[2024-01-25 18:25:20,715] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:25:20,717] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:25:20,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg709890b0-3e84-4558-a0ab-8f3632e86410/dqc_reference
[2024-01-25 18:25:21,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:25:21,891] [INFO] Task started: Prodigal
[2024-01-25 18:25:21,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg17c723b1-f76e-415e-a01e-48c7f8bc243b/GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna.gz | prodigal -d GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/cds.fna -a GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:25:32,082] [INFO] Task succeeded: Prodigal
[2024-01-25 18:25:32,082] [INFO] Task started: HMMsearch
[2024-01-25 18:25:32,082] [INFO] Running command: hmmsearch --tblout GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg709890b0-3e84-4558-a0ab-8f3632e86410/dqc_reference/reference_markers.hmm GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:25:32,285] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:25:32,286] [INFO] Found 6/6 markers.
[2024-01-25 18:25:32,317] [INFO] Query marker FASTA was written to GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/markers.fasta
[2024-01-25 18:25:32,317] [INFO] Task started: Blastn
[2024-01-25 18:25:32,317] [INFO] Running command: blastn -query GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg709890b0-3e84-4558-a0ab-8f3632e86410/dqc_reference/reference_markers.fasta -out GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:25:33,063] [INFO] Task succeeded: Blastn
[2024-01-25 18:25:33,066] [INFO] Selected 11 target genomes.
[2024-01-25 18:25:33,066] [INFO] Target genome list was writen to GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/target_genomes.txt
[2024-01-25 18:25:33,095] [INFO] Task started: fastANI
[2024-01-25 18:25:33,095] [INFO] Running command: fastANI --query /var/lib/cwl/stg17c723b1-f76e-415e-a01e-48c7f8bc243b/GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna.gz --refList GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/target_genomes.txt --output GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:25:42,004] [INFO] Task succeeded: fastANI
[2024-01-25 18:25:42,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg709890b0-3e84-4558-a0ab-8f3632e86410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:25:42,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg709890b0-3e84-4558-a0ab-8f3632e86410/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:25:42,012] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:25:42,012] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:25:42,012] [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
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	100.0	1241	1243	95	conclusive
Kushneria marisflavi	strain=DSM 15357	GCA_003610515.1	157779	157779	type	True	86.4182	992	1243	95	below_threshold
Kushneria marisflavi	strain=SW32	GCA_002157205.1	157779	157779	type	True	86.3196	1032	1243	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	85.7746	1022	1243	95	below_threshold
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	85.546	991	1243	95	below_threshold
Kushneria pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	84.9113	1002	1243	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.5534	203	1243	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.4407	230	1243	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	77.3557	202	1243	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	77.318	202	1243	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.1133	195	1243	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:25:42,014] [INFO] DFAST Taxonomy check result was written to GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/tc_result.tsv
[2024-01-25 18:25:42,014] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:25:42,014] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:25:42,014] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg709890b0-3e84-4558-a0ab-8f3632e86410/dqc_reference/checkm_data
[2024-01-25 18:25:42,015] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:25:42,052] [INFO] Task started: CheckM
[2024-01-25 18:25:42,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/checkm_input GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/checkm_result
[2024-01-25 18:26:14,544] [INFO] Task succeeded: CheckM
[2024-01-25 18:26:14,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:26:14,566] [INFO] ===== Completeness check finished =====
[2024-01-25 18:26:14,566] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:26:14,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/markers.fasta)
[2024-01-25 18:26:14,567] [INFO] Task started: Blastn
[2024-01-25 18:26:14,568] [INFO] Running command: blastn -query GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stg709890b0-3e84-4558-a0ab-8f3632e86410/dqc_reference/reference_markers_gtdb.fasta -out GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:26:15,866] [INFO] Task succeeded: Blastn
[2024-01-25 18:26:15,869] [INFO] Selected 6 target genomes.
[2024-01-25 18:26:15,869] [INFO] Target genome list was writen to GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:26:15,895] [INFO] Task started: fastANI
[2024-01-25 18:26:15,896] [INFO] Running command: fastANI --query /var/lib/cwl/stg17c723b1-f76e-415e-a01e-48c7f8bc243b/GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna.gz --refList GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:26:21,629] [INFO] Task succeeded: fastANI
[2024-01-25 18:26:21,634] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:26:21,634] [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_900312995.1	s__Kushneria phyllosphaerae	100.0	1241	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002157205.1	s__Kushneria marisflavi	86.3196	1032	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003385845.1	s__Kushneria indalinina	85.7682	1023	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002155145.1	s__Kushneria konosiri	85.546	991	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652795.1	s__Kushneria pakistanensis	84.9113	1002	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112585.1	s__Kushneria avicenniae	84.1912	937	1243	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:26:21,636] [INFO] GTDB search result was written to GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-25 18:26:21,636] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:26:21,639] [INFO] DFAST_QC result json was written to GCF_900312995.1_Kushneria_sp_EAod3_Prokka_genomic.fna/dqc_result.json
[2024-01-25 18:26:21,639] [INFO] DFAST_QC completed!
[2024-01-25 18:26:21,639] [INFO] Total running time: 0h1m1s