[2024-01-24 13:33:40,831] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:40,833] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:40,834] [INFO] DQC Reference Directory: /var/lib/cwl/stg826eb285-aeee-493d-95e5-66c4fa711268/dqc_reference
[2024-01-24 13:33:42,232] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,233] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,233] [INFO] Running command: gunzip -c /var/lib/cwl/stgc46135b7-957a-4c55-bfdc-3989bed2f8be/GCF_009769165.1_ASM976916v1_genomic.fna.gz | prodigal -d GCF_009769165.1_ASM976916v1_genomic.fna/cds.fna -a GCF_009769165.1_ASM976916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:57,938] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:57,938] [INFO] Task started: HMMsearch
[2024-01-24 13:33:57,938] [INFO] Running command: hmmsearch --tblout GCF_009769165.1_ASM976916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg826eb285-aeee-493d-95e5-66c4fa711268/dqc_reference/reference_markers.hmm GCF_009769165.1_ASM976916v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:58,257] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:58,258] [INFO] Found 6/6 markers.
[2024-01-24 13:33:58,301] [INFO] Query marker FASTA was written to GCF_009769165.1_ASM976916v1_genomic.fna/markers.fasta
[2024-01-24 13:33:58,302] [INFO] Task started: Blastn
[2024-01-24 13:33:58,302] [INFO] Running command: blastn -query GCF_009769165.1_ASM976916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826eb285-aeee-493d-95e5-66c4fa711268/dqc_reference/reference_markers.fasta -out GCF_009769165.1_ASM976916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:59,337] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:59,340] [INFO] Selected 12 target genomes.
[2024-01-24 13:33:59,341] [INFO] Target genome list was writen to GCF_009769165.1_ASM976916v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:59,350] [INFO] Task started: fastANI
[2024-01-24 13:33:59,350] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46135b7-957a-4c55-bfdc-3989bed2f8be/GCF_009769165.1_ASM976916v1_genomic.fna.gz --refList GCF_009769165.1_ASM976916v1_genomic.fna/target_genomes.txt --output GCF_009769165.1_ASM976916v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:14,476] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:14,477] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg826eb285-aeee-493d-95e5-66c4fa711268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:14,478] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg826eb285-aeee-493d-95e5-66c4fa711268/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:14,489] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:34:14,489] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:34:14,490] [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 hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	100.0	1652	1653	95	conclusive
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	99.963	1594	1653	95	conclusive
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	92.3723	976	1653	95	below_threshold
Xanthomonas translucens	strain=DSM 18974	GCA_000331775.1	343	343	type	True	92.2524	937	1653	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	90.8521	1029	1653	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	90.6897	1099	1653	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	88.8747	1145	1653	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	82.5761	774	1653	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	82.5315	776	1653	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	82.3734	969	1653	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	82.224	953	1653	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	82.1557	957	1653	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:14,491] [INFO] DFAST Taxonomy check result was written to GCF_009769165.1_ASM976916v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:14,492] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:14,492] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:14,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg826eb285-aeee-493d-95e5-66c4fa711268/dqc_reference/checkm_data
[2024-01-24 13:34:14,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:14,551] [INFO] Task started: CheckM
[2024-01-24 13:34:14,551] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009769165.1_ASM976916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009769165.1_ASM976916v1_genomic.fna/checkm_input GCF_009769165.1_ASM976916v1_genomic.fna/checkm_result
[2024-01-24 13:35:11,752] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:11,753] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:11,772] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:11,772] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:11,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009769165.1_ASM976916v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:11,773] [INFO] Task started: Blastn
[2024-01-24 13:35:11,773] [INFO] Running command: blastn -query GCF_009769165.1_ASM976916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg826eb285-aeee-493d-95e5-66c4fa711268/dqc_reference/reference_markers_gtdb.fasta -out GCF_009769165.1_ASM976916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:13,936] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:13,939] [INFO] Selected 10 target genomes.
[2024-01-24 13:35:13,939] [INFO] Target genome list was writen to GCF_009769165.1_ASM976916v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:13,960] [INFO] Task started: fastANI
[2024-01-24 13:35:13,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgc46135b7-957a-4c55-bfdc-3989bed2f8be/GCF_009769165.1_ASM976916v1_genomic.fna.gz --refList GCF_009769165.1_ASM976916v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009769165.1_ASM976916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:26,711] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:26,724] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:35:26,725] [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_009769165.1	s__Xanthomonas_A hyacinthi	100.0	1652	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_007829315.1	s__Xanthomonas_A translucens_A	93.4452	1247	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014236855.1	s__Xanthomonas_A sp014236855	93.2674	1248	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	95.82	95.01	0.91	0.88	7	-
GCF_014197395.1	s__Xanthomonas_A translucens_B	92.4715	1243	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331775.1	s__Xanthomonas_A translucens	92.2704	936	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.09	95.18	0.88	0.77	59	-
GCF_014236795.1	s__Xanthomonas_A theicola	90.6849	1098	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	99.99	99.99	1.00	1.00	2	-
GCF_010093225.1	s__Pseudoxanthomonas koreensis	83.1652	687	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	82.5746	772	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010093205.1	s__Pseudoxanthomonas daejeonensis	82.2248	756	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297225.1	s__Luteimonas_B sp004297225	80.3281	474	1653	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:35:26,726] [INFO] GTDB search result was written to GCF_009769165.1_ASM976916v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:26,727] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:26,730] [INFO] DFAST_QC result json was written to GCF_009769165.1_ASM976916v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:26,730] [INFO] DFAST_QC completed!
[2024-01-24 13:35:26,730] [INFO] Total running time: 0h1m46s