[2024-01-24 13:12:39,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:39,107] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:39,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a22e9d4-71af-478a-8f85-259a6b06e4a6/dqc_reference
[2024-01-24 13:12:40,437] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,438] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,438] [INFO] Running command: gunzip -c /var/lib/cwl/stge34566dd-b986-41a4-a580-4997c260f678/GCF_003064105.1_ASM306410v1_genomic.fna.gz | prodigal -d GCF_003064105.1_ASM306410v1_genomic.fna/cds.fna -a GCF_003064105.1_ASM306410v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:58,480] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:58,480] [INFO] Task started: HMMsearch
[2024-01-24 13:12:58,480] [INFO] Running command: hmmsearch --tblout GCF_003064105.1_ASM306410v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a22e9d4-71af-478a-8f85-259a6b06e4a6/dqc_reference/reference_markers.hmm GCF_003064105.1_ASM306410v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:58,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:58,838] [INFO] Found 6/6 markers.
[2024-01-24 13:12:58,886] [INFO] Query marker FASTA was written to GCF_003064105.1_ASM306410v1_genomic.fna/markers.fasta
[2024-01-24 13:12:58,887] [INFO] Task started: Blastn
[2024-01-24 13:12:58,887] [INFO] Running command: blastn -query GCF_003064105.1_ASM306410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a22e9d4-71af-478a-8f85-259a6b06e4a6/dqc_reference/reference_markers.fasta -out GCF_003064105.1_ASM306410v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:59,844] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:59,847] [INFO] Selected 8 target genomes.
[2024-01-24 13:12:59,847] [INFO] Target genome list was writen to GCF_003064105.1_ASM306410v1_genomic.fna/target_genomes.txt
[2024-01-24 13:12:59,851] [INFO] Task started: fastANI
[2024-01-24 13:12:59,851] [INFO] Running command: fastANI --query /var/lib/cwl/stge34566dd-b986-41a4-a580-4997c260f678/GCF_003064105.1_ASM306410v1_genomic.fna.gz --refList GCF_003064105.1_ASM306410v1_genomic.fna/target_genomes.txt --output GCF_003064105.1_ASM306410v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:15,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:15,213] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a22e9d4-71af-478a-8f85-259a6b06e4a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:15,213] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a22e9d4-71af-478a-8f85-259a6b06e4a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:15,223] [INFO] Found 8 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:13:15,223] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:13:15,224] [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 hortorum	strain=WHRI 7744	GCA_003064105.1	56454	56454	suspected-type	True	100.0	1669	1678	95	inconclusive
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	96.1161	1410	1678	95	inconclusive
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	96.0755	1413	1678	95	inconclusive
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	95.0969	1420	1678	95	inconclusive
Xanthomonas populi	strain=CFBP1817	GCA_002940065.1	53414	53414	type	True	90.6908	1107	1678	95	below_threshold
Xanthomonas nasturtii	strain=WHRI 8853	GCA_001660815.1	1843581	1843581	type	True	88.1136	1268	1678	95	below_threshold
Xanthomonas fragariae	strain=PD 885	GCA_900380235.1	48664	48664	type	True	87.1603	992	1678	95	below_threshold
Xanthomonas fragariae	strain=PD885	GCA_900183975.1	48664	48664	type	True	86.8503	1092	1678	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:15,225] [INFO] DFAST Taxonomy check result was written to GCF_003064105.1_ASM306410v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:15,226] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:15,226] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:15,226] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a22e9d4-71af-478a-8f85-259a6b06e4a6/dqc_reference/checkm_data
[2024-01-24 13:13:15,227] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:15,284] [INFO] Task started: CheckM
[2024-01-24 13:13:15,284] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003064105.1_ASM306410v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003064105.1_ASM306410v1_genomic.fna/checkm_input GCF_003064105.1_ASM306410v1_genomic.fna/checkm_result
[2024-01-24 13:14:09,869] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:09,870] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,893] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:09,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:09,894] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003064105.1_ASM306410v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:09,894] [INFO] Task started: Blastn
[2024-01-24 13:14:09,894] [INFO] Running command: blastn -query GCF_003064105.1_ASM306410v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a22e9d4-71af-478a-8f85-259a6b06e4a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003064105.1_ASM306410v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:11,611] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:11,615] [INFO] Selected 8 target genomes.
[2024-01-24 13:14:11,615] [INFO] Target genome list was writen to GCF_003064105.1_ASM306410v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:11,622] [INFO] Task started: fastANI
[2024-01-24 13:14:11,623] [INFO] Running command: fastANI --query /var/lib/cwl/stge34566dd-b986-41a4-a580-4997c260f678/GCF_003064105.1_ASM306410v1_genomic.fna.gz --refList GCF_003064105.1_ASM306410v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003064105.1_ASM306410v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:26,745] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:26,760] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:14:26,760] [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_003064105.1	s__Xanthomonas hortorum	100.0	1669	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	96.84	96.16	0.86	0.83	8	inconclusive
GCF_002939985.1	s__Xanthomonas hortorum_A	96.0555	1381	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	96.0883	98.80	97.51	0.93	0.89	28	-
GCF_905142465.1	s__Xanthomonas sp905142465	95.2137	1413	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.1927	99.49	99.23	0.97	0.96	4	inconclusive
GCF_001423495.1	s__Xanthomonas sp001423495	92.5988	1355	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002940065.1	s__Xanthomonas populi	90.6884	1107	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002939945.1	s__Xanthomonas arboricola_A	90.086	1267	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	95.91	95.91	0.90	0.90	2	-
GCF_003353015.1	s__Xanthomonas arboricola_E	89.5863	1310	1678	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660815.1	s__Xanthomonas nasturtii	88.1126	1269	1678	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 13:14:26,762] [INFO] GTDB search result was written to GCF_003064105.1_ASM306410v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:26,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:26,770] [INFO] DFAST_QC result json was written to GCF_003064105.1_ASM306410v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:26,771] [INFO] DFAST_QC completed!
[2024-01-24 13:14:26,771] [INFO] Total running time: 0h1m48s