[2024-01-24 13:22:30,935] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:30,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:30,936] [INFO] DQC Reference Directory: /var/lib/cwl/stg68945294-e4ef-4cd9-8eaa-f184e4d8886b/dqc_reference
[2024-01-24 13:22:32,203] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,205] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,205] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b047990-7468-45cd-99ea-a692157e29fc/GCF_002940085.1_ASM294008v1_genomic.fna.gz | prodigal -d GCF_002940085.1_ASM294008v1_genomic.fna/cds.fna -a GCF_002940085.1_ASM294008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:47,911] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:47,912] [INFO] Task started: HMMsearch
[2024-01-24 13:22:47,912] [INFO] Running command: hmmsearch --tblout GCF_002940085.1_ASM294008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68945294-e4ef-4cd9-8eaa-f184e4d8886b/dqc_reference/reference_markers.hmm GCF_002940085.1_ASM294008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:48,192] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:48,194] [INFO] Found 6/6 markers.
[2024-01-24 13:22:48,237] [INFO] Query marker FASTA was written to GCF_002940085.1_ASM294008v1_genomic.fna/markers.fasta
[2024-01-24 13:22:48,238] [INFO] Task started: Blastn
[2024-01-24 13:22:48,238] [INFO] Running command: blastn -query GCF_002940085.1_ASM294008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68945294-e4ef-4cd9-8eaa-f184e4d8886b/dqc_reference/reference_markers.fasta -out GCF_002940085.1_ASM294008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:49,263] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:49,267] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:49,267] [INFO] Target genome list was writen to GCF_002940085.1_ASM294008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:49,683] [INFO] Task started: fastANI
[2024-01-24 13:22:49,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b047990-7468-45cd-99ea-a692157e29fc/GCF_002940085.1_ASM294008v1_genomic.fna.gz --refList GCF_002940085.1_ASM294008v1_genomic.fna/target_genomes.txt --output GCF_002940085.1_ASM294008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:05,625] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:05,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68945294-e4ef-4cd9-8eaa-f184e4d8886b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:05,626] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68945294-e4ef-4cd9-8eaa-f184e4d8886b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:05,641] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:05,641] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:05,642] [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 sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	100.0	1617	1619	95	conclusive
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	94.3292	1454	1619	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	88.7727	1160	1619	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	88.7407	1159	1619	95	below_threshold
Xanthomonas translucens	strain=DSM 18974	GCA_000331775.1	343	343	type	True	88.3393	954	1619	95	below_threshold
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	88.3209	985	1619	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	88.1827	1008	1619	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	87.7665	1083	1619	95	below_threshold
Xanthomonas albilineans	strain=CFBP2523	GCA_002939705.1	29447	29447	type	True	84.2057	911	1619	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	82.1461	977	1619	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	81.9081	993	1619	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	81.8649	981	1619	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:05,643] [INFO] DFAST Taxonomy check result was written to GCF_002940085.1_ASM294008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:05,644] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:05,644] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:05,644] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68945294-e4ef-4cd9-8eaa-f184e4d8886b/dqc_reference/checkm_data
[2024-01-24 13:23:05,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:05,695] [INFO] Task started: CheckM
[2024-01-24 13:23:05,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002940085.1_ASM294008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002940085.1_ASM294008v1_genomic.fna/checkm_input GCF_002940085.1_ASM294008v1_genomic.fna/checkm_result
[2024-01-24 13:24:00,498] [INFO] Task succeeded: CheckM
[2024-01-24 13:24:00,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:24:00,531] [INFO] ===== Completeness check finished =====
[2024-01-24 13:24:00,532] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:24:00,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002940085.1_ASM294008v1_genomic.fna/markers.fasta)
[2024-01-24 13:24:00,533] [INFO] Task started: Blastn
[2024-01-24 13:24:00,533] [INFO] Running command: blastn -query GCF_002940085.1_ASM294008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68945294-e4ef-4cd9-8eaa-f184e4d8886b/dqc_reference/reference_markers_gtdb.fasta -out GCF_002940085.1_ASM294008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:24:02,514] [INFO] Task succeeded: Blastn
[2024-01-24 13:24:02,518] [INFO] Selected 5 target genomes.
[2024-01-24 13:24:02,518] [INFO] Target genome list was writen to GCF_002940085.1_ASM294008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:24:02,528] [INFO] Task started: fastANI
[2024-01-24 13:24:02,529] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b047990-7468-45cd-99ea-a692157e29fc/GCF_002940085.1_ASM294008v1_genomic.fna.gz --refList GCF_002940085.1_ASM294008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002940085.1_ASM294008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:24:12,422] [INFO] Task succeeded: fastANI
[2024-01-24 13:24:12,433] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:24:12,434] [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_002940085.1	s__Xanthomonas_A sacchari	100.0	1617	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.45	95.41	0.95	0.91	6	conclusive
GCF_008119715.1	s__Xanthomonas_A sontii	94.5826	1282	1619	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_014206815.1	s__Xanthomonas_A sacchari_B	94.1035	1428	1619	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	93.8132	1413	1619	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_014199795.1	s__Xanthomonas_A sp014199795	93.6085	1435	1619	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:24:12,435] [INFO] GTDB search result was written to GCF_002940085.1_ASM294008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:24:12,436] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:24:12,439] [INFO] DFAST_QC result json was written to GCF_002940085.1_ASM294008v1_genomic.fna/dqc_result.json
[2024-01-24 13:24:12,440] [INFO] DFAST_QC completed!
[2024-01-24 13:24:12,440] [INFO] Total running time: 0h1m42s