[2024-01-24 12:06:24,000] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,005] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,005] [INFO] DQC Reference Directory: /var/lib/cwl/stga0926fb6-7e99-4c75-a73b-30fec1c7100f/dqc_reference
[2024-01-24 12:06:25,318] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,319] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,320] [INFO] Running command: gunzip -c /var/lib/cwl/stgac8e9a03-971e-4260-b2e5-2b4c37c5daea/GCF_013112235.1_ASM1311223v1_genomic.fna.gz | prodigal -d GCF_013112235.1_ASM1311223v1_genomic.fna/cds.fna -a GCF_013112235.1_ASM1311223v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:43,082] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:43,082] [INFO] Task started: HMMsearch
[2024-01-24 12:06:43,083] [INFO] Running command: hmmsearch --tblout GCF_013112235.1_ASM1311223v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0926fb6-7e99-4c75-a73b-30fec1c7100f/dqc_reference/reference_markers.hmm GCF_013112235.1_ASM1311223v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:43,341] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:43,342] [INFO] Found 6/6 markers.
[2024-01-24 12:06:43,385] [INFO] Query marker FASTA was written to GCF_013112235.1_ASM1311223v1_genomic.fna/markers.fasta
[2024-01-24 12:06:43,386] [INFO] Task started: Blastn
[2024-01-24 12:06:43,386] [INFO] Running command: blastn -query GCF_013112235.1_ASM1311223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0926fb6-7e99-4c75-a73b-30fec1c7100f/dqc_reference/reference_markers.fasta -out GCF_013112235.1_ASM1311223v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:44,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:44,292] [INFO] Selected 12 target genomes.
[2024-01-24 12:06:44,292] [INFO] Target genome list was writen to GCF_013112235.1_ASM1311223v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:44,297] [INFO] Task started: fastANI
[2024-01-24 12:06:44,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgac8e9a03-971e-4260-b2e5-2b4c37c5daea/GCF_013112235.1_ASM1311223v1_genomic.fna.gz --refList GCF_013112235.1_ASM1311223v1_genomic.fna/target_genomes.txt --output GCF_013112235.1_ASM1311223v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:59,854] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:59,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0926fb6-7e99-4c75-a73b-30fec1c7100f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:59,855] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0926fb6-7e99-4c75-a73b-30fec1c7100f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:59,865] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 12:06:59,865] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:59,865] [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 euvesicatoria pv. alfalfae	strain=CFBP 3836	GCA_000488955.1	359387	456327	pathovar	True	98.637	1577	1677	95	conclusive
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP3836	GCA_017724035.1	359387	456327	pathovar	True	98.5598	1591	1677	95	conclusive
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	98.4713	1529	1677	95	conclusive
Xanthomonas euvesicatoria	strain=LMG 27970	GCA_001401555.1	456327	456327	type	True	98.0521	1102	1677	95	conclusive
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	94.39	1500	1677	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	94.334	1507	1677	95	below_threshold
Xanthomonas phaseoli	strain=CFBP2534	GCA_017745345.1	1985254	1985254	pathovar	True	94.261	1471	1677	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001402235.1	1985254	1985254	pathovar	True	94.1463	1350	1677	95	below_threshold
Xanthomonas phaseoli	strain=LMG 695	GCA_001564415.1	1985254	1985254	pathovar	True	94.1269	1534	1677	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	87.0907	1366	1677	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	87.0395	1334	1677	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.8748	962	1677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:59,867] [INFO] DFAST Taxonomy check result was written to GCF_013112235.1_ASM1311223v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:59,868] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:59,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:59,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0926fb6-7e99-4c75-a73b-30fec1c7100f/dqc_reference/checkm_data
[2024-01-24 12:06:59,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:59,915] [INFO] Task started: CheckM
[2024-01-24 12:06:59,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013112235.1_ASM1311223v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013112235.1_ASM1311223v1_genomic.fna/checkm_input GCF_013112235.1_ASM1311223v1_genomic.fna/checkm_result
[2024-01-24 12:08:09,618] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:09,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:09,637] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:09,637] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:09,637] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013112235.1_ASM1311223v1_genomic.fna/markers.fasta)
[2024-01-24 12:08:09,638] [INFO] Task started: Blastn
[2024-01-24 12:08:09,638] [INFO] Running command: blastn -query GCF_013112235.1_ASM1311223v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0926fb6-7e99-4c75-a73b-30fec1c7100f/dqc_reference/reference_markers_gtdb.fasta -out GCF_013112235.1_ASM1311223v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:11,274] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:11,279] [INFO] Selected 9 target genomes.
[2024-01-24 12:08:11,279] [INFO] Target genome list was writen to GCF_013112235.1_ASM1311223v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:11,287] [INFO] Task started: fastANI
[2024-01-24 12:08:11,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgac8e9a03-971e-4260-b2e5-2b4c37c5daea/GCF_013112235.1_ASM1311223v1_genomic.fna.gz --refList GCF_013112235.1_ASM1311223v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013112235.1_ASM1311223v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:23,629] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:23,637] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:23,637] [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_013112235.1	s__Xanthomonas perforans	100.0	1675	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	conclusive
GCF_008801575.1	s__Xanthomonas cissicola	94.5551	1434	1677	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	94.1371	1524	1677	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	93.3592	1234	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_000772705.2	s__Xanthomonas vasicola	90.3826	1392	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	-
GCF_002846205.1	s__Xanthomonas prunicola	90.1127	1435	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_001660815.1	s__Xanthomonas nasturtii	89.1616	1351	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.97	98.97	0.95	0.95	2	-
GCF_000802365.1	s__Xanthomonas cannabis	87.5098	1254	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_001642575.1	s__Xanthomonas floridensis	87.0258	1377	1677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:23,639] [INFO] GTDB search result was written to GCF_013112235.1_ASM1311223v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:23,639] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:23,642] [INFO] DFAST_QC result json was written to GCF_013112235.1_ASM1311223v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:23,643] [INFO] DFAST_QC completed!
[2024-01-24 12:08:23,643] [INFO] Total running time: 0h1m60s