[2024-01-24 15:18:18,751] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:18,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:18,753] [INFO] DQC Reference Directory: /var/lib/cwl/stg4103d6e6-488e-459b-94e0-9e8fc10b9e01/dqc_reference
[2024-01-24 15:18:20,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:20,042] [INFO] Task started: Prodigal
[2024-01-24 15:18:20,042] [INFO] Running command: gunzip -c /var/lib/cwl/stgde5d05f1-248a-44a5-9b67-de1c9eb91ce8/GCF_001401595.1_Xaa_LMG982_genomic.fna.gz | prodigal -d GCF_001401595.1_Xaa_LMG982_genomic.fna/cds.fna -a GCF_001401595.1_Xaa_LMG982_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:33,254] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:33,255] [INFO] Task started: HMMsearch
[2024-01-24 15:18:33,255] [INFO] Running command: hmmsearch --tblout GCF_001401595.1_Xaa_LMG982_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4103d6e6-488e-459b-94e0-9e8fc10b9e01/dqc_reference/reference_markers.hmm GCF_001401595.1_Xaa_LMG982_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:33,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:33,531] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgde5d05f1-248a-44a5-9b67-de1c9eb91ce8/GCF_001401595.1_Xaa_LMG982_genomic.fna.gz]
[2024-01-24 15:18:33,585] [INFO] Query marker FASTA was written to GCF_001401595.1_Xaa_LMG982_genomic.fna/markers.fasta
[2024-01-24 15:18:33,586] [INFO] Task started: Blastn
[2024-01-24 15:18:33,586] [INFO] Running command: blastn -query GCF_001401595.1_Xaa_LMG982_genomic.fna/markers.fasta -db /var/lib/cwl/stg4103d6e6-488e-459b-94e0-9e8fc10b9e01/dqc_reference/reference_markers.fasta -out GCF_001401595.1_Xaa_LMG982_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:34,478] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:34,484] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:34,485] [INFO] Target genome list was writen to GCF_001401595.1_Xaa_LMG982_genomic.fna/target_genomes.txt
[2024-01-24 15:18:34,493] [INFO] Task started: fastANI
[2024-01-24 15:18:34,493] [INFO] Running command: fastANI --query /var/lib/cwl/stgde5d05f1-248a-44a5-9b67-de1c9eb91ce8/GCF_001401595.1_Xaa_LMG982_genomic.fna.gz --refList GCF_001401595.1_Xaa_LMG982_genomic.fna/target_genomes.txt --output GCF_001401595.1_Xaa_LMG982_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:50,280] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:50,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4103d6e6-488e-459b-94e0-9e8fc10b9e01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:50,281] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4103d6e6-488e-459b-94e0-9e8fc10b9e01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:50,300] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:50,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:50,301] [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 axonopodis subcluster 9.3	strain=LMG 982	GCA_001401595.1	1982678	53413	suspected-type	True	100.0	1062	1081	95	conclusive
Xanthomonas axonopodis	strain=DSM 3585	GCA_001304695.1	53413	53413	suspected-type	True	99.9615	1065	1081	95	conclusive
Xanthomonas phaseoli	strain=CFBP2534	GCA_017745345.1	1985254	1985254	pathovar	True	93.7023	1001	1081	95	below_threshold
Xanthomonas phaseoli	strain=NCPPB 3035	GCA_000774035.2	1985254	1985254	pathovar	True	93.6754	997	1081	95	below_threshold
Xanthomonas phaseoli	strain=LMG784	GCA_001482665.1	1985254	1985254	pathovar	True	93.646	989	1081	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	93.3805	1009	1081	95	below_threshold
Xanthomonas citri	strain=CFBP 2526	GCA_000495275.1	346	346	pathovar	True	93.365	1005	1081	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	93.3637	1006	1081	95	below_threshold
Xanthomonas citri	strain=CFBP 2913	GCA_002688625.1	346	346	pathovar	True	93.3409	1019	1081	95	below_threshold
Xanthomonas citri	strain=LMG 859	GCA_000285775.1	346	346	pathovar	True	93.3297	972	1081	95	below_threshold
Xanthomonas citri	strain=LMG9322	GCA_002018575.1	346	346	suspected-type	True	93.3113	980	1081	95	below_threshold
Xanthomonas citri	strain=LMG867	GCA_020011255.1	346	346	pathovar	True	93.2512	961	1081	95	below_threshold
