[2024-01-24 13:22:10,388] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,390] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg437a1d4e-f2f4-4369-9f2b-fc5c71e9964a/dqc_reference
[2024-01-24 13:22:11,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:11,709] [INFO] Task started: Prodigal
[2024-01-24 13:22:11,709] [INFO] Running command: gunzip -c /var/lib/cwl/stgcc08b6dd-c2fa-4cb2-ac03-a5092e4f9263/GCF_014652795.1_ASM1465279v1_genomic.fna.gz | prodigal -d GCF_014652795.1_ASM1465279v1_genomic.fna/cds.fna -a GCF_014652795.1_ASM1465279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:23,269] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:23,269] [INFO] Task started: HMMsearch
[2024-01-24 13:22:23,269] [INFO] Running command: hmmsearch --tblout GCF_014652795.1_ASM1465279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg437a1d4e-f2f4-4369-9f2b-fc5c71e9964a/dqc_reference/reference_markers.hmm GCF_014652795.1_ASM1465279v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:23,557] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:23,558] [INFO] Found 6/6 markers.
[2024-01-24 13:22:23,587] [INFO] Query marker FASTA was written to GCF_014652795.1_ASM1465279v1_genomic.fna/markers.fasta
[2024-01-24 13:22:23,588] [INFO] Task started: Blastn
[2024-01-24 13:22:23,588] [INFO] Running command: blastn -query GCF_014652795.1_ASM1465279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg437a1d4e-f2f4-4369-9f2b-fc5c71e9964a/dqc_reference/reference_markers.fasta -out GCF_014652795.1_ASM1465279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:24,438] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:24,630] [INFO] Selected 14 target genomes.
[2024-01-24 13:22:24,631] [INFO] Target genome list was writen to GCF_014652795.1_ASM1465279v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:24,637] [INFO] Task started: fastANI
[2024-01-24 13:22:24,637] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc08b6dd-c2fa-4cb2-ac03-a5092e4f9263/GCF_014652795.1_ASM1465279v1_genomic.fna.gz --refList GCF_014652795.1_ASM1465279v1_genomic.fna/target_genomes.txt --output GCF_014652795.1_ASM1465279v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:35,844] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:35,844] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg437a1d4e-f2f4-4369-9f2b-fc5c71e9964a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:35,844] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg437a1d4e-f2f4-4369-9f2b-fc5c71e9964a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:35,856] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:35,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:35,857] [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 pakistanensis	strain=KCTC 42082	GCA_014652795.1	1508770	1508770	type	True	100.0	1170	1170	95	conclusive
Kushneria indalinina	strain=DSM 14324	GCA_003385845.1	184067	184067	type	True	86.8429	999	1170	95	below_threshold
Kushneria phyllosphaerae	strain=EAod3	GCA_900312995.1	2100822	2100822	type	True	84.8917	982	1170	95	below_threshold
Kushneria avicenniae	strain=DSM 23439	GCA_900112585.1	402385	402385	type	True	84.2906	938	1170	95	below_threshold
Kushneria marisflavi	strain=SW32	GCA_002157205.1	157779	157779	type	True	84.1155	943	1170	95	below_threshold
Kushneria marisflavi	strain=DSM 15357	GCA_003610515.1	157779	157779	type	True	84.0874	928	1170	95	below_threshold
Kushneria konosiri	strain=X49	GCA_002155145.1	698828	698828	type	True	83.903	905	1170	95	below_threshold
Kushneria aurantia	strain=DSM 21353	GCA_000382245.1	504092	504092	type	True	78.8591	478	1170	95	below_threshold
Kushneria phosphatilytica	strain=YCWA18	GCA_001854625.1	657387	657387	type	True	77.8993	314	1170	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	77.7581	195	1170	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.5893	206	1170	95	below_threshold
Halomonas antri	strain=Y3S6	GCA_019430905.1	2846777	2846777	type	True	77.5719	202	1170	95	below_threshold
Halomonas sulfidivorans	strain=MCCC 1A13718	GCA_017868935.1	2733488	2733488	type	True	77.5131	211	1170	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	77.3191	223	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:35,858] [INFO] DFAST Taxonomy check result was written to GCF_014652795.1_ASM1465279v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:35,859] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:35,859] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:35,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg437a1d4e-f2f4-4369-9f2b-fc5c71e9964a/dqc_reference/checkm_data
[2024-01-24 13:22:35,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:35,899] [INFO] Task started: CheckM
[2024-01-24 13:22:35,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014652795.1_ASM1465279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014652795.1_ASM1465279v1_genomic.fna/checkm_input GCF_014652795.1_ASM1465279v1_genomic.fna/checkm_result
[2024-01-24 13:23:14,643] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:14,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:14,660] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:14,661] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:14,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014652795.1_ASM1465279v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:14,662] [INFO] Task started: Blastn
[2024-01-24 13:23:14,662] [INFO] Running command: blastn -query GCF_014652795.1_ASM1465279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg437a1d4e-f2f4-4369-9f2b-fc5c71e9964a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014652795.1_ASM1465279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:16,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:16,026] [INFO] Selected 8 target genomes.
[2024-01-24 13:23:16,026] [INFO] Target genome list was writen to GCF_014652795.1_ASM1465279v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:16,038] [INFO] Task started: fastANI
[2024-01-24 13:23:16,038] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc08b6dd-c2fa-4cb2-ac03-a5092e4f9263/GCF_014652795.1_ASM1465279v1_genomic.fna.gz --refList GCF_014652795.1_ASM1465279v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014652795.1_ASM1465279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:22,627] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:22,634] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:22,635] [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_014652795.1	s__Kushneria pakistanensis	100.0	1170	1170	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_003385845.1	s__Kushneria indalinina	86.8447	998	1170	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	84.8979	981	1170	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	84.2783	938	1170	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	84.1301	942	1170	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	83.9219	904	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382245.1	s__Kushneria aurantia	78.8765	476	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008247605.1	s__Kushneria phosphatilytica	78.0593	319	1170	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Kushneria	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:22,636] [INFO] GTDB search result was written to GCF_014652795.1_ASM1465279v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:22,637] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:22,640] [INFO] DFAST_QC result json was written to GCF_014652795.1_ASM1465279v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:22,640] [INFO] DFAST_QC completed!
[2024-01-24 13:23:22,640] [INFO] Total running time: 0h1m12s