[2024-01-24 13:57:13,069] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:13,071] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:13,072] [INFO] DQC Reference Directory: /var/lib/cwl/stgf976e3af-a0e4-4854-830b-c2f97271afe4/dqc_reference
[2024-01-24 13:57:14,287] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:14,288] [INFO] Task started: Prodigal
[2024-01-24 13:57:14,288] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8b1ce95-07d9-430d-8225-7520b399da57/GCF_002197665.1_ASM219766v1_genomic.fna.gz | prodigal -d GCF_002197665.1_ASM219766v1_genomic.fna/cds.fna -a GCF_002197665.1_ASM219766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:25,167] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:25,167] [INFO] Task started: HMMsearch
[2024-01-24 13:57:25,168] [INFO] Running command: hmmsearch --tblout GCF_002197665.1_ASM219766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf976e3af-a0e4-4854-830b-c2f97271afe4/dqc_reference/reference_markers.hmm GCF_002197665.1_ASM219766v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:25,408] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:25,410] [INFO] Found 6/6 markers.
[2024-01-24 13:57:25,442] [INFO] Query marker FASTA was written to GCF_002197665.1_ASM219766v1_genomic.fna/markers.fasta
[2024-01-24 13:57:25,442] [INFO] Task started: Blastn
[2024-01-24 13:57:25,442] [INFO] Running command: blastn -query GCF_002197665.1_ASM219766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf976e3af-a0e4-4854-830b-c2f97271afe4/dqc_reference/reference_markers.fasta -out GCF_002197665.1_ASM219766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:26,499] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:26,503] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:26,503] [INFO] Target genome list was writen to GCF_002197665.1_ASM219766v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:26,509] [INFO] Task started: fastANI
[2024-01-24 13:57:26,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b1ce95-07d9-430d-8225-7520b399da57/GCF_002197665.1_ASM219766v1_genomic.fna.gz --refList GCF_002197665.1_ASM219766v1_genomic.fna/target_genomes.txt --output GCF_002197665.1_ASM219766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:35,105] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:35,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf976e3af-a0e4-4854-830b-c2f97271afe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:35,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf976e3af-a0e4-4854-830b-c2f97271afe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:35,115] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:35,115] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:35,116] [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 mucosissima	strain=DSM 17494	GCA_002197665.1	370959	370959	type	True	100.0	1185	1187	95	conclusive
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	84.3185	839	1187	95	below_threshold
Sphingomonas jeddahensis	strain=G39	GCA_001981525.1	1915074	1915074	type	True	82.4922	699	1187	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	81.0749	627	1187	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	80.204	427	1187	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.5988	528	1187	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.3095	480	1187	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.3031	488	1187	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.2498	477	1187	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	79.1324	429	1187	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.0864	440	1187	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:35,117] [INFO] DFAST Taxonomy check result was written to GCF_002197665.1_ASM219766v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:35,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:35,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:35,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf976e3af-a0e4-4854-830b-c2f97271afe4/dqc_reference/checkm_data
[2024-01-24 13:57:35,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:35,159] [INFO] Task started: CheckM
[2024-01-24 13:57:35,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002197665.1_ASM219766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002197665.1_ASM219766v1_genomic.fna/checkm_input GCF_002197665.1_ASM219766v1_genomic.fna/checkm_result
[2024-01-24 13:58:12,148] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:12,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:12,175] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:12,176] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:12,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002197665.1_ASM219766v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:12,177] [INFO] Task started: Blastn
[2024-01-24 13:58:12,177] [INFO] Running command: blastn -query GCF_002197665.1_ASM219766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf976e3af-a0e4-4854-830b-c2f97271afe4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002197665.1_ASM219766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:14,381] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:14,384] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:14,384] [INFO] Target genome list was writen to GCF_002197665.1_ASM219766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:14,394] [INFO] Task started: fastANI
[2024-01-24 13:58:14,395] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8b1ce95-07d9-430d-8225-7520b399da57/GCF_002197665.1_ASM219766v1_genomic.fna.gz --refList GCF_002197665.1_ASM219766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002197665.1_ASM219766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:23,349] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:23,357] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:23,357] [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_002197665.1	s__Sphingomonas mucosissima	100.0	1185	1187	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_002197685.1	s__Sphingomonas dokdonensis	84.3185	839	1187	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	83.7039	840	1187	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	83.1599	717	1187	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	82.4922	699	1187	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	81.6836	669	1187	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	81.578	656	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374835.1	s__Sphingomonas ginsenosidimutans	79.7342	517	1187	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.62	98.43	0.85	0.81	6	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.3832	494	1187	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 13:58:23,359] [INFO] GTDB search result was written to GCF_002197665.1_ASM219766v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:23,360] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:23,363] [INFO] DFAST_QC result json was written to GCF_002197665.1_ASM219766v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:23,363] [INFO] DFAST_QC completed!
[2024-01-24 13:58:23,363] [INFO] Total running time: 0h1m10s