[2024-01-24 13:40:44,022] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,024] [INFO] DQC Reference Directory: /var/lib/cwl/stg81e14b91-158e-4b2f-8930-b686a3f0042a/dqc_reference
[2024-01-24 13:40:45,480] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,481] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,481] [INFO] Running command: gunzip -c /var/lib/cwl/stg15ea6eaf-178a-46ce-af50-a3e8711a604b/GCF_001598455.1_ASM159845v1_genomic.fna.gz | prodigal -d GCF_001598455.1_ASM159845v1_genomic.fna/cds.fna -a GCF_001598455.1_ASM159845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:58,143] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:58,144] [INFO] Task started: HMMsearch
[2024-01-24 13:40:58,144] [INFO] Running command: hmmsearch --tblout GCF_001598455.1_ASM159845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81e14b91-158e-4b2f-8930-b686a3f0042a/dqc_reference/reference_markers.hmm GCF_001598455.1_ASM159845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:58,442] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:58,444] [INFO] Found 6/6 markers.
[2024-01-24 13:40:58,493] [INFO] Query marker FASTA was written to GCF_001598455.1_ASM159845v1_genomic.fna/markers.fasta
[2024-01-24 13:40:58,494] [INFO] Task started: Blastn
[2024-01-24 13:40:58,494] [INFO] Running command: blastn -query GCF_001598455.1_ASM159845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81e14b91-158e-4b2f-8930-b686a3f0042a/dqc_reference/reference_markers.fasta -out GCF_001598455.1_ASM159845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:59,489] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:59,493] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:59,493] [INFO] Target genome list was writen to GCF_001598455.1_ASM159845v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:59,501] [INFO] Task started: fastANI
[2024-01-24 13:40:59,502] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ea6eaf-178a-46ce-af50-a3e8711a604b/GCF_001598455.1_ASM159845v1_genomic.fna.gz --refList GCF_001598455.1_ASM159845v1_genomic.fna/target_genomes.txt --output GCF_001598455.1_ASM159845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:14,422] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:14,423] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81e14b91-158e-4b2f-8930-b686a3f0042a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:14,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81e14b91-158e-4b2f-8930-b686a3f0042a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:14,438] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:14,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:14,438] [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 pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	100.0	1409	1414	95	conclusive
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	89.1344	1144	1414	95	below_threshold
Sphingomonas asaccharolytica	strain=NBRC 15499	GCA_001598355.1	40681	40681	type	True	88.499	1021	1414	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	81.92	727	1414	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	79.6121	592	1414	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.6106	593	1414	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	79.6086	577	1414	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.516	554	1414	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.3446	599	1414	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.3313	519	1414	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.2515	457	1414	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.1926	555	1414	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.188	486	1414	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.1753	535	1414	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.0936	508	1414	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.5763	464	1414	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:14,440] [INFO] DFAST Taxonomy check result was written to GCF_001598455.1_ASM159845v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:14,440] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:14,440] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:14,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81e14b91-158e-4b2f-8930-b686a3f0042a/dqc_reference/checkm_data
[2024-01-24 13:41:14,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:14,486] [INFO] Task started: CheckM
[2024-01-24 13:41:14,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001598455.1_ASM159845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001598455.1_ASM159845v1_genomic.fna/checkm_input GCF_001598455.1_ASM159845v1_genomic.fna/checkm_result
[2024-01-24 13:41:54,581] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:54,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:54,600] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:54,600] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:54,601] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001598455.1_ASM159845v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:54,601] [INFO] Task started: Blastn
[2024-01-24 13:41:54,601] [INFO] Running command: blastn -query GCF_001598455.1_ASM159845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg81e14b91-158e-4b2f-8930-b686a3f0042a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001598455.1_ASM159845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:56,406] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:56,410] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:56,410] [INFO] Target genome list was writen to GCF_001598455.1_ASM159845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:56,419] [INFO] Task started: fastANI
[2024-01-24 13:41:56,419] [INFO] Running command: fastANI --query /var/lib/cwl/stg15ea6eaf-178a-46ce-af50-a3e8711a604b/GCF_001598455.1_ASM159845v1_genomic.fna.gz --refList GCF_001598455.1_ASM159845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001598455.1_ASM159845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:06,986] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:07,000] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:07,000] [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_001598455.1	s__Sphingomonas pruni	100.0	1409	1414	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_001598415.1	s__Sphingomonas mali	89.1567	1142	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598355.1	s__Sphingomonas asaccharolytica	88.4776	1022	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859635.1	s__Sphingomonas panacisoli	81.9103	728	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004799495.1	s__Sphingomonas sp004799495	81.9046	680	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	81.5722	655	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304615.1	s__Sphingomonas sp017304615	81.4683	671	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	79.6099	592	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018449795.1	s__Sphingomonas sp018449795	79.4842	571	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	79.413	590	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.3686	494	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_014641735.1	s__Sphingomonas metalli	79.2665	456	1414	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:07,002] [INFO] GTDB search result was written to GCF_001598455.1_ASM159845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:07,002] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:07,006] [INFO] DFAST_QC result json was written to GCF_001598455.1_ASM159845v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:07,007] [INFO] DFAST_QC completed!
[2024-01-24 13:42:07,007] [INFO] Total running time: 0h1m23s