[2024-01-24 13:40:43,504] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:43,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:43,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg39ff385d-cbc3-40e8-8873-bd7c9604c74b/dqc_reference
[2024-01-24 13:40:44,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:44,889] [INFO] Task started: Prodigal
[2024-01-24 13:40:44,889] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1222284-38dd-4a55-b2fc-bab9334e14b9/GCF_002155145.1_ASM215514v1_genomic.fna.gz | prodigal -d GCF_002155145.1_ASM215514v1_genomic.fna/cds.fna -a GCF_002155145.1_ASM215514v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:56,596] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:56,596] [INFO] Task started: HMMsearch
[2024-01-24 13:40:56,597] [INFO] Running command: hmmsearch --tblout GCF_002155145.1_ASM215514v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39ff385d-cbc3-40e8-8873-bd7c9604c74b/dqc_reference/reference_markers.hmm GCF_002155145.1_ASM215514v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:56,949] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:56,951] [INFO] Found 6/6 markers.
[2024-01-24 13:40:56,989] [INFO] Query marker FASTA was written to GCF_002155145.1_ASM215514v1_genomic.fna/markers.fasta
[2024-01-24 13:40:56,989] [INFO] Task started: Blastn
[2024-01-24 13:40:56,989] [INFO] Running command: blastn -query GCF_002155145.1_ASM215514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39ff385d-cbc3-40e8-8873-bd7c9604c74b/dqc_reference/reference_markers.fasta -out GCF_002155145.1_ASM215514v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:57,858] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:57,861] [INFO] Selected 12 target genomes.
[2024-01-24 13:40:57,862] [INFO] Target genome list was writen to GCF_002155145.1_ASM215514v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:57,866] [INFO] Task started: fastANI
[2024-01-24 13:40:57,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1222284-38dd-4a55-b2fc-bab9334e14b9/GCF_002155145.1_ASM215514v1_genomic.fna.gz --refList GCF_002155145.1_ASM215514v1_genomic.fna/target_genomes.txt --output GCF_002155145.1_ASM215514v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:08,003] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:08,004] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39ff385d-cbc3-40e8-8873-bd7c9604c74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:08,004] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39ff385d-cbc3-40e8-8873-bd7c9604c74b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:08,015] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:08,015] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:08,015] [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 konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	100.0	1191	1194	95	conclusive
Kushneria marisflavi	strain=SW32	GCA_002157205.1	157779	157779	type	True	90.3406	1082	1194	95	below_threshold
Kushneria marisflavi	strain=DSM 15357	GCA_003610515.1	157779	157779	type	True	90.284	1062	1194	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	85.4816	1008	1194	95	below_threshold
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	84.4932	982	1194	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	84.3126	952	1194	95	below_threshold
Kushneria pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	84.1331	900	1194	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.9952	201	1194	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.8808	210	1194	95	below_threshold
Larsenimonas salina	strain=CCM 8464	GCA_023736155.1	1295565	1295565	type	True	77.8045	247	1194	95	below_threshold
Halomonas zhangzhouensis	strain=MCCC 1A11036	GCA_021404465.1	2733481	2733481	type	True	77.5473	179	1194	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.4537	213	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:08,016] [INFO] DFAST Taxonomy check result was written to GCF_002155145.1_ASM215514v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:08,017] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:08,017] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:08,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39ff385d-cbc3-40e8-8873-bd7c9604c74b/dqc_reference/checkm_data
[2024-01-24 13:41:08,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:08,057] [INFO] Task started: CheckM
[2024-01-24 13:41:08,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155145.1_ASM215514v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155145.1_ASM215514v1_genomic.fna/checkm_input GCF_002155145.1_ASM215514v1_genomic.fna/checkm_result
[2024-01-24 13:41:47,209] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:47,210] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.24%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:47,229] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:47,230] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:47,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155145.1_ASM215514v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:47,231] [INFO] Task started: Blastn
[2024-01-24 13:41:47,231] [INFO] Running command: blastn -query GCF_002155145.1_ASM215514v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39ff385d-cbc3-40e8-8873-bd7c9604c74b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155145.1_ASM215514v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:48,608] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:48,613] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:48,613] [INFO] Target genome list was writen to GCF_002155145.1_ASM215514v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:48,633] [INFO] Task started: fastANI
[2024-01-24 13:41:48,633] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1222284-38dd-4a55-b2fc-bab9334e14b9/GCF_002155145.1_ASM215514v1_genomic.fna.gz --refList GCF_002155145.1_ASM215514v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155145.1_ASM215514v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:55,818] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:55,831] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:55,831] [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_002155145.1	s__Kushneria konosiri	100.0	1191	1194	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	90.3243	1082	1194	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900312995.1	s__Kushneria phyllosphaerae	85.4816	1008	1194	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	84.4921	982	1194	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	84.3126	952	1194	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	84.1228	901	1194	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	77.6047	195	1194	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 13:41:55,833] [INFO] GTDB search result was written to GCF_002155145.1_ASM215514v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:55,833] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:55,836] [INFO] DFAST_QC result json was written to GCF_002155145.1_ASM215514v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:55,836] [INFO] DFAST_QC completed!
[2024-01-24 13:41:55,836] [INFO] Total running time: 0h1m12s