[2024-01-24 12:36:24,192] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,194] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,195] [INFO] DQC Reference Directory: /var/lib/cwl/stgacf0a67e-23cf-457d-abdd-4a0c7346775a/dqc_reference
[2024-01-24 12:36:25,583] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:25,584] [INFO] Task started: Prodigal
[2024-01-24 12:36:25,585] [INFO] Running command: gunzip -c /var/lib/cwl/stgec0be67e-2430-4390-a523-757bb3befa05/GCF_022669045.1_ASM2266904v1_genomic.fna.gz | prodigal -d GCF_022669045.1_ASM2266904v1_genomic.fna/cds.fna -a GCF_022669045.1_ASM2266904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:40,570] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:40,570] [INFO] Task started: HMMsearch
[2024-01-24 12:36:40,570] [INFO] Running command: hmmsearch --tblout GCF_022669045.1_ASM2266904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgacf0a67e-23cf-457d-abdd-4a0c7346775a/dqc_reference/reference_markers.hmm GCF_022669045.1_ASM2266904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:40,852] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:40,854] [INFO] Found 6/6 markers.
[2024-01-24 12:36:40,899] [INFO] Query marker FASTA was written to GCF_022669045.1_ASM2266904v1_genomic.fna/markers.fasta
[2024-01-24 12:36:40,900] [INFO] Task started: Blastn
[2024-01-24 12:36:40,900] [INFO] Running command: blastn -query GCF_022669045.1_ASM2266904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf0a67e-23cf-457d-abdd-4a0c7346775a/dqc_reference/reference_markers.fasta -out GCF_022669045.1_ASM2266904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:41,946] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:41,951] [INFO] Selected 12 target genomes.
[2024-01-24 12:36:41,951] [INFO] Target genome list was writen to GCF_022669045.1_ASM2266904v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:41,960] [INFO] Task started: fastANI
[2024-01-24 12:36:41,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgec0be67e-2430-4390-a523-757bb3befa05/GCF_022669045.1_ASM2266904v1_genomic.fna.gz --refList GCF_022669045.1_ASM2266904v1_genomic.fna/target_genomes.txt --output GCF_022669045.1_ASM2266904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:57,522] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:57,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgacf0a67e-23cf-457d-abdd-4a0c7346775a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:57,522] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgacf0a67e-23cf-457d-abdd-4a0c7346775a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:57,533] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:36:57,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:36:57,533] [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 indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	100.0	1582	1584	95	conclusive
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	94.3165	1436	1584	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	88.9296	1148	1584	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	88.9277	1157	1584	95	below_threshold
Xanthomonas translucens	strain=DSM 18974	GCA_000331775.1	343	343	type	True	88.4123	945	1584	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	88.3919	984	1584	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	88.1518	1023	1584	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	87.8401	1091	1584	95	below_threshold
Xanthomonas albilineans	strain=CFBP2523	GCA_002939705.1	29447	29447	type	True	84.5768	886	1584	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	82.2819	977	1584	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	82.0826	961	1584	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	82.0022	990	1584	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:57,534] [INFO] DFAST Taxonomy check result was written to GCF_022669045.1_ASM2266904v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:57,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:57,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:57,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgacf0a67e-23cf-457d-abdd-4a0c7346775a/dqc_reference/checkm_data
[2024-01-24 12:36:57,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:57,584] [INFO] Task started: CheckM
[2024-01-24 12:36:57,584] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022669045.1_ASM2266904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022669045.1_ASM2266904v1_genomic.fna/checkm_input GCF_022669045.1_ASM2266904v1_genomic.fna/checkm_result
[2024-01-24 12:37:50,456] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:50,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:50,480] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:50,480] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:50,481] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022669045.1_ASM2266904v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:50,481] [INFO] Task started: Blastn
[2024-01-24 12:37:50,481] [INFO] Running command: blastn -query GCF_022669045.1_ASM2266904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgacf0a67e-23cf-457d-abdd-4a0c7346775a/dqc_reference/reference_markers_gtdb.fasta -out GCF_022669045.1_ASM2266904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:52,529] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:52,533] [INFO] Selected 5 target genomes.
[2024-01-24 12:37:52,533] [INFO] Target genome list was writen to GCF_022669045.1_ASM2266904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:52,539] [INFO] Task started: fastANI
[2024-01-24 12:37:52,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgec0be67e-2430-4390-a523-757bb3befa05/GCF_022669045.1_ASM2266904v1_genomic.fna.gz --refList GCF_022669045.1_ASM2266904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022669045.1_ASM2266904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:01,593] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:01,602] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:01,603] [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_014206815.1	s__Xanthomonas_A sacchari_B	96.701	1461	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002940085.1	s__Xanthomonas_A sacchari	94.3165	1436	1584	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_014199795.1	s__Xanthomonas_A sp014199795	93.8735	1434	1584	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_008119715.1	s__Xanthomonas_A sontii	93.849	1257	1584	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_001043115.1	s__Xanthomonas_A sp001043115	93.844	1389	1584	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	96.72	96.71	0.90	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:01,604] [INFO] GTDB search result was written to GCF_022669045.1_ASM2266904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:01,605] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:01,609] [INFO] DFAST_QC result json was written to GCF_022669045.1_ASM2266904v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:01,610] [INFO] DFAST_QC completed!
[2024-01-24 12:38:01,610] [INFO] Total running time: 0h1m37s