[2024-01-24 12:14:48,817] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:48,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:48,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f9c73cb-bdc3-4cb8-8d63-93d696c37936/dqc_reference
[2024-01-24 12:14:50,129] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:50,130] [INFO] Task started: Prodigal
[2024-01-24 12:14:50,130] [INFO] Running command: gunzip -c /var/lib/cwl/stg138d2d03-9ba7-4622-a4f0-382107ebbd4a/GCF_002940065.1_ASM294006v1_genomic.fna.gz | prodigal -d GCF_002940065.1_ASM294006v1_genomic.fna/cds.fna -a GCF_002940065.1_ASM294006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:04,006] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:04,006] [INFO] Task started: HMMsearch
[2024-01-24 12:15:04,006] [INFO] Running command: hmmsearch --tblout GCF_002940065.1_ASM294006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f9c73cb-bdc3-4cb8-8d63-93d696c37936/dqc_reference/reference_markers.hmm GCF_002940065.1_ASM294006v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:04,347] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:04,349] [INFO] Found 6/6 markers.
[2024-01-24 12:15:04,392] [INFO] Query marker FASTA was written to GCF_002940065.1_ASM294006v1_genomic.fna/markers.fasta
[2024-01-24 12:15:04,392] [INFO] Task started: Blastn
[2024-01-24 12:15:04,393] [INFO] Running command: blastn -query GCF_002940065.1_ASM294006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f9c73cb-bdc3-4cb8-8d63-93d696c37936/dqc_reference/reference_markers.fasta -out GCF_002940065.1_ASM294006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:05,185] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:05,189] [INFO] Selected 7 target genomes.
[2024-01-24 12:15:05,189] [INFO] Target genome list was writen to GCF_002940065.1_ASM294006v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:05,193] [INFO] Task started: fastANI
[2024-01-24 12:15:05,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg138d2d03-9ba7-4622-a4f0-382107ebbd4a/GCF_002940065.1_ASM294006v1_genomic.fna.gz --refList GCF_002940065.1_ASM294006v1_genomic.fna/target_genomes.txt --output GCF_002940065.1_ASM294006v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:16,762] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:16,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f9c73cb-bdc3-4cb8-8d63-93d696c37936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:16,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f9c73cb-bdc3-4cb8-8d63-93d696c37936/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:16,774] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:16,774] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:16,775] [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 populi	strain=CFBP1817	GCA_002940065.1	53414	53414	type	True	100.0	1287	1293	95	conclusive
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	91.015	1148	1293	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	91.004	1157	1293	95	below_threshold
Xanthomonas hortorum	strain=WHRI 7744	GCA_003064105.1	56454	56454	suspected-type	True	90.8935	1106	1293	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	90.5902	1153	1293	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	86.5818	919	1293	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	86.3862	996	1293	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:16,777] [INFO] DFAST Taxonomy check result was written to GCF_002940065.1_ASM294006v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:16,777] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:16,778] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:16,778] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f9c73cb-bdc3-4cb8-8d63-93d696c37936/dqc_reference/checkm_data
[2024-01-24 12:15:16,781] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:16,827] [INFO] Task started: CheckM
[2024-01-24 12:15:16,828] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002940065.1_ASM294006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002940065.1_ASM294006v1_genomic.fna/checkm_input GCF_002940065.1_ASM294006v1_genomic.fna/checkm_result
[2024-01-24 12:16:00,288] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:00,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:00,315] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:00,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:00,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002940065.1_ASM294006v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:00,316] [INFO] Task started: Blastn
[2024-01-24 12:16:00,317] [INFO] Running command: blastn -query GCF_002940065.1_ASM294006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f9c73cb-bdc3-4cb8-8d63-93d696c37936/dqc_reference/reference_markers_gtdb.fasta -out GCF_002940065.1_ASM294006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:01,593] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:01,598] [INFO] Selected 6 target genomes.
[2024-01-24 12:16:01,598] [INFO] Target genome list was writen to GCF_002940065.1_ASM294006v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:01,605] [INFO] Task started: fastANI
[2024-01-24 12:16:01,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg138d2d03-9ba7-4622-a4f0-382107ebbd4a/GCF_002940065.1_ASM294006v1_genomic.fna.gz --refList GCF_002940065.1_ASM294006v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002940065.1_ASM294006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:11,125] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:11,134] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:11,134] [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_002940065.1	s__Xanthomonas populi	100.0	1287	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002939985.1	s__Xanthomonas hortorum_A	90.9777	1142	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	98.80	97.51	0.93	0.89	28	-
GCF_003064105.1	s__Xanthomonas hortorum	90.8501	1110	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	96.84	96.16	0.86	0.83	8	-
GCF_905142465.1	s__Xanthomonas sp905142465	90.6506	1144	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.1927	99.49	99.23	0.97	0.96	4	-
GCF_001423495.1	s__Xanthomonas sp001423495	90.5671	1109	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900476395.1	s__Xanthomonas euroxanthea	88.5808	1116	1293	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.09	97.74	0.93	0.92	25	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:11,138] [INFO] GTDB search result was written to GCF_002940065.1_ASM294006v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:11,140] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:11,144] [INFO] DFAST_QC result json was written to GCF_002940065.1_ASM294006v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:11,144] [INFO] DFAST_QC completed!
[2024-01-24 12:16:11,144] [INFO] Total running time: 0h1m22s