[2024-01-24 14:23:05,253] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:05,255] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:05,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg21cea4d6-6e23-4a24-8d9b-ba8f47086c9a/dqc_reference
[2024-01-24 14:23:06,629] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:06,630] [INFO] Task started: Prodigal
[2024-01-24 14:23:06,630] [INFO] Running command: gunzip -c /var/lib/cwl/stg69108d3b-050d-4183-baa6-70e8c2aa4c91/GCF_009829075.1_ASM982907v1_genomic.fna.gz | prodigal -d GCF_009829075.1_ASM982907v1_genomic.fna/cds.fna -a GCF_009829075.1_ASM982907v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:21,036] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:21,036] [INFO] Task started: HMMsearch
[2024-01-24 14:23:21,036] [INFO] Running command: hmmsearch --tblout GCF_009829075.1_ASM982907v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21cea4d6-6e23-4a24-8d9b-ba8f47086c9a/dqc_reference/reference_markers.hmm GCF_009829075.1_ASM982907v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:21,371] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:21,373] [INFO] Found 6/6 markers.
[2024-01-24 14:23:21,405] [INFO] Query marker FASTA was written to GCF_009829075.1_ASM982907v1_genomic.fna/markers.fasta
[2024-01-24 14:23:21,405] [INFO] Task started: Blastn
[2024-01-24 14:23:21,406] [INFO] Running command: blastn -query GCF_009829075.1_ASM982907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21cea4d6-6e23-4a24-8d9b-ba8f47086c9a/dqc_reference/reference_markers.fasta -out GCF_009829075.1_ASM982907v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:22,025] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:22,028] [INFO] Selected 9 target genomes.
[2024-01-24 14:23:22,029] [INFO] Target genome list was writen to GCF_009829075.1_ASM982907v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:22,033] [INFO] Task started: fastANI
[2024-01-24 14:23:22,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg69108d3b-050d-4183-baa6-70e8c2aa4c91/GCF_009829075.1_ASM982907v1_genomic.fna.gz --refList GCF_009829075.1_ASM982907v1_genomic.fna/target_genomes.txt --output GCF_009829075.1_ASM982907v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:30,029] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:30,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21cea4d6-6e23-4a24-8d9b-ba8f47086c9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:30,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21cea4d6-6e23-4a24-8d9b-ba8f47086c9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:30,045] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:30,046] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:30,046] [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
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	100.0	1166	1172	95	conclusive
Sphingobacterium cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	83.9969	735	1172	95	below_threshold
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	83.9191	743	1172	95	below_threshold
Sphingobacterium litopenaei	strain=DN04309	GCA_014692495.1	2763500	2763500	type	True	82.2412	644	1172	95	below_threshold
Sphingobacterium alimentarium	strain=DSM 22362	GCA_004342685.1	797292	797292	type	True	80.8345	459	1172	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	78.9918	288	1172	95	below_threshold
Sphingobacterium chungjuense	strain=IMCC25678	GCA_011316935.1	2675553	2675553	type	True	77.9343	99	1172	95	below_threshold
Pedobacter fastidiosus	strain=CCM 8938	GCA_014306625.1	2765361	2765361	type	True	76.0463	61	1172	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:30,071] [INFO] DFAST Taxonomy check result was written to GCF_009829075.1_ASM982907v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:30,072] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:30,072] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:30,073] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21cea4d6-6e23-4a24-8d9b-ba8f47086c9a/dqc_reference/checkm_data
[2024-01-24 14:23:30,074] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:30,148] [INFO] Task started: CheckM
[2024-01-24 14:23:30,148] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009829075.1_ASM982907v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009829075.1_ASM982907v1_genomic.fna/checkm_input GCF_009829075.1_ASM982907v1_genomic.fna/checkm_result
[2024-01-24 14:24:14,412] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:14,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:14,432] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:14,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:14,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009829075.1_ASM982907v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:14,434] [INFO] Task started: Blastn
[2024-01-24 14:24:14,434] [INFO] Running command: blastn -query GCF_009829075.1_ASM982907v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg21cea4d6-6e23-4a24-8d9b-ba8f47086c9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_009829075.1_ASM982907v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:15,266] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:15,269] [INFO] Selected 6 target genomes.
[2024-01-24 14:24:15,269] [INFO] Target genome list was writen to GCF_009829075.1_ASM982907v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:15,276] [INFO] Task started: fastANI
[2024-01-24 14:24:15,276] [INFO] Running command: fastANI --query /var/lib/cwl/stg69108d3b-050d-4183-baa6-70e8c2aa4c91/GCF_009829075.1_ASM982907v1_genomic.fna.gz --refList GCF_009829075.1_ASM982907v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009829075.1_ASM982907v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:20,361] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:20,375] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:20,376] [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_009829075.1	s__Sphingobacterium composti	100.0	1166	1172	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008520265.1	s__Sphingobacterium cavernae	84.0203	735	1172	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_009829085.1	s__Sphingobacterium bovisgrunnientis	83.9065	745	1172	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_011043515.1	s__Sphingobacterium sp011043515	82.0544	615	1172	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.84	98.84	0.89	0.89	2	-
GCF_004342685.1	s__Sphingobacterium alimentarium	80.8265	461	1172	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009557615.1	s__Sphingobacterium sp009557615	77.9532	154	1172	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:20,378] [INFO] GTDB search result was written to GCF_009829075.1_ASM982907v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:20,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:20,382] [INFO] DFAST_QC result json was written to GCF_009829075.1_ASM982907v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:20,383] [INFO] DFAST_QC completed!
[2024-01-24 14:24:20,383] [INFO] Total running time: 0h1m15s