[2024-01-24 14:07:14,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:14,792] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:14,792] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f1d965d-46a0-4d82-a607-050251045f19/dqc_reference
[2024-01-24 14:07:16,077] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:16,078] [INFO] Task started: Prodigal
[2024-01-24 14:07:16,078] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fb03cde-fd35-4928-b44e-c8d68ee8d0c6/GCF_002197685.1_ASM219768v1_genomic.fna.gz | prodigal -d GCF_002197685.1_ASM219768v1_genomic.fna/cds.fna -a GCF_002197685.1_ASM219768v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:26,679] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:26,679] [INFO] Task started: HMMsearch
[2024-01-24 14:07:26,680] [INFO] Running command: hmmsearch --tblout GCF_002197685.1_ASM219768v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f1d965d-46a0-4d82-a607-050251045f19/dqc_reference/reference_markers.hmm GCF_002197685.1_ASM219768v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:26,948] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:26,949] [INFO] Found 6/6 markers.
[2024-01-24 14:07:26,988] [INFO] Query marker FASTA was written to GCF_002197685.1_ASM219768v1_genomic.fna/markers.fasta
[2024-01-24 14:07:26,988] [INFO] Task started: Blastn
[2024-01-24 14:07:26,988] [INFO] Running command: blastn -query GCF_002197685.1_ASM219768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f1d965d-46a0-4d82-a607-050251045f19/dqc_reference/reference_markers.fasta -out GCF_002197685.1_ASM219768v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:28,106] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:28,110] [INFO] Selected 13 target genomes.
[2024-01-24 14:07:28,111] [INFO] Target genome list was writen to GCF_002197685.1_ASM219768v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:28,116] [INFO] Task started: fastANI
[2024-01-24 14:07:28,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb03cde-fd35-4928-b44e-c8d68ee8d0c6/GCF_002197685.1_ASM219768v1_genomic.fna.gz --refList GCF_002197685.1_ASM219768v1_genomic.fna/target_genomes.txt --output GCF_002197685.1_ASM219768v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:38,470] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:38,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f1d965d-46a0-4d82-a607-050251045f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:38,471] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f1d965d-46a0-4d82-a607-050251045f19/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:38,486] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:38,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:38,487] [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 dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	100.0	1143	1143	95	conclusive
Sphingomonas mucosissima	strain=DSM 17494	GCA_002197665.1	370959	370959	type	True	84.2332	839	1143	95	below_threshold
Sphingomonas jeddahensis	strain=G39	GCA_001981525.1	1915074	1915074	type	True	83.3605	743	1143	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	81.712	681	1143	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	80.9446	513	1143	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	80.5536	595	1143	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.254	572	1143	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.2287	564	1143	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	80.1509	542	1143	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	80.0746	509	1143	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.9721	523	1143	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.9543	564	1143	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.8546	516	1143	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:38,488] [INFO] DFAST Taxonomy check result was written to GCF_002197685.1_ASM219768v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:38,489] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:38,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:38,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f1d965d-46a0-4d82-a607-050251045f19/dqc_reference/checkm_data
[2024-01-24 14:07:38,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:38,530] [INFO] Task started: CheckM
[2024-01-24 14:07:38,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002197685.1_ASM219768v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002197685.1_ASM219768v1_genomic.fna/checkm_input GCF_002197685.1_ASM219768v1_genomic.fna/checkm_result
[2024-01-24 14:08:12,055] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:12,056] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:12,073] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:12,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:12,074] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002197685.1_ASM219768v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:12,074] [INFO] Task started: Blastn
[2024-01-24 14:08:12,074] [INFO] Running command: blastn -query GCF_002197685.1_ASM219768v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f1d965d-46a0-4d82-a607-050251045f19/dqc_reference/reference_markers_gtdb.fasta -out GCF_002197685.1_ASM219768v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:14,226] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:14,234] [INFO] Selected 9 target genomes.
[2024-01-24 14:08:14,234] [INFO] Target genome list was writen to GCF_002197685.1_ASM219768v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:14,273] [INFO] Task started: fastANI
[2024-01-24 14:08:14,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fb03cde-fd35-4928-b44e-c8d68ee8d0c6/GCF_002197685.1_ASM219768v1_genomic.fna.gz --refList GCF_002197685.1_ASM219768v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002197685.1_ASM219768v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:22,974] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:22,983] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:22,984] [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_002197685.1	s__Sphingomonas dokdonensis	100.0	1143	1143	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_002197665.1	s__Sphingomonas mucosissima	84.2361	839	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109205.1	s__Sphingomonas sp900109205	83.8633	854	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.87	0.87	2	-
GCF_000980895.1	s__Sphingomonas olei	83.6832	772	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.98	97.88	0.87	0.83	3	-
GCF_001981525.1	s__Sphingomonas jeddahensis	83.3487	744	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002117915.1	s__Sphingomonas sp002117915	82.9397	756	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014217605.1	s__Sphingomonas sp014217605	82.7569	750	1143	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	81.0279	571	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_014204695.1	s__Sphingomonas sp001897045	80.4442	580	1143	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:22,985] [INFO] GTDB search result was written to GCF_002197685.1_ASM219768v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:22,986] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:22,989] [INFO] DFAST_QC result json was written to GCF_002197685.1_ASM219768v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:22,990] [INFO] DFAST_QC completed!
[2024-01-24 14:08:22,990] [INFO] Total running time: 0h1m8s