[2024-01-24 14:15:02,626] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:02,628] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:02,628] [INFO] DQC Reference Directory: /var/lib/cwl/stg002cdb02-b285-45c7-bd72-8527c093e0e7/dqc_reference
[2024-01-24 14:15:04,069] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:04,070] [INFO] Task started: Prodigal
[2024-01-24 14:15:04,070] [INFO] Running command: gunzip -c /var/lib/cwl/stg8fd23c95-ccf5-4303-8d03-8fbd1138f7c8/GCF_002939705.1_ASM293970v1_genomic.fna.gz | prodigal -d GCF_002939705.1_ASM293970v1_genomic.fna/cds.fna -a GCF_002939705.1_ASM293970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:18,120] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:18,120] [INFO] Task started: HMMsearch
[2024-01-24 14:15:18,121] [INFO] Running command: hmmsearch --tblout GCF_002939705.1_ASM293970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg002cdb02-b285-45c7-bd72-8527c093e0e7/dqc_reference/reference_markers.hmm GCF_002939705.1_ASM293970v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:18,437] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:18,439] [INFO] Found 6/6 markers.
[2024-01-24 14:15:18,477] [INFO] Query marker FASTA was written to GCF_002939705.1_ASM293970v1_genomic.fna/markers.fasta
[2024-01-24 14:15:18,478] [INFO] Task started: Blastn
[2024-01-24 14:15:18,478] [INFO] Running command: blastn -query GCF_002939705.1_ASM293970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg002cdb02-b285-45c7-bd72-8527c093e0e7/dqc_reference/reference_markers.fasta -out GCF_002939705.1_ASM293970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:19,400] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:19,403] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:19,404] [INFO] Target genome list was writen to GCF_002939705.1_ASM293970v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:19,410] [INFO] Task started: fastANI
[2024-01-24 14:15:19,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fd23c95-ccf5-4303-8d03-8fbd1138f7c8/GCF_002939705.1_ASM293970v1_genomic.fna.gz --refList GCF_002939705.1_ASM293970v1_genomic.fna/target_genomes.txt --output GCF_002939705.1_ASM293970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:31,104] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:31,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg002cdb02-b285-45c7-bd72-8527c093e0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:31,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg002cdb02-b285-45c7-bd72-8527c093e0e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:31,114] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:31,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:31,115] [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
Xanthomonas albilineans	strain=CFBP2523	GCA_002939705.1	29447	29447	type	True	100.0	1176	1177	95	conclusive
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	84.5353	891	1177	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	84.4116	899	1177	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	83.836	830	1177	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	83.7841	838	1177	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	83.7533	755	1177	95	below_threshold
Xanthomonas translucens	strain=DSM 18974	GCA_000331775.1	343	343	type	True	83.6724	740	1177	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	83.4745	778	1177	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	83.2478	829	1177	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	79.8896	611	1177	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	79.8861	644	1177	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	79.7537	622	1177	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:31,116] [INFO] DFAST Taxonomy check result was written to GCF_002939705.1_ASM293970v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:31,117] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:31,117] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:31,117] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg002cdb02-b285-45c7-bd72-8527c093e0e7/dqc_reference/checkm_data
[2024-01-24 14:15:31,118] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:31,159] [INFO] Task started: CheckM
[2024-01-24 14:15:31,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002939705.1_ASM293970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002939705.1_ASM293970v1_genomic.fna/checkm_input GCF_002939705.1_ASM293970v1_genomic.fna/checkm_result
[2024-01-24 14:16:14,427] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:14,428] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:14,445] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:14,445] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:14,445] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002939705.1_ASM293970v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:14,446] [INFO] Task started: Blastn
[2024-01-24 14:16:14,446] [INFO] Running command: blastn -query GCF_002939705.1_ASM293970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg002cdb02-b285-45c7-bd72-8527c093e0e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002939705.1_ASM293970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:16,111] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:16,116] [INFO] Selected 11 target genomes.
[2024-01-24 14:16:16,116] [INFO] Target genome list was writen to GCF_002939705.1_ASM293970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:16,158] [INFO] Task started: fastANI
[2024-01-24 14:16:16,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fd23c95-ccf5-4303-8d03-8fbd1138f7c8/GCF_002939705.1_ASM293970v1_genomic.fna.gz --refList GCF_002939705.1_ASM293970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002939705.1_ASM293970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:27,528] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:27,543] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:27,543] [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_002939705.1	s__Xanthomonas_A albilineans	100.0	1176	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.54	98.32	0.96	0.93	17	conclusive
GCF_000963005.1	s__Xanthomonas_A sp000963005	90.5159	1035	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.55	96.55	0.90	0.90	2	-
GCF_014206815.1	s__Xanthomonas_A sacchari_B	84.5791	906	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001043115.1	s__Xanthomonas_A sp001043115	84.4997	885	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
GCF_008119715.1	s__Xanthomonas_A sontii	84.4381	819	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.63	96.72	0.89	0.85	12	-
GCF_014199795.1	s__Xanthomonas_A sp014199795	84.4375	903	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
GCF_002940085.1	s__Xanthomonas_A sacchari	84.41	900	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.45	95.41	0.95	0.91	6	-
GCF_007829315.1	s__Xanthomonas_A translucens_A	84.0959	877	1177	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_014236855.1	s__Xanthomonas_A sp014236855	83.9183	880	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	95.82	95.01	0.91	0.88	7	-
GCF_014197395.1	s__Xanthomonas_A translucens_B	83.7686	876	1177	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_014236795.1	s__Xanthomonas_A theicola	83.2328	830	1177	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:27,545] [INFO] GTDB search result was written to GCF_002939705.1_ASM293970v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:27,545] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:27,548] [INFO] DFAST_QC result json was written to GCF_002939705.1_ASM293970v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:27,549] [INFO] DFAST_QC completed!
[2024-01-24 14:16:27,549] [INFO] Total running time: 0h1m25s