Xanthomonas euvesicatoria	strain=LMG 27970	GCA_001401555.1	456327	456327	type	True	92.8821	803	1081	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	86.5929	960	1081	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	85.29	760	1081	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	85.161	801	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:50,305] [INFO] DFAST Taxonomy check result was written to GCF_001401595.1_Xaa_LMG982_genomic.fna/tc_result.tsv
[2024-01-24 15:18:50,305] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:50,306] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:50,306] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4103d6e6-488e-459b-94e0-9e8fc10b9e01/dqc_reference/checkm_data
[2024-01-24 15:18:50,307] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:50,363] [INFO] Task started: CheckM
[2024-01-24 15:18:50,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001401595.1_Xaa_LMG982_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001401595.1_Xaa_LMG982_genomic.fna/checkm_input GCF_001401595.1_Xaa_LMG982_genomic.fna/checkm_result
[2024-01-24 15:19:32,024] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:32,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.71%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 15:19:32,054] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:32,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:32,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001401595.1_Xaa_LMG982_genomic.fna/markers.fasta)
[2024-01-24 15:19:32,055] [INFO] Task started: Blastn
[2024-01-24 15:19:32,055] [INFO] Running command: blastn -query GCF_001401595.1_Xaa_LMG982_genomic.fna/markers.fasta -db /var/lib/cwl/stg4103d6e6-488e-459b-94e0-9e8fc10b9e01/dqc_reference/reference_markers_gtdb.fasta -out GCF_001401595.1_Xaa_LMG982_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:33,618] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:33,622] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:33,623] [INFO] Target genome list was writen to GCF_001401595.1_Xaa_LMG982_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:33,630] [INFO] Task started: fastANI
[2024-01-24 15:19:33,631] [INFO] Running command: fastANI --query /var/lib/cwl/stgde5d05f1-248a-44a5-9b67-de1c9eb91ce8/GCF_001401595.1_Xaa_LMG982_genomic.fna.gz --refList GCF_001401595.1_Xaa_LMG982_genomic.fna/target_genomes_gtdb.txt --output GCF_001401595.1_Xaa_LMG982_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:43,558] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:43,571] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:43,571] [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_001304695.1	s__Xanthomonas axonopodis	99.9615	1065	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.43	97.90	0.94	0.92	5	conclusive
GCF_003999565.1	s__Xanthomonas phaseoli	93.6434	1018	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.19	96.38	0.95	0.90	158	-
GCF_013112235.1	s__Xanthomonas perforans	93.4906	1015	1081	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	93.2664	983	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	97.71	95.83	0.91	0.86	247	-
GCF_000772705.2	s__Xanthomonas vasicola	89.8519	994	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.75	98.20	0.95	0.92	113	-
GCF_004136375.1	s__Xanthomonas oryzae	89.4531	939	1081	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	88.9855	953	1081	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	87.1218	892	1081	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	96.66	96.40	0.92	0.89	21	-
GCF_000454545.1	s__Xanthomonas cassavae	86.6767	946	1081	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 15:19:43,573] [INFO] GTDB search result was written to GCF_001401595.1_Xaa_LMG982_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:43,574] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:43,578] [INFO] DFAST_QC result json was written to GCF_001401595.1_Xaa_LMG982_genomic.fna/dqc_result.json
[2024-01-24 15:19:43,578] [INFO] DFAST_QC completed!
[2024-01-24 15:19:43,578] [INFO] Total running time: 0h1m25s