[2024-01-24 11:44:05,456] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,458] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,458] [INFO] DQC Reference Directory: /var/lib/cwl/stgfa1700d8-3ac0-4759-8475-d55d43f1a42d/dqc_reference
[2024-01-24 11:44:08,836] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,837] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,837] [INFO] Running command: gunzip -c /var/lib/cwl/stg8caa7e73-b96e-42a1-9fd4-09a285aea65e/GCF_002157205.1_ASM215720v1_genomic.fna.gz | prodigal -d GCF_002157205.1_ASM215720v1_genomic.fna/cds.fna -a GCF_002157205.1_ASM215720v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:20,283] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:20,284] [INFO] Task started: HMMsearch
[2024-01-24 11:44:20,284] [INFO] Running command: hmmsearch --tblout GCF_002157205.1_ASM215720v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfa1700d8-3ac0-4759-8475-d55d43f1a42d/dqc_reference/reference_markers.hmm GCF_002157205.1_ASM215720v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:20,544] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:20,545] [INFO] Found 6/6 markers.
[2024-01-24 11:44:20,584] [INFO] Query marker FASTA was written to GCF_002157205.1_ASM215720v1_genomic.fna/markers.fasta
[2024-01-24 11:44:20,585] [INFO] Task started: Blastn
[2024-01-24 11:44:20,585] [INFO] Running command: blastn -query GCF_002157205.1_ASM215720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa1700d8-3ac0-4759-8475-d55d43f1a42d/dqc_reference/reference_markers.fasta -out GCF_002157205.1_ASM215720v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:21,397] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:21,400] [INFO] Selected 11 target genomes.
[2024-01-24 11:44:21,400] [INFO] Target genome list was writen to GCF_002157205.1_ASM215720v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:21,405] [INFO] Task started: fastANI
[2024-01-24 11:44:21,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caa7e73-b96e-42a1-9fd4-09a285aea65e/GCF_002157205.1_ASM215720v1_genomic.fna.gz --refList GCF_002157205.1_ASM215720v1_genomic.fna/target_genomes.txt --output GCF_002157205.1_ASM215720v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:30,091] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:30,091] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfa1700d8-3ac0-4759-8475-d55d43f1a42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:30,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfa1700d8-3ac0-4759-8475-d55d43f1a42d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:30,102] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:44:30,102] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:30,102] [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 marisflavi	strain=SW32	GCA_002157205.1	157779	157779	type	True	100.0	1220	1222	95	conclusive
Kushneria marisflavi	strain=DSM 15357	GCA_003610515.1	157779	157779	type	True	99.997	1208	1222	95	conclusive
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	90.2445	1099	1222	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	86.3269	994	1222	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	84.5813	973	1222	95	below_threshold
Kushneria pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	84.0091	962	1222	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.136	189	1222	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.0253	198	1222	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	77.7038	196	1222	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.702	195	1222	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	77.5409	193	1222	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:30,104] [INFO] DFAST Taxonomy check result was written to GCF_002157205.1_ASM215720v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:30,104] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:30,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:30,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfa1700d8-3ac0-4759-8475-d55d43f1a42d/dqc_reference/checkm_data
[2024-01-24 11:44:30,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:30,140] [INFO] Task started: CheckM
[2024-01-24 11:44:30,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002157205.1_ASM215720v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002157205.1_ASM215720v1_genomic.fna/checkm_input GCF_002157205.1_ASM215720v1_genomic.fna/checkm_result
[2024-01-24 11:45:07,748] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:07,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,766] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:07,766] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:07,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002157205.1_ASM215720v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:07,767] [INFO] Task started: Blastn
[2024-01-24 11:45:07,767] [INFO] Running command: blastn -query GCF_002157205.1_ASM215720v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfa1700d8-3ac0-4759-8475-d55d43f1a42d/dqc_reference/reference_markers_gtdb.fasta -out GCF_002157205.1_ASM215720v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:09,107] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:09,111] [INFO] Selected 6 target genomes.
[2024-01-24 11:45:09,112] [INFO] Target genome list was writen to GCF_002157205.1_ASM215720v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:09,117] [INFO] Task started: fastANI
[2024-01-24 11:45:09,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caa7e73-b96e-42a1-9fd4-09a285aea65e/GCF_002157205.1_ASM215720v1_genomic.fna.gz --refList GCF_002157205.1_ASM215720v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002157205.1_ASM215720v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:14,690] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:14,703] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:14,703] [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_002157205.1	s__Kushneria marisflavi	100.0	1221	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002155145.1	s__Kushneria konosiri	90.2571	1100	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900312995.1	s__Kushneria phyllosphaerae	86.3269	994	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385845.1	s__Kushneria indalinina	84.5858	972	1222	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	84.1919	965	1222	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	84.0091	962	1222	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:14,706] [INFO] GTDB search result was written to GCF_002157205.1_ASM215720v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:14,706] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:14,711] [INFO] DFAST_QC result json was written to GCF_002157205.1_ASM215720v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:14,711] [INFO] DFAST_QC completed!
[2024-01-24 11:45:14,712] [INFO] Total running time: 0h1m9s