[2024-01-24 12:48:20,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:48:20,318] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:48:20,318] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeade9b2-dea9-456e-8a49-cffde00af3fe/dqc_reference
[2024-01-24 12:48:21,505] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:48:21,505] [INFO] Task started: Prodigal
[2024-01-24 12:48:21,506] [INFO] Running command: gunzip -c /var/lib/cwl/stg1c448efc-9ba7-4a7b-8f6e-c3e05e0e1b0e/GCF_002939925.1_ASM293992v1_genomic.fna.gz | prodigal -d GCF_002939925.1_ASM293992v1_genomic.fna/cds.fna -a GCF_002939925.1_ASM293992v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:48:38,853] [INFO] Task succeeded: Prodigal
[2024-01-24 12:48:38,853] [INFO] Task started: HMMsearch
[2024-01-24 12:48:38,853] [INFO] Running command: hmmsearch --tblout GCF_002939925.1_ASM293992v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeade9b2-dea9-456e-8a49-cffde00af3fe/dqc_reference/reference_markers.hmm GCF_002939925.1_ASM293992v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:48:39,156] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:48:39,158] [INFO] Found 6/6 markers.
[2024-01-24 12:48:39,203] [INFO] Query marker FASTA was written to GCF_002939925.1_ASM293992v1_genomic.fna/markers.fasta
[2024-01-24 12:48:39,203] [INFO] Task started: Blastn
[2024-01-24 12:48:39,203] [INFO] Running command: blastn -query GCF_002939925.1_ASM293992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeade9b2-dea9-456e-8a49-cffde00af3fe/dqc_reference/reference_markers.fasta -out GCF_002939925.1_ASM293992v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:48:40,081] [INFO] Task succeeded: Blastn
[2024-01-24 12:48:40,085] [INFO] Selected 10 target genomes.
[2024-01-24 12:48:40,086] [INFO] Target genome list was writen to GCF_002939925.1_ASM293992v1_genomic.fna/target_genomes.txt
[2024-01-24 12:48:40,116] [INFO] Task started: fastANI
[2024-01-24 12:48:40,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c448efc-9ba7-4a7b-8f6e-c3e05e0e1b0e/GCF_002939925.1_ASM293992v1_genomic.fna.gz --refList GCF_002939925.1_ASM293992v1_genomic.fna/target_genomes.txt --output GCF_002939925.1_ASM293992v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:48:53,875] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:53,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeade9b2-dea9-456e-8a49-cffde00af3fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:48:53,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeade9b2-dea9-456e-8a49-cffde00af3fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:48:53,890] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 12:48:53,890] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:48:53,890] [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 vasicola	strain=CFBP2543	GCA_002939925.1	56459	56459	type	True	100.0	1584	1586	95	conclusive
Xanthomonas vasicola	strain=NCPPB 2417	GCA_000772705.2	56459	56459	type	True	99.9929	1579	1586	95	conclusive
Xanthomonas vasicola	strain=SAM119	GCA_002191955.1	56459	56459	pathovar	True	98.684	1475	1586	95	conclusive
Xanthomonas vasicola	strain=SAM119	GCA_003015715.1	56459	56459	pathovar	True	98.6796	1491	1586	95	conclusive
Xanthomonas vasicola	strain=NCPPB 2649	GCA_000770355.2	56459	56459	pathovar	True	98.5493	1506	1586	95	conclusive
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	90.3131	1339	1586	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	90.2505	1383	1586	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	86.7584	1286	1586	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	86.7484	1281	1586	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.7376	1311	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:48:53,892] [INFO] DFAST Taxonomy check result was written to GCF_002939925.1_ASM293992v1_genomic.fna/tc_result.tsv
[2024-01-24 12:48:53,893] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:48:53,893] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:48:53,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeade9b2-dea9-456e-8a49-cffde00af3fe/dqc_reference/checkm_data
[2024-01-24 12:48:53,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:48:53,944] [INFO] Task started: CheckM
[2024-01-24 12:48:53,944] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002939925.1_ASM293992v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002939925.1_ASM293992v1_genomic.fna/checkm_input GCF_002939925.1_ASM293992v1_genomic.fna/checkm_result
[2024-01-24 12:49:44,557] [INFO] Task succeeded: CheckM
[2024-01-24 12:49:44,559] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:49:44,584] [INFO] ===== Completeness check finished =====
[2024-01-24 12:49:44,584] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:49:44,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002939925.1_ASM293992v1_genomic.fna/markers.fasta)
[2024-01-24 12:49:44,585] [INFO] Task started: Blastn
[2024-01-24 12:49:44,585] [INFO] Running command: blastn -query GCF_002939925.1_ASM293992v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeade9b2-dea9-456e-8a49-cffde00af3fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_002939925.1_ASM293992v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:49:46,155] [INFO] Task succeeded: Blastn
[2024-01-24 12:49:46,159] [INFO] Selected 9 target genomes.
[2024-01-24 12:49:46,159] [INFO] Target genome list was writen to GCF_002939925.1_ASM293992v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:49:46,174] [INFO] Task started: fastANI
[2024-01-24 12:49:46,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg1c448efc-9ba7-4a7b-8f6e-c3e05e0e1b0e/GCF_002939925.1_ASM293992v1_genomic.fna.gz --refList GCF_002939925.1_ASM293992v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002939925.1_ASM293992v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:49:59,232] [INFO] Task succeeded: fastANI
[2024-01-24 12:49:59,249] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:49:59,250] [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_000772705.2	s__Xanthomonas vasicola	99.9929	1579	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	conclusive
GCF_002846205.1	s__Xanthomonas prunicola	91.2571	1361	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_004136375.1	s__Xanthomonas oryzae	90.8044	1258	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
GCF_013112235.1	s__Xanthomonas perforans	90.3864	1387	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_008801575.1	s__Xanthomonas cissicola	90.3082	1359	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_003999565.1	s__Xanthomonas phaseoli	89.7949	1377	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_001304695.1	s__Xanthomonas axonopodis	89.7533	1193	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_900092025.1	s__Xanthomonas bromi	89.5775	1296	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001660815.1	s__Xanthomonas nasturtii	89.0175	1287	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:49:59,252] [INFO] GTDB search result was written to GCF_002939925.1_ASM293992v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:49:59,253] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:49:59,258] [INFO] DFAST_QC result json was written to GCF_002939925.1_ASM293992v1_genomic.fna/dqc_result.json
[2024-01-24 12:49:59,258] [INFO] DFAST_QC completed!
[2024-01-24 12:49:59,258] [INFO] Total running time: 0h1m39s