list was writen to GCF_003053745.1_ASM305374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:20,997] [INFO] Task started: fastANI
[2024-01-25 20:08:20,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg4f9dd28e-7b60-480e-be16-5ed4df2b9949/GCF_003053745.1_ASM305374v1_genomic.fna.gz --refList GCF_003053745.1_ASM305374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003053745.1_ASM305374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:39,459] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:39,469] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:39,469] [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_003053745.1	s__Sphingomonas faeni	100.0	1441	1441	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_003610375.1	s__Sphingomonas sp003610375	93.7556	1192	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_004340965.1	s__Sphingomonas sp004340965	93.6657	1221	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421745.1	s__Sphingomonas sp001421745	93.5886	1175	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795835.1	s__Sphingomonas sp004795835	93.4928	1158	1441	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	93.2849	1140	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050745.1	s__Sphingomonas sp003050745	90.9413	990	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.19	95.12	0.89	0.88	3	-
GCF_900115295.1	s__Sphingomonas sp900115295	90.1825	1069	1441	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	89.6222	992	1441	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	89.5701	970	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341085.1	s__Sphingomonas sp004341085	89.5566	1004	1441	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	89.4803	982	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688625.1	s__Sphingomonas sp003688625	89.4761	958	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004340945.1	s__Sphingomonas sp004340945	89.202	978	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.25	95.25	0.84	0.84	2	-
GCF_014358075.1	s__Sphingomonas albertensis	88.9661	912	1441	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:39,471] [INFO] GTDB search result was written to GCF_003053745.1_ASM305374v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:39,471] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:39,474] [INFO] DFAST_QC result json was written to GCF_003053745.1_ASM305374v1_genomic.fna/dqc_result.json
[2024-01-25 20:08:39,474] [INFO] DFAST_QC completed!
[2024-01-25 20:08:39,474] [INFO] Total running time: 0h1m19s