[2024-01-25 17:47:50,765] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:47:50,767] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:47:50,767] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8fa0f20-dde4-4257-8967-72d1cc5d4a47/dqc_reference
[2024-01-25 17:47:51,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:47:51,899] [INFO] Task started: Prodigal
[2024-01-25 17:47:51,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg511cfc06-b721-42d2-8152-7a8f0df83e2b/GCF_000331775.1_ASM33177v1_genomic.fna.gz | prodigal -d GCF_000331775.1_ASM33177v1_genomic.fna/cds.fna -a GCF_000331775.1_ASM33177v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:02,831] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:02,831] [INFO] Task started: HMMsearch
[2024-01-25 17:48:02,831] [INFO] Running command: hmmsearch --tblout GCF_000331775.1_ASM33177v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8fa0f20-dde4-4257-8967-72d1cc5d4a47/dqc_reference/reference_markers.hmm GCF_000331775.1_ASM33177v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:03,090] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:03,092] [INFO] Found 6/6 markers.
[2024-01-25 17:48:03,129] [INFO] Query marker FASTA was written to GCF_000331775.1_ASM33177v1_genomic.fna/markers.fasta
[2024-01-25 17:48:03,130] [INFO] Task started: Blastn
[2024-01-25 17:48:03,130] [INFO] Running command: blastn -query GCF_000331775.1_ASM33177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8fa0f20-dde4-4257-8967-72d1cc5d4a47/dqc_reference/reference_markers.fasta -out GCF_000331775.1_ASM33177v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:04,103] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:04,105] [INFO] Selected 11 target genomes.
[2024-01-25 17:48:04,106] [INFO] Target genome list was writen to GCF_000331775.1_ASM33177v1_genomic.fna/target_genomes.txt
[2024-01-25 17:48:04,123] [INFO] Task started: fastANI
[2024-01-25 17:48:04,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg511cfc06-b721-42d2-8152-7a8f0df83e2b/GCF_000331775.1_ASM33177v1_genomic.fna.gz --refList GCF_000331775.1_ASM33177v1_genomic.fna/target_genomes.txt --output GCF_000331775.1_ASM33177v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:17,097] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:17,097] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8fa0f20-dde4-4257-8967-72d1cc5d4a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:17,098] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8fa0f20-dde4-4257-8967-72d1cc5d4a47/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:17,105] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:48:17,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:17,106] [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 translucens	strain=DSM 18974	GCA_000331775.1	343	343	type	True	100.0	1202	1217	95	conclusive
Xanthomonas translucens	strain=ATCC 19319	GCA_020880735.1	343	343	type	True	99.8187	1104	1217	95	conclusive
Xanthomonas hyacinthi	strain=CFBP1156	GCA_002939895.1	56455	56455	type	True	92.4718	948	1217	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	92.3766	957	1217	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	89.9564	847	1217	95	below_threshold
Xanthomonas indica	strain=PPL560	GCA_022669045.1	2912242	2912242	type	True	88.5015	973	1217	95	below_threshold
Xanthomonas sacchari	strain=CFBP4641	GCA_002940085.1	56458	56458	suspected-type	True	88.4152	974	1217	95	below_threshold
Stenotrophomonas daejeonensis	strain=JCM 16244	GCA_001431505.1	659018	659018	type	True	83.8095	600	1217	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	82.2884	815	1217	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	82.1418	759	1217	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	81.8201	790	1217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:17,107] [INFO] DFAST Taxonomy check result was written to GCF_000331775.1_ASM33177v1_genomic.fna/tc_result.tsv
[2024-01-25 17:48:17,108] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:17,108] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:17,108] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8fa0f20-dde4-4257-8967-72d1cc5d4a47/dqc_reference/checkm_data
[2024-01-25 17:48:17,109] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:17,154] [INFO] Task started: CheckM
[2024-01-25 17:48:17,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000331775.1_ASM33177v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000331775.1_ASM33177v1_genomic.fna/checkm_input GCF_000331775.1_ASM33177v1_genomic.fna/checkm_result
[2024-01-25 17:48:53,504] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:53,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:53,519] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:53,519] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:53,520] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000331775.1_ASM33177v1_genomic.fna/markers.fasta)
[2024-01-25 17:48:53,520] [INFO] Task started: Blastn
[2024-01-25 17:48:53,520] [INFO] Running command: blastn -query GCF_000331775.1_ASM33177v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8fa0f20-dde4-4257-8967-72d1cc5d4a47/dqc_reference/reference_markers_gtdb.fasta -out GCF_000331775.1_ASM33177v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:55,451] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:55,454] [INFO] Selected 7 target genomes.
[2024-01-25 17:48:55,454] [INFO] Target genome list was writen to GCF_000331775.1_ASM33177v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:55,459] [INFO] Task started: fastANI
[2024-01-25 17:48:55,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg511cfc06-b721-42d2-8152-7a8f0df83e2b/GCF_000331775.1_ASM33177v1_genomic.fna.gz --refList GCF_000331775.1_ASM33177v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000331775.1_ASM33177v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:04,630] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:04,636] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:04,636] [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_000331775.1	s__Xanthomonas_A translucens	100.0	1202	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	97.09	95.18	0.88	0.77	59	conclusive
GCF_014236855.1	s__Xanthomonas_A sp014236855	93.1632	1033	1217	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_007829315.1	s__Xanthomonas_A translucens_A	92.4068	1010	1217	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_009769165.1	s__Xanthomonas_A hyacinthi	92.3327	960	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014197395.1	s__Xanthomonas_A translucens_B	92.0055	1013	1217	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_014236795.1	s__Xanthomonas_A theicola	89.7956	907	1217	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_014199795.1	s__Xanthomonas_A sp014199795	88.3917	978	1217	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_A	95.0	98.20	98.15	0.95	0.95	4	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:04,637] [INFO] GTDB search result was written to GCF_000331775.1_ASM33177v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:04,637] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:04,640] [INFO] DFAST_QC result json was written to GCF_000331775.1_ASM33177v1_genomic.fna/dqc_result.json
[2024-01-25 17:49:04,640] [INFO] DFAST_QC completed!
[2024-01-25 17:49:04,640] [INFO] Total running time: 0h1m14s