[2024-01-24 11:43:42,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,358] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,358] [INFO] DQC Reference Directory: /var/lib/cwl/stg03024845-4797-4037-95df-299da2a31ad4/dqc_reference
[2024-01-24 11:43:43,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,831] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,832] [INFO] Running command: gunzip -c /var/lib/cwl/stg70eaa0bb-ef53-4eb1-84ed-665a30035658/GCF_001401655.1_Xcc_LMG9322_genomic.fna.gz | prodigal -d GCF_001401655.1_Xcc_LMG9322_genomic.fna/cds.fna -a GCF_001401655.1_Xcc_LMG9322_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:59,094] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:59,094] [INFO] Task started: HMMsearch
[2024-01-24 11:43:59,095] [INFO] Running command: hmmsearch --tblout GCF_001401655.1_Xcc_LMG9322_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03024845-4797-4037-95df-299da2a31ad4/dqc_reference/reference_markers.hmm GCF_001401655.1_Xcc_LMG9322_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:59,531] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:59,533] [INFO] Found 6/6 markers.
[2024-01-24 11:43:59,581] [INFO] Query marker FASTA was written to GCF_001401655.1_Xcc_LMG9322_genomic.fna/markers.fasta
[2024-01-24 11:43:59,581] [INFO] Task started: Blastn
[2024-01-24 11:43:59,581] [INFO] Running command: blastn -query GCF_001401655.1_Xcc_LMG9322_genomic.fna/markers.fasta -db /var/lib/cwl/stg03024845-4797-4037-95df-299da2a31ad4/dqc_reference/reference_markers.fasta -out GCF_001401655.1_Xcc_LMG9322_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:00,488] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:00,491] [INFO] Selected 15 target genomes.
[2024-01-24 11:44:00,492] [INFO] Target genome list was writen to GCF_001401655.1_Xcc_LMG9322_genomic.fna/target_genomes.txt
[2024-01-24 11:44:00,497] [INFO] Task started: fastANI
[2024-01-24 11:44:00,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg70eaa0bb-ef53-4eb1-84ed-665a30035658/GCF_001401655.1_Xcc_LMG9322_genomic.fna.gz --refList GCF_001401655.1_Xcc_LMG9322_genomic.fna/target_genomes.txt --output GCF_001401655.1_Xcc_LMG9322_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:16,893] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:16,893] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03024845-4797-4037-95df-299da2a31ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:16,894] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03024845-4797-4037-95df-299da2a31ad4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:16,907] [INFO] Found 15 fastANI hits (11 hits with ANI > threshold)
[2024-01-24 11:44:16,908] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:44:16,908] [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 citri	strain=LMG 9322	GCA_001401655.1	346	346	suspected-type	True	100.0	1301	1313	95	inconclusive
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	99.977	1280	1313	95	inconclusive
Xanthomonas citri	strain=LMG 941	GCA_000263335.1	346	346	pathovar	True	98.785	1172	1313	95	inconclusive
Xanthomonas citri	strain=CFBP 2526	GCA_000495275.1	346	346	pathovar	True	98.7792	1218	1313	95	inconclusive
Xanthomonas citri	strain=LMG712	GCA_002019125.1	346	346	pathovar	True	98.7493	1200	1313	95	inconclusive
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	98.7104	1225	1313	95	inconclusive
Xanthomonas citri	strain=LMG 965	GCA_000723725.1	346	346	pathovar	True	98.6708	1212	1313	95	inconclusive
Xanthomonas citri	strain=LMG 859	GCA_000285775.1	346	346	pathovar	True	98.6345	1155	1313	95	inconclusive
Xanthomonas cissicola	strain=CCUG 18839	GCA_008801575.1	86186	86186	suspected-type	True	98.3963	1180	1313	95	inconclusive
Xanthomonas cissicola	strain=LMG21719	GCA_002019225.1	86186	86186	suspected-type	True	98.3688	1161	1313	95	inconclusive
Xanthomonas citri	strain=WHRI 5232	GCA_003064125.1	346	346	pathovar	True	98.3673	1207	1313	95	inconclusive
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	94.2427	1144	1313	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.8415	1076	1313	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.4715	800	1313	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.1532	857	1313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:16,910] [INFO] DFAST Taxonomy check result was written to GCF_001401655.1_Xcc_LMG9322_genomic.fna/tc_result.tsv
[2024-01-24 11:44:16,910] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:16,911] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:16,911] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03024845-4797-4037-95df-299da2a31ad4/dqc_reference/checkm_data
[2024-01-24 11:44:16,912] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:16,965] [INFO] Task started: CheckM
[2024-01-24 11:44:16,966] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001401655.1_Xcc_LMG9322_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001401655.1_Xcc_LMG9322_genomic.fna/checkm_input GCF_001401655.1_Xcc_LMG9322_genomic.fna/checkm_result
[2024-01-24 11:45:05,950] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:05,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:05,977] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:05,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:05,978] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001401655.1_Xcc_LMG9322_genomic.fna/markers.fasta)
[2024-01-24 11:45:05,978] [INFO] Task started: Blastn
[2024-01-24 11:45:05,979] [INFO] Running command: blastn -query GCF_001401655.1_Xcc_LMG9322_genomic.fna/markers.fasta -db /var/lib/cwl/stg03024845-4797-4037-95df-299da2a31ad4/dqc_reference/reference_markers_gtdb.fasta -out GCF_001401655.1_Xcc_LMG9322_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:07,661] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:07,665] [INFO] Selected 8 target genomes.
[2024-01-24 11:45:07,665] [INFO] Target genome list was writen to GCF_001401655.1_Xcc_LMG9322_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:07,673] [INFO] Task started: fastANI
[2024-01-24 11:45:07,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg70eaa0bb-ef53-4eb1-84ed-665a30035658/GCF_001401655.1_Xcc_LMG9322_genomic.fna.gz --refList GCF_001401655.1_Xcc_LMG9322_genomic.fna/target_genomes_gtdb.txt --output GCF_001401655.1_Xcc_LMG9322_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:17,696] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:17,711] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:17,711] [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_008801575.1	s__Xanthomonas cissicola	98.3963	1180	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	conclusive
GCF_013112235.1	s__Xanthomonas perforans	94.3658	1163	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.28	96.72	0.95	0.89	246	-
GCF_003999565.1	s__Xanthomonas phaseoli	93.7463	1156	1313	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	93.1491	975	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	-
GCF_002846205.1	s__Xanthomonas prunicola	90.0315	1130	1313	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	89.5167	974	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.14	96.34	0.95	0.82	364	-
GCF_001660815.1	s__Xanthomonas nasturtii	89.175	1056	1313	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	87.3704	998	1313	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:17,713] [INFO] GTDB search result was written to GCF_001401655.1_Xcc_LMG9322_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:17,713] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:17,716] [INFO] DFAST_QC result json was written to GCF_001401655.1_Xcc_LMG9322_genomic.fna/dqc_result.json
[2024-01-24 11:45:17,716] [INFO] DFAST_QC completed!
[2024-01-24 11:45:17,716] [INFO] Total running time: 0h1m35s