[2024-01-24 13:31:41,652] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:41,653] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:41,653] [INFO] DQC Reference Directory: /var/lib/cwl/stgdb472437-71cc-47af-a097-11c2286f5106/dqc_reference
[2024-01-24 13:31:42,864] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:42,864] [INFO] Task started: Prodigal
[2024-01-24 13:31:42,865] [INFO] Running command: gunzip -c /var/lib/cwl/stg66f16598-770b-4f2e-a4fd-d54e58c69bd9/GCF_004283755.1_ASM428375v1_genomic.fna.gz | prodigal -d GCF_004283755.1_ASM428375v1_genomic.fna/cds.fna -a GCF_004283755.1_ASM428375v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:56,309] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:56,309] [INFO] Task started: HMMsearch
[2024-01-24 13:31:56,309] [INFO] Running command: hmmsearch --tblout GCF_004283755.1_ASM428375v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdb472437-71cc-47af-a097-11c2286f5106/dqc_reference/reference_markers.hmm GCF_004283755.1_ASM428375v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:56,606] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:56,609] [INFO] Found 6/6 markers.
[2024-01-24 13:31:56,659] [INFO] Query marker FASTA was written to GCF_004283755.1_ASM428375v1_genomic.fna/markers.fasta
[2024-01-24 13:31:56,660] [INFO] Task started: Blastn
[2024-01-24 13:31:56,660] [INFO] Running command: blastn -query GCF_004283755.1_ASM428375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb472437-71cc-47af-a097-11c2286f5106/dqc_reference/reference_markers.fasta -out GCF_004283755.1_ASM428375v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:57,697] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:57,704] [INFO] Selected 18 target genomes.
[2024-01-24 13:31:57,704] [INFO] Target genome list was writen to GCF_004283755.1_ASM428375v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:57,735] [INFO] Task started: fastANI
[2024-01-24 13:31:57,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f16598-770b-4f2e-a4fd-d54e58c69bd9/GCF_004283755.1_ASM428375v1_genomic.fna.gz --refList GCF_004283755.1_ASM428375v1_genomic.fna/target_genomes.txt --output GCF_004283755.1_ASM428375v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:16,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:16,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdb472437-71cc-47af-a097-11c2286f5106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:16,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdb472437-71cc-47af-a097-11c2286f5106/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:16,189] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:16,189] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:16,190] [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
Pseudoxanthomonas winnipegensis	strain=NML 130738	GCA_004283755.1	2480810	2480810	type	True	100.0	1488	1489	95	conclusive
Pseudoxanthomonas spadix	strain=DSM 18855	GCA_003703395.1	415229	415229	type	True	85.5897	841	1489	95	below_threshold
Pseudoxanthomonas composti	strain=GSS15	GCA_004122095.1	2137479	2137479	type	True	83.9153	953	1489	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	82.6675	895	1489	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	82.5054	868	1489	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	82.5002	861	1489	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	82.3773	721	1489	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	82.192	685	1489	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	82.1895	714	1489	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	81.9746	695	1489	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	81.6333	731	1489	95	below_threshold
Stenotrophomonas bentonitica	strain=DSM 103927	GCA_013185915.1	1450134	1450134	type	True	81.522	710	1489	95	below_threshold
Stenotrophomonas pavanii	strain=DSM 25135	GCA_001431565.1	487698	487698	type	True	81.2934	710	1489	95	below_threshold
Stenotrophomonas pavanii	strain=LMG 25348	GCA_900101175.1	487698	487698	type	True	81.1656	745	1489	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.0627	496	1489	95	below_threshold
Pseudoxanthomonas indica	strain=CCM 7430	GCA_014635165.1	428993	428993	type	True	80.8016	664	1489	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	80.5491	687	1489	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	80.1611	719	1489	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:16,191] [INFO] DFAST Taxonomy check result was written to GCF_004283755.1_ASM428375v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:16,192] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:16,192] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:16,192] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdb472437-71cc-47af-a097-11c2286f5106/dqc_reference/checkm_data
[2024-01-24 13:32:16,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:16,239] [INFO] Task started: CheckM
[2024-01-24 13:32:16,239] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004283755.1_ASM428375v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004283755.1_ASM428375v1_genomic.fna/checkm_input GCF_004283755.1_ASM428375v1_genomic.fna/checkm_result
[2024-01-24 13:33:01,015] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:01,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:01,035] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:01,035] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:01,035] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004283755.1_ASM428375v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:01,036] [INFO] Task started: Blastn
[2024-01-24 13:33:01,036] [INFO] Running command: blastn -query GCF_004283755.1_ASM428375v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdb472437-71cc-47af-a097-11c2286f5106/dqc_reference/reference_markers_gtdb.fasta -out GCF_004283755.1_ASM428375v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:03,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:03,054] [INFO] Selected 8 target genomes.
[2024-01-24 13:33:03,054] [INFO] Target genome list was writen to GCF_004283755.1_ASM428375v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:03,112] [INFO] Task started: fastANI
[2024-01-24 13:33:03,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg66f16598-770b-4f2e-a4fd-d54e58c69bd9/GCF_004283755.1_ASM428375v1_genomic.fna.gz --refList GCF_004283755.1_ASM428375v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004283755.1_ASM428375v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:13,658] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:13,668] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:13,668] [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_004284195.1	s__Pseudoxanthomonas_A sp004284195	97.3446	1328	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	97.94	97.04	0.92	0.87	11	conclusive
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	94.0708	1226	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
GCF_900109775.1	s__Pseudoxanthomonas_A sp900109775	85.9484	1061	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003703395.1	s__Pseudoxanthomonas_A spadix	85.6158	839	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.25	98.51	0.95	0.90	3	-
GCF_004122095.1	s__Pseudoxanthomonas_A composti	83.9405	951	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007829315.1	s__Xanthomonas_A translucens_A	82.6732	914	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004216795.1	s__Stenotrophomonas_A sp004216795	82.433	795	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007667275.1	s__Stenotrophomonas maltophilia_AE	81.1522	728	1489	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Stenotrophomonas	95.0	98.01	98.01	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:13,670] [INFO] GTDB search result was written to GCF_004283755.1_ASM428375v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:13,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:13,677] [INFO] DFAST_QC result json was written to GCF_004283755.1_ASM428375v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:13,677] [INFO] DFAST_QC completed!
[2024-01-24 13:33:13,677] [INFO] Total running time: 0h1m32s