[2024-01-24 10:57:19,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:19,807] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:19,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d10fc34-f4fa-4c95-a398-cbaa19d3717a/dqc_reference
[2024-01-24 10:57:22,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,298] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,299] [INFO] Running command: gunzip -c /var/lib/cwl/stg60f7bb9b-696c-4199-b497-79b4009f5ac0/GCF_003385845.1_ASM338584v1_genomic.fna.gz | prodigal -d GCF_003385845.1_ASM338584v1_genomic.fna/cds.fna -a GCF_003385845.1_ASM338584v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:33,562] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:33,563] [INFO] Task started: HMMsearch
[2024-01-24 10:57:33,563] [INFO] Running command: hmmsearch --tblout GCF_003385845.1_ASM338584v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d10fc34-f4fa-4c95-a398-cbaa19d3717a/dqc_reference/reference_markers.hmm GCF_003385845.1_ASM338584v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:33,814] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:33,815] [INFO] Found 6/6 markers.
[2024-01-24 10:57:33,853] [INFO] Query marker FASTA was written to GCF_003385845.1_ASM338584v1_genomic.fna/markers.fasta
[2024-01-24 10:57:33,853] [INFO] Task started: Blastn
[2024-01-24 10:57:33,853] [INFO] Running command: blastn -query GCF_003385845.1_ASM338584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d10fc34-f4fa-4c95-a398-cbaa19d3717a/dqc_reference/reference_markers.fasta -out GCF_003385845.1_ASM338584v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:34,612] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:34,616] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:34,616] [INFO] Target genome list was writen to GCF_003385845.1_ASM338584v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:34,803] [INFO] Task started: fastANI
[2024-01-24 10:57:34,803] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f7bb9b-696c-4199-b497-79b4009f5ac0/GCF_003385845.1_ASM338584v1_genomic.fna.gz --refList GCF_003385845.1_ASM338584v1_genomic.fna/target_genomes.txt --output GCF_003385845.1_ASM338584v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:45,626] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:45,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d10fc34-f4fa-4c95-a398-cbaa19d3717a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:45,628] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d10fc34-f4fa-4c95-a398-cbaa19d3717a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:45,646] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:57:45,647] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:45,647] [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 indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	100.0	1244	1245	95	conclusive
Kushneria pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	86.8519	1007	1245	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	85.8706	1011	1245	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	85.0801	975	1245	95	below_threshold
Kushneria marisflavi	strain=SW32	GCA_002157205.1	157779	157779	type	True	84.5915	983	1245	95	below_threshold
Kushneria marisflavi	strain=DSM 15357	GCA_003610515.1	157779	157779	type	True	84.4612	1004	1245	95	below_threshold
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	84.4587	973	1245	95	below_threshold
Larsenimonas suaedae	strain=DSM 22428	GCA_023712105.1	1851019	1851019	type	True	78.0126	256	1245	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	77.813	252	1245	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.7165	261	1245	95	below_threshold
Larsenimonas salina	strain=CCM 8464	GCA_023736155.1	1295565	1295565	type	True	77.7062	249	1245	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	77.7026	224	1245	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.679	265	1245	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.1487	233	1245	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:45,648] [INFO] DFAST Taxonomy check result was written to GCF_003385845.1_ASM338584v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:45,649] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:45,649] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:45,649] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d10fc34-f4fa-4c95-a398-cbaa19d3717a/dqc_reference/checkm_data
[2024-01-24 10:57:45,650] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:45,687] [INFO] Task started: CheckM
[2024-01-24 10:57:45,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003385845.1_ASM338584v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003385845.1_ASM338584v1_genomic.fna/checkm_input GCF_003385845.1_ASM338584v1_genomic.fna/checkm_result
[2024-01-24 10:58:22,956] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:22,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:22,978] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:22,979] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:22,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003385845.1_ASM338584v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:22,980] [INFO] Task started: Blastn
[2024-01-24 10:58:22,980] [INFO] Running command: blastn -query GCF_003385845.1_ASM338584v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d10fc34-f4fa-4c95-a398-cbaa19d3717a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003385845.1_ASM338584v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:24,134] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:24,138] [INFO] Selected 10 target genomes.
[2024-01-24 10:58:24,138] [INFO] Target genome list was writen to GCF_003385845.1_ASM338584v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:24,162] [INFO] Task started: fastANI
[2024-01-24 10:58:24,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg60f7bb9b-696c-4199-b497-79b4009f5ac0/GCF_003385845.1_ASM338584v1_genomic.fna.gz --refList GCF_003385845.1_ASM338584v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003385845.1_ASM338584v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:32,323] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:32,332] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:32,332] [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_003385845.1	s__Kushneria indalinina	100.0	1244	1245	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_014652795.1	s__Kushneria pakistanensis	86.8519	1007	1245	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	85.8819	1010	1245	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	85.0801	975	1245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002157205.1	s__Kushneria marisflavi	84.5915	983	1245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002155145.1	s__Kushneria konosiri	84.4461	973	1245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798905.1	s__Halomonas borealis	77.8237	232	1245	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:32,333] [INFO] GTDB search result was written to GCF_003385845.1_ASM338584v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:32,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:32,338] [INFO] DFAST_QC result json was written to GCF_003385845.1_ASM338584v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:32,338] [INFO] DFAST_QC completed!
[2024-01-24 10:58:32,339] [INFO] Total running time: 0h1m13s