[2024-01-24 15:10:48,141] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:48,143] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:48,143] [INFO] DQC Reference Directory: /var/lib/cwl/stge68c3b7d-6bf1-4d80-ab42-9e916ba45e12/dqc_reference
[2024-01-24 15:10:51,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:51,749] [INFO] Task started: Prodigal
[2024-01-24 15:10:51,750] [INFO] Running command: gunzip -c /var/lib/cwl/stg2be18a38-c492-4a5b-8376-8f649d9483a1/GCF_008520265.1_ASM852026v1_genomic.fna.gz | prodigal -d GCF_008520265.1_ASM852026v1_genomic.fna/cds.fna -a GCF_008520265.1_ASM852026v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:11:07,957] [INFO] Task succeeded: Prodigal
[2024-01-24 15:11:07,957] [INFO] Task started: HMMsearch
[2024-01-24 15:11:07,957] [INFO] Running command: hmmsearch --tblout GCF_008520265.1_ASM852026v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge68c3b7d-6bf1-4d80-ab42-9e916ba45e12/dqc_reference/reference_markers.hmm GCF_008520265.1_ASM852026v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:11:08,278] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:11:08,279] [INFO] Found 6/6 markers.
[2024-01-24 15:11:08,317] [INFO] Query marker FASTA was written to GCF_008520265.1_ASM852026v1_genomic.fna/markers.fasta
[2024-01-24 15:11:08,318] [INFO] Task started: Blastn
[2024-01-24 15:11:08,318] [INFO] Running command: blastn -query GCF_008520265.1_ASM852026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68c3b7d-6bf1-4d80-ab42-9e916ba45e12/dqc_reference/reference_markers.fasta -out GCF_008520265.1_ASM852026v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:08,950] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:08,955] [INFO] Selected 10 target genomes.
[2024-01-24 15:11:08,956] [INFO] Target genome list was writen to GCF_008520265.1_ASM852026v1_genomic.fna/target_genomes.txt
[2024-01-24 15:11:08,961] [INFO] Task started: fastANI
[2024-01-24 15:11:08,962] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be18a38-c492-4a5b-8376-8f649d9483a1/GCF_008520265.1_ASM852026v1_genomic.fna.gz --refList GCF_008520265.1_ASM852026v1_genomic.fna/target_genomes.txt --output GCF_008520265.1_ASM852026v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:18,279] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:18,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge68c3b7d-6bf1-4d80-ab42-9e916ba45e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:18,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge68c3b7d-6bf1-4d80-ab42-9e916ba45e12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:18,297] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:11:18,297] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:11:18,297] [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 cavernae	strain=5.0403-2	GCA_008520265.1	2592657	2592657	type	True	100.0	1290	1297	95	inconclusive
Sphingobacterium bovisgrunnientis	strain=KCTC 52685	GCA_009829085.1	1874697	1874697	type	True	96.1593	1033	1297	95	inconclusive
Sphingobacterium composti Ten et al. 2007 non Yoo et al. 2007	strain=KCTC 12578	GCA_009829075.1	363260	363260	type	True	84.116	721	1297	95	below_threshold
Sphingobacterium litopenaei	strain=DN04309	GCA_014692495.1	2763500	2763500	type	True	83.484	741	1297	95	below_threshold
Sphingobacterium alimentarium	strain=DSM 22362	GCA_004342685.1	797292	797292	type	True	80.6787	503	1297	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	79.2061	291	1297	95	below_threshold
Sphingobacterium detergens	strain=CECT 7938	GCA_003610355.1	1145106	1145106	type	True	78.251	151	1297	95	below_threshold
Sphingobacterium griseoflavum	strain=CGMCC 1.12966	GCA_014653155.1	1474952	1474952	type	True	77.9306	100	1297	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:18,299] [INFO] DFAST Taxonomy check result was written to GCF_008520265.1_ASM852026v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:18,299] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:18,300] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:18,300] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge68c3b7d-6bf1-4d80-ab42-9e916ba45e12/dqc_reference/checkm_data
[2024-01-24 15:11:18,301] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:18,348] [INFO] Task started: CheckM
[2024-01-24 15:11:18,348] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008520265.1_ASM852026v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008520265.1_ASM852026v1_genomic.fna/checkm_input GCF_008520265.1_ASM852026v1_genomic.fna/checkm_result
[2024-01-24 15:12:07,254] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:07,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:07,278] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:07,278] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:07,278] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008520265.1_ASM852026v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:07,279] [INFO] Task started: Blastn
[2024-01-24 15:12:07,279] [INFO] Running command: blastn -query GCF_008520265.1_ASM852026v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge68c3b7d-6bf1-4d80-ab42-9e916ba45e12/dqc_reference/reference_markers_gtdb.fasta -out GCF_008520265.1_ASM852026v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:08,117] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:08,126] [INFO] Selected 9 target genomes.
[2024-01-24 15:12:08,126] [INFO] Target genome list was writen to GCF_008520265.1_ASM852026v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:08,135] [INFO] Task started: fastANI
[2024-01-24 15:12:08,135] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be18a38-c492-4a5b-8376-8f649d9483a1/GCF_008520265.1_ASM852026v1_genomic.fna.gz --refList GCF_008520265.1_ASM852026v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008520265.1_ASM852026v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:16,112] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:16,126] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:16,127] [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_008520265.1	s__Sphingobacterium cavernae	100.0	1290	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	conclusive
GCF_009829085.1	s__Sphingobacterium bovisgrunnientis	96.1425	1034	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	96.1642	N/A	N/A	N/A	N/A	1	-
GCF_009829075.1	s__Sphingobacterium composti	84.1124	720	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011043515.1	s__Sphingobacterium sp011043515	82.8176	714	1297	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	80.7061	499	1297	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	78.5694	165	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002245855.1	s__Sphingobacterium cellulitidis	78.3571	179	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	98.02	97.95	0.91	0.90	4	-
GCF_003610355.1	s__Sphingobacterium detergens	78.2769	150	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653155.1	s__Sphingobacterium griseoflavum	77.9219	101	1297	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:16,130] [INFO] GTDB search result was written to GCF_008520265.1_ASM852026v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:16,131] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:16,136] [INFO] DFAST_QC result json was written to GCF_008520265.1_ASM852026v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:16,137] [INFO] DFAST_QC completed!
[2024-01-24 15:12:16,137] [INFO] Total running time: 0h1m28s