[2023-06-29 06:53:45,435] [INFO] DFAST_QC pipeline started.
[2023-06-29 06:53:45,442] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 06:53:45,443] [INFO] DQC Reference Directory: /var/lib/cwl/stg13328489-67ad-4608-9831-8efe95cc3d17/dqc_reference
[2023-06-29 06:53:47,907] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 06:53:47,909] [INFO] Task started: Prodigal
[2023-06-29 06:53:47,909] [INFO] Running command: gunzip -c /var/lib/cwl/stg491338ea-c30a-4f84-bd49-632ab35dfcea/GCA_020442005.1_ASM2044200v1_genomic.fna.gz | prodigal -d GCA_020442005.1_ASM2044200v1_genomic.fna/cds.fna -a GCA_020442005.1_ASM2044200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 06:53:56,487] [INFO] Task succeeded: Prodigal
[2023-06-29 06:53:56,487] [INFO] Task started: HMMsearch
[2023-06-29 06:53:56,487] [INFO] Running command: hmmsearch --tblout GCA_020442005.1_ASM2044200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg13328489-67ad-4608-9831-8efe95cc3d17/dqc_reference/reference_markers.hmm GCA_020442005.1_ASM2044200v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 06:53:56,734] [INFO] Task succeeded: HMMsearch
[2023-06-29 06:53:56,735] [WARNING] Found 1/6 markers. [/var/lib/cwl/stg491338ea-c30a-4f84-bd49-632ab35dfcea/GCA_020442005.1_ASM2044200v1_genomic.fna.gz]
[2023-06-29 06:53:56,774] [INFO] Query marker FASTA was written to GCA_020442005.1_ASM2044200v1_genomic.fna/markers.fasta
[2023-06-29 06:53:56,775] [INFO] Task started: Blastn
[2023-06-29 06:53:56,775] [INFO] Running command: blastn -query GCA_020442005.1_ASM2044200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13328489-67ad-4608-9831-8efe95cc3d17/dqc_reference/reference_markers.fasta -out GCA_020442005.1_ASM2044200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:53:57,262] [INFO] Task succeeded: Blastn
[2023-06-29 06:53:57,267] [INFO] Selected 5 target genomes.
[2023-06-29 06:53:57,267] [INFO] Target genome list was writen to GCA_020442005.1_ASM2044200v1_genomic.fna/target_genomes.txt
[2023-06-29 06:53:57,268] [INFO] Task started: fastANI
[2023-06-29 06:53:57,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg491338ea-c30a-4f84-bd49-632ab35dfcea/GCA_020442005.1_ASM2044200v1_genomic.fna.gz --refList GCA_020442005.1_ASM2044200v1_genomic.fna/target_genomes.txt --output GCA_020442005.1_ASM2044200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 06:54:01,161] [INFO] Task succeeded: fastANI
[2023-06-29 06:54:01,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg13328489-67ad-4608-9831-8efe95cc3d17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 06:54:01,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg13328489-67ad-4608-9831-8efe95cc3d17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 06:54:01,168] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 06:54:01,168] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 06:54:01,169] [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
Kaistia adipata	strain=DSM 17808	GCA_000423225.1	166954	166954	type	True	75.7745	135	814	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	75.732	130	814	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	75.5927	128	814	95	below_threshold
Phreatobacter cathodiphilus	strain=S-12	GCA_003008515.1	1868589	1868589	type	True	75.5339	142	814	95	below_threshold
Methylobacterium tardum	strain=DSM 19566	GCA_023546765.1	374432	374432	type	True	75.0713	86	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 06:54:01,170] [INFO] DFAST Taxonomy check result was written to GCA_020442005.1_ASM2044200v1_genomic.fna/tc_result.tsv
[2023-06-29 06:54:01,171] [INFO] ===== Taxonomy check completed =====
[2023-06-29 06:54:01,171] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 06:54:01,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg13328489-67ad-4608-9831-8efe95cc3d17/dqc_reference/checkm_data
[2023-06-29 06:54:01,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 06:54:01,215] [INFO] Task started: CheckM
[2023-06-29 06:54:01,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020442005.1_ASM2044200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020442005.1_ASM2044200v1_genomic.fna/checkm_input GCA_020442005.1_ASM2044200v1_genomic.fna/checkm_result
[2023-06-29 06:54:30,108] [INFO] Task succeeded: CheckM
[2023-06-29 06:54:30,109] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 31.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 06:54:30,134] [INFO] ===== Completeness check finished =====
[2023-06-29 06:54:30,134] [INFO] ===== Start GTDB Search =====
[2023-06-29 06:54:30,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020442005.1_ASM2044200v1_genomic.fna/markers.fasta)
[2023-06-29 06:54:30,135] [INFO] Task started: Blastn
[2023-06-29 06:54:30,135] [INFO] Running command: blastn -query GCA_020442005.1_ASM2044200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg13328489-67ad-4608-9831-8efe95cc3d17/dqc_reference/reference_markers_gtdb.fasta -out GCA_020442005.1_ASM2044200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 06:54:30,597] [INFO] Task succeeded: Blastn
[2023-06-29 06:54:30,601] [INFO] Selected 5 target genomes.
[2023-06-29 06:54:30,601] [INFO] Target genome list was writen to GCA_020442005.1_ASM2044200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 06:54:30,604] [INFO] Task started: fastANI
[2023-06-29 06:54:30,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg491338ea-c30a-4f84-bd49-632ab35dfcea/GCA_020442005.1_ASM2044200v1_genomic.fna.gz --refList GCA_020442005.1_ASM2044200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020442005.1_ASM2044200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 06:54:34,129] [INFO] Task succeeded: fastANI
[2023-06-29 06:54:34,138] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 06:54:34,138] [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_014199915.1	s__Prosthecomicrobium pneumaticum	75.9512	152	814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Prosthecomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016428755.1	s__Bosea sp016428755	75.6054	111	814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Bosea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464235.1	s__Phreatobacter sp001464235	75.5918	115	814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793505.1	s__GCA-013693735 sp016793505	75.5326	152	814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__GCA-013693735	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003008515.1	s__Phreatobacter cathodiphilus	75.5293	143	814	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Phreatobacteraceae;g__Phreatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 06:54:34,140] [INFO] GTDB search result was written to GCA_020442005.1_ASM2044200v1_genomic.fna/result_gtdb.tsv
[2023-06-29 06:54:34,140] [INFO] ===== GTDB Search completed =====
[2023-06-29 06:54:34,145] [INFO] DFAST_QC result json was written to GCA_020442005.1_ASM2044200v1_genomic.fna/dqc_result.json
[2023-06-29 06:54:34,146] [INFO] DFAST_QC completed!
[2023-06-29 06:54:34,146] [INFO] Total running time: 0h0m49s