[2024-01-24 13:32:34,840] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,842] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f6efbac-bfc6-4739-b304-452e6c0dcbd6/dqc_reference
[2024-01-24 13:32:36,382] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:36,384] [INFO] Task started: Prodigal
[2024-01-24 13:32:36,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg671a8564-ed7d-4316-b440-9e1651f030b6/GCF_002939895.1_ASM293989v1_genomic.fna.gz | prodigal -d GCF_002939895.1_ASM293989v1_genomic.fna/cds.fna -a GCF_002939895.1_ASM293989v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:52,076] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:52,077] [INFO] Task started: HMMsearch
[2024-01-24 13:32:52,077] [INFO] Running command: hmmsearch --tblout GCF_002939895.1_ASM293989v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f6efbac-bfc6-4739-b304-452e6c0dcbd6/dqc_reference/reference_markers.hmm GCF_002939895.1_ASM293989v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:52,471] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:52,472] [INFO] Found 6/6 markers.
[2024-01-24 13:32:52,576] [INFO] Query marker FASTA was written to GCF_002939895.1_ASM293989v1_genomic.fna/markers.fasta
[2024-01-24 13:32:52,576] [INFO] Task started: Blastn
[2024-01-24 13:32:52,576] [INFO] Running command: blastn -query GCF_002939895.1_ASM293989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6efbac-bfc6-4739-b304-452e6c0dcbd6/dqc_reference/reference_markers.fasta -out GCF_002939895.1_ASM293989v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:53,719] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:53,732] [INFO] Selected 12 target genomes.
[2024-01-24 13:32:53,733] [INFO] Target genome list was writen to GCF_002939895.1_ASM293989v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:53,762] [INFO] Task started: fastANI
[2024-01-24 13:32:53,763] [INFO] Running command: fastANI --query /var/lib/cwl/stg671a8564-ed7d-4316-b440-9e1651f030b6/GCF_002939895.1_ASM293989v1_genomic.fna.gz --refList GCF_002939895.1_ASM293989v1_genomic.fna/target_genomes.txt --output GCF_002939895.1_ASM293989v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:09,425] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:09,426] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f6efbac-bfc6-4739-b304-452e6c0dcbd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:09,426] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f6efbac-bfc6-4739-b304-452e6c0dcbd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:09,437] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:33:09,438] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:09,438] [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=CFBP1156	GCA_002939895.1	56455	56455	type	True	100.0	1591	1598	95	conclusive
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	99.9969	1597	1598	95	conclusive
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	92.4762	977	1598	95	below_threshold
Xanthomonas translucens	strain=DSM 18974	GCA_000331775.1	343	343	type	True	92.2921	943	1598	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	90.8121	1017	1598	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	90.485	1107	1598	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	88.8009	1168	1598	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	82.6485	754	1598	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	82.6321	747	1598	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	82.378	971	1598	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	82.186	950	1598	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	82.1364	949	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:09,440] [INFO] DFAST Taxonomy check result was written to GCF_002939895.1_ASM293989v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:09,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:09,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:09,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f6efbac-bfc6-4739-b304-452e6c0dcbd6/dqc_reference/checkm_data
[2024-01-24 13:33:09,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:09,492] [INFO] Task started: CheckM
[2024-01-24 13:33:09,492] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002939895.1_ASM293989v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002939895.1_ASM293989v1_genomic.fna/checkm_input GCF_002939895.1_ASM293989v1_genomic.fna/checkm_result
[2024-01-24 13:34:00,723] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:00,725] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:00,748] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:00,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:00,748] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002939895.1_ASM293989v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:00,749] [INFO] Task started: Blastn
[2024-01-24 13:34:00,749] [INFO] Running command: blastn -query GCF_002939895.1_ASM293989v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f6efbac-bfc6-4739-b304-452e6c0dcbd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002939895.1_ASM293989v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:02,867] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:02,871] [INFO] Selected 10 target genomes.
[2024-01-24 13:34:02,872] [INFO] Target genome list was writen to GCF_002939895.1_ASM293989v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:02,884] [INFO] Task started: fastANI
[2024-01-24 13:34:02,884] [INFO] Running command: fastANI --query /var/lib/cwl/stg671a8564-ed7d-4316-b440-9e1651f030b6/GCF_002939895.1_ASM293989v1_genomic.fna.gz --refList GCF_002939895.1_ASM293989v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002939895.1_ASM293989v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:15,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:15,866] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:15,866] [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	99.9969	1597	1598	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	93.3418	1251	1598	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	93.3216	1229	1598	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	92.5229	1243	1598	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	92.2545	945	1598	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	90.4308	1110	1598	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	83.1437	693	1598	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	82.6788	743	1598	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	82.3195	740	1598	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	80.5732	452	1598	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 13:34:15,868] [INFO] GTDB search result was written to GCF_002939895.1_ASM293989v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:15,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:15,872] [INFO] DFAST_QC result json was written to GCF_002939895.1_ASM293989v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:15,872] [INFO] DFAST_QC completed!
[2024-01-24 13:34:15,872] [INFO] Total running time: 0h1m41s