[2024-01-24 14:19:19,012] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:19,019] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:19,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dbce2aa-d83e-432d-98a5-9f8a244ead2a/dqc_reference
[2024-01-24 14:19:20,361] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,362] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,363] [INFO] Running command: gunzip -c /var/lib/cwl/stgc5f70200-cc64-4fd6-9bb9-f34cf04d4b51/GCF_003049725.1_ASM304972v1_genomic.fna.gz | prodigal -d GCF_003049725.1_ASM304972v1_genomic.fna/cds.fna -a GCF_003049725.1_ASM304972v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:31,248] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:31,248] [INFO] Task started: HMMsearch
[2024-01-24 14:19:31,248] [INFO] Running command: hmmsearch --tblout GCF_003049725.1_ASM304972v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dbce2aa-d83e-432d-98a5-9f8a244ead2a/dqc_reference/reference_markers.hmm GCF_003049725.1_ASM304972v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:31,566] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:31,568] [INFO] Found 6/6 markers.
[2024-01-24 14:19:31,609] [INFO] Query marker FASTA was written to GCF_003049725.1_ASM304972v1_genomic.fna/markers.fasta
[2024-01-24 14:19:31,610] [INFO] Task started: Blastn
[2024-01-24 14:19:31,610] [INFO] Running command: blastn -query GCF_003049725.1_ASM304972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbce2aa-d83e-432d-98a5-9f8a244ead2a/dqc_reference/reference_markers.fasta -out GCF_003049725.1_ASM304972v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:32,648] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:32,651] [INFO] Selected 12 target genomes.
[2024-01-24 14:19:32,652] [INFO] Target genome list was writen to GCF_003049725.1_ASM304972v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:32,677] [INFO] Task started: fastANI
[2024-01-24 14:19:32,677] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5f70200-cc64-4fd6-9bb9-f34cf04d4b51/GCF_003049725.1_ASM304972v1_genomic.fna.gz --refList GCF_003049725.1_ASM304972v1_genomic.fna/target_genomes.txt --output GCF_003049725.1_ASM304972v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:42,814] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:42,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dbce2aa-d83e-432d-98a5-9f8a244ead2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:42,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dbce2aa-d83e-432d-98a5-9f8a244ead2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:42,826] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:42,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:42,826] [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
Oceanimonas marisflavi	strain=102-Na3	GCA_003049725.1	2059724	2059724	type	True	100.0	1083	1086	95	conclusive
Oceanimonas doudoroffii	strain=ATCC 27123	GCA_002242685.1	84158	84158	type	True	88.5258	883	1086	95	below_threshold
Oceanimonas smirnovii	strain=ATCC BAA-899	GCA_000381965.1	264574	264574	type	True	85.0013	755	1086	95	below_threshold
Oceanimonas baumannii	strain=ATCC 700832	GCA_002245495.1	129578	129578	type	True	83.8158	796	1086	95	below_threshold
Oceanimonas baumannii	strain=DSM 15594	GCA_004365405.1	129578	129578	type	True	83.8084	789	1086	95	below_threshold
Zobellella denitrificans	strain=ZD1	GCA_002237365.1	347534	347534	type	True	83.2474	720	1086	95	below_threshold
Zobellella endophytica	strain=59N8	GCA_003012775.1	2116700	2116700	type	True	82.6896	748	1086	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_021602585.1	2740518	2740518	type	True	76.6534	135	1086	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	76.6361	120	1086	95	below_threshold
Pseudomonas faucium	strain=BML-PP048	GCA_013373935.1	2740518	2740518	type	True	76.6197	130	1086	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.5275	169	1086	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	76.231	130	1086	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:42,828] [INFO] DFAST Taxonomy check result was written to GCF_003049725.1_ASM304972v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:42,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:42,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:42,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dbce2aa-d83e-432d-98a5-9f8a244ead2a/dqc_reference/checkm_data
[2024-01-24 14:19:42,831] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:42,879] [INFO] Task started: CheckM
[2024-01-24 14:19:42,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003049725.1_ASM304972v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003049725.1_ASM304972v1_genomic.fna/checkm_input GCF_003049725.1_ASM304972v1_genomic.fna/checkm_result
[2024-01-24 14:20:17,636] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:17,637] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:17,662] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:17,663] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:17,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003049725.1_ASM304972v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:17,664] [INFO] Task started: Blastn
[2024-01-24 14:20:17,664] [INFO] Running command: blastn -query GCF_003049725.1_ASM304972v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dbce2aa-d83e-432d-98a5-9f8a244ead2a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003049725.1_ASM304972v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:19,365] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:19,370] [INFO] Selected 9 target genomes.
[2024-01-24 14:20:19,370] [INFO] Target genome list was writen to GCF_003049725.1_ASM304972v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:19,376] [INFO] Task started: fastANI
[2024-01-24 14:20:19,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5f70200-cc64-4fd6-9bb9-f34cf04d4b51/GCF_003049725.1_ASM304972v1_genomic.fna.gz --refList GCF_003049725.1_ASM304972v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003049725.1_ASM304972v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:27,668] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:27,676] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:27,677] [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_003049725.1	s__Oceanimonas marisflavi	100.0	1083	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002242685.1	s__Oceanimonas doudoroffii	88.5413	882	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	98.80	98.80	0.94	0.94	2	-
GCF_000243075.1	s__Oceanimonas sp000243075	87.7645	870	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381965.1	s__Oceanimonas smirnovii	84.9906	756	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002245495.1	s__Oceanimonas baumannii	83.8072	797	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Oceanimonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003012795.1	s__Zobellella_D taiwanensis	83.5917	741	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237365.1	s__Zobellella denitrificans	83.2811	716	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella	95.0	98.78	98.78	0.93	0.93	2	-
GCF_003012775.1	s__Zobellella_C endophytica	82.7	746	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075035.1	s__Zobellella_A maritima	80.774	635	1086	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Aeromonadaceae;g__Zobellella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:27,679] [INFO] GTDB search result was written to GCF_003049725.1_ASM304972v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:27,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:27,683] [INFO] DFAST_QC result json was written to GCF_003049725.1_ASM304972v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:27,683] [INFO] DFAST_QC completed!
[2024-01-24 14:20:27,683] [INFO] Total running time: 0h1m9s