[2024-01-24 15:18:37,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:37,777] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:37,777] [INFO] DQC Reference Directory: /var/lib/cwl/stg37f5c772-cc77-4fc3-bd13-1ec9186314c5/dqc_reference
[2024-01-24 15:18:39,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:39,084] [INFO] Task started: Prodigal
[2024-01-24 15:18:39,085] [INFO] Running command: gunzip -c /var/lib/cwl/stg00d46058-6074-4729-bd1c-69f8040ca08f/GCF_016773205.1_ASM1677320v1_genomic.fna.gz | prodigal -d GCF_016773205.1_ASM1677320v1_genomic.fna/cds.fna -a GCF_016773205.1_ASM1677320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:58,994] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:58,995] [INFO] Task started: HMMsearch
[2024-01-24 15:18:58,995] [INFO] Running command: hmmsearch --tblout GCF_016773205.1_ASM1677320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg37f5c772-cc77-4fc3-bd13-1ec9186314c5/dqc_reference/reference_markers.hmm GCF_016773205.1_ASM1677320v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:59,526] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:59,528] [INFO] Found 6/6 markers.
[2024-01-24 15:18:59,584] [INFO] Query marker FASTA was written to GCF_016773205.1_ASM1677320v1_genomic.fna/markers.fasta
[2024-01-24 15:18:59,584] [INFO] Task started: Blastn
[2024-01-24 15:18:59,584] [INFO] Running command: blastn -query GCF_016773205.1_ASM1677320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37f5c772-cc77-4fc3-bd13-1ec9186314c5/dqc_reference/reference_markers.fasta -out GCF_016773205.1_ASM1677320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:00,624] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:00,630] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:00,631] [INFO] Target genome list was writen to GCF_016773205.1_ASM1677320v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:00,637] [INFO] Task started: fastANI
[2024-01-24 15:19:00,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d46058-6074-4729-bd1c-69f8040ca08f/GCF_016773205.1_ASM1677320v1_genomic.fna.gz --refList GCF_016773205.1_ASM1677320v1_genomic.fna/target_genomes.txt --output GCF_016773205.1_ASM1677320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:20,565] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:20,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg37f5c772-cc77-4fc3-bd13-1ec9186314c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:20,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg37f5c772-cc77-4fc3-bd13-1ec9186314c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:20,581] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:20,581] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:20,581] [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
Belnapia arida	strain=T18	GCA_016773205.1	2804533	2804533	type	True	100.0	2208	2213	95	conclusive
Belnapia moabensis	strain=DSM 16746	GCA_000745835.1	365533	365533	type	True	90.4567	1598	2213	95	below_threshold
Belnapia rosea	strain=CGMCC 1.10758	GCA_900104205.1	938405	938405	type	True	87.0307	1448	2213	95	below_threshold
Belnapia rosea	strain=CPCC 100156	GCA_900101615.1	938405	938405	type	True	86.9528	1463	2213	95	below_threshold
Belnapia mucosa	strain=T6	GCA_016775475.1	2804532	2804532	type	True	85.9485	1412	2213	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	81.2815	1086	2213	95	below_threshold
Roseomonas alkaliterrae	strain=DSM 25895	GCA_014199195.1	1452450	1452450	type	True	79.1838	752	2213	95	below_threshold
Roseomonas hellenica	strain=LMG 31523	GCA_018129085.1	2687306	2687306	type	True	79.1219	874	2213	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	78.9278	634	2213	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	78.7291	697	2213	95	below_threshold
Roseomonas marmotae	strain=1318	GCA_017654485.1	2768161	2768161	type	True	78.4941	614	2213	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	78.0761	617	2213	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	77.909	637	2213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:20,583] [INFO] DFAST Taxonomy check result was written to GCF_016773205.1_ASM1677320v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:20,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:20,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:20,584] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg37f5c772-cc77-4fc3-bd13-1ec9186314c5/dqc_reference/checkm_data
[2024-01-24 15:19:20,585] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:20,657] [INFO] Task started: CheckM
[2024-01-24 15:19:20,658] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016773205.1_ASM1677320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016773205.1_ASM1677320v1_genomic.fna/checkm_input GCF_016773205.1_ASM1677320v1_genomic.fna/checkm_result
[2024-01-24 15:20:20,791] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:20,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:20,818] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:20,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:20,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016773205.1_ASM1677320v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:20,819] [INFO] Task started: Blastn
[2024-01-24 15:20:20,819] [INFO] Running command: blastn -query GCF_016773205.1_ASM1677320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg37f5c772-cc77-4fc3-bd13-1ec9186314c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_016773205.1_ASM1677320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:22,415] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:22,425] [INFO] Selected 6 target genomes.
[2024-01-24 15:20:22,425] [INFO] Target genome list was writen to GCF_016773205.1_ASM1677320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:22,430] [INFO] Task started: fastANI
[2024-01-24 15:20:22,430] [INFO] Running command: fastANI --query /var/lib/cwl/stg00d46058-6074-4729-bd1c-69f8040ca08f/GCF_016773205.1_ASM1677320v1_genomic.fna.gz --refList GCF_016773205.1_ASM1677320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016773205.1_ASM1677320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:34,726] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:34,739] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:34,739] [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_016773205.1	s__Belnapia sp016773205	100.0	2208	2213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000802185.1	s__Belnapia sp000802185	92.4775	1719	2213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745835.1	s__Belnapia moabensis	90.484	1595	2213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805545.1	s__Belnapia sp902805545	89.9741	1252	2213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101615.1	s__Belnapia rosea	86.9693	1462	2213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	98.36	98.36	0.89	0.89	2	-
GCF_016775475.1	s__Belnapia sp016775475	85.9479	1412	2213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Belnapia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:34,741] [INFO] GTDB search result was written to GCF_016773205.1_ASM1677320v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:34,741] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:34,745] [INFO] DFAST_QC result json was written to GCF_016773205.1_ASM1677320v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:34,745] [INFO] DFAST_QC completed!
[2024-01-24 15:20:34,745] [INFO] Total running time: 0h1m57s