[2024-01-24 13:28:39,952] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:39,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:39,954] [INFO] DQC Reference Directory: /var/lib/cwl/stg4843a80d-8d62-4550-aade-17503eb3345f/dqc_reference
[2024-01-24 13:28:41,213] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:41,214] [INFO] Task started: Prodigal
[2024-01-24 13:28:41,215] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b202492-1c3d-494a-9aa3-0a8c2861f47e/GCF_014196745.1_ASM1419674v1_genomic.fna.gz | prodigal -d GCF_014196745.1_ASM1419674v1_genomic.fna/cds.fna -a GCF_014196745.1_ASM1419674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:57,635] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:57,635] [INFO] Task started: HMMsearch
[2024-01-24 13:28:57,636] [INFO] Running command: hmmsearch --tblout GCF_014196745.1_ASM1419674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4843a80d-8d62-4550-aade-17503eb3345f/dqc_reference/reference_markers.hmm GCF_014196745.1_ASM1419674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:57,918] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:57,920] [INFO] Found 6/6 markers.
[2024-01-24 13:28:57,965] [INFO] Query marker FASTA was written to GCF_014196745.1_ASM1419674v1_genomic.fna/markers.fasta
[2024-01-24 13:28:57,965] [INFO] Task started: Blastn
[2024-01-24 13:28:57,965] [INFO] Running command: blastn -query GCF_014196745.1_ASM1419674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4843a80d-8d62-4550-aade-17503eb3345f/dqc_reference/reference_markers.fasta -out GCF_014196745.1_ASM1419674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:58,984] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:58,987] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:58,988] [INFO] Target genome list was writen to GCF_014196745.1_ASM1419674v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:59,004] [INFO] Task started: fastANI
[2024-01-24 13:28:59,004] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b202492-1c3d-494a-9aa3-0a8c2861f47e/GCF_014196745.1_ASM1419674v1_genomic.fna.gz --refList GCF_014196745.1_ASM1419674v1_genomic.fna/target_genomes.txt --output GCF_014196745.1_ASM1419674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:29:14,632] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:14,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4843a80d-8d62-4550-aade-17503eb3345f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:29:14,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4843a80d-8d62-4550-aade-17503eb3345f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:29:14,646] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:29:14,646] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:29:14,646] [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 kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	100.0	1834	1834	95	conclusive
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	87.7839	1134	1834	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	82.901	943	1834	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	82.8475	946	1834	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	82.2762	819	1834	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	81.8741	828	1834	95	below_threshold
Sphingomonas pokkalii	strain=L3B27	GCA_003096275.1	2175090	2175090	type	True	81.563	715	1834	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	81.4944	919	1834	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	81.2158	717	1834	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	81.1459	840	1834	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	80.5345	668	1834	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.6408	612	1834	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.3952	641	1834	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.3672	662	1834	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.1028	555	1834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:29:14,648] [INFO] DFAST Taxonomy check result was written to GCF_014196745.1_ASM1419674v1_genomic.fna/tc_result.tsv
[2024-01-24 13:29:14,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:29:14,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:29:14,650] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4843a80d-8d62-4550-aade-17503eb3345f/dqc_reference/checkm_data
[2024-01-24 13:29:14,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:29:14,706] [INFO] Task started: CheckM
[2024-01-24 13:29:14,706] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014196745.1_ASM1419674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014196745.1_ASM1419674v1_genomic.fna/checkm_input GCF_014196745.1_ASM1419674v1_genomic.fna/checkm_result
[2024-01-24 13:30:04,219] [INFO] Task succeeded: CheckM
[2024-01-24 13:30:04,221] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:30:04,238] [INFO] ===== Completeness check finished =====
[2024-01-24 13:30:04,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:30:04,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014196745.1_ASM1419674v1_genomic.fna/markers.fasta)
[2024-01-24 13:30:04,239] [INFO] Task started: Blastn
[2024-01-24 13:30:04,240] [INFO] Running command: blastn -query GCF_014196745.1_ASM1419674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4843a80d-8d62-4550-aade-17503eb3345f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014196745.1_ASM1419674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:06,288] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:06,292] [INFO] Selected 8 target genomes.
[2024-01-24 13:30:06,293] [INFO] Target genome list was writen to GCF_014196745.1_ASM1419674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:30:06,301] [INFO] Task started: fastANI
[2024-01-24 13:30:06,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b202492-1c3d-494a-9aa3-0a8c2861f47e/GCF_014196745.1_ASM1419674v1_genomic.fna.gz --refList GCF_014196745.1_ASM1419674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014196745.1_ASM1419674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:30:16,690] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:16,705] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:30:16,706] [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_014196745.1	s__Sphingomonas kyeonggiensis	100.0	1834	1834	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_014204495.1	s__Sphingomonas kyeonggiensis_A	89.5786	1328	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096895.1	s__Sphingomonas sp003096895	88.475	1191	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	87.8734	1126	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	87.8471	1107	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	87.7819	1134	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCF_013416555.1	s__Sphingomonas sp013416555	87.6745	1131	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005503355.1	s__Sphingomonas sp005503355	87.44	1138	1834	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:30:16,708] [INFO] GTDB search result was written to GCF_014196745.1_ASM1419674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:30:16,708] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:30:16,713] [INFO] DFAST_QC result json was written to GCF_014196745.1_ASM1419674v1_genomic.fna/dqc_result.json
[2024-01-24 13:30:16,713] [INFO] DFAST_QC completed!
[2024-01-24 13:30:16,714] [INFO] Total running time: 0h1m37s