[2024-01-24 15:17:48,929] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:48,932] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:48,932] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f64e99e-db29-4389-8e38-c411dc6942f3/dqc_reference
[2024-01-24 15:17:51,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,534] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e7d0865-7764-4625-a08b-1b25b0b0089c/GCF_001010415.1_ASM101041v1_genomic.fna.gz | prodigal -d GCF_001010415.1_ASM101041v1_genomic.fna/cds.fna -a GCF_001010415.1_ASM101041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:05,750] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:05,750] [INFO] Task started: HMMsearch
[2024-01-24 15:18:05,751] [INFO] Running command: hmmsearch --tblout GCF_001010415.1_ASM101041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f64e99e-db29-4389-8e38-c411dc6942f3/dqc_reference/reference_markers.hmm GCF_001010415.1_ASM101041v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:06,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:06,025] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0e7d0865-7764-4625-a08b-1b25b0b0089c/GCF_001010415.1_ASM101041v1_genomic.fna.gz]
[2024-01-24 15:18:06,063] [INFO] Query marker FASTA was written to GCF_001010415.1_ASM101041v1_genomic.fna/markers.fasta
[2024-01-24 15:18:06,063] [INFO] Task started: Blastn
[2024-01-24 15:18:06,063] [INFO] Running command: blastn -query GCF_001010415.1_ASM101041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f64e99e-db29-4389-8e38-c411dc6942f3/dqc_reference/reference_markers.fasta -out GCF_001010415.1_ASM101041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:06,893] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:06,897] [INFO] Selected 15 target genomes.
[2024-01-24 15:18:06,897] [INFO] Target genome list was writen to GCF_001010415.1_ASM101041v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:06,904] [INFO] Task started: fastANI
[2024-01-24 15:18:06,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e7d0865-7764-4625-a08b-1b25b0b0089c/GCF_001010415.1_ASM101041v1_genomic.fna.gz --refList GCF_001010415.1_ASM101041v1_genomic.fna/target_genomes.txt --output GCF_001010415.1_ASM101041v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:24,549] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:24,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f64e99e-db29-4389-8e38-c411dc6942f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:24,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f64e99e-db29-4389-8e38-c411dc6942f3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:24,562] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:24,563] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:24,563] [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 pisi	strain=DSM 18956	GCA_001010415.1	56457	56457	type	True	100.0	1323	1328	95	conclusive
Xanthomonas dyei	strain=CFBP7245	GCA_002939865.1	743699	743699	type	True	91.7894	1117	1328	95	below_threshold
Xanthomonas vesicatoria	strain=LMG911	GCA_001908725.1	56460	56460	type	True	90.6392	1110	1328	95	below_threshold
Xanthomonas vesicatoria	strain=ATCC 35937	GCA_000192025.2	56460	56460	type	True	90.6323	1051	1328	95	below_threshold
Xanthomonas floridensis	strain=WHRI 8848	GCA_001642575.1	1843580	1843580	type	True	89.6358	1129	1328	95	below_threshold
Xanthomonas prunicola	strain=CFBP 8353	GCA_002846205.1	2053930	2053930	type	True	88.4214	1056	1328	95	below_threshold
Xanthomonas cassavae	strain=NCPPB 101	GCA_020783895.1	56450	56450	type	True	88.0112	997	1328	95	below_threshold
Xanthomonas cassavae	strain=CFBP 4642	GCA_000454545.1	56450	56450	type	True	87.9114	1020	1328	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	87.7694	1053	1328	95	below_threshold
Xanthomonas hortorum	strain=CFBP2533	GCA_012922215.1	56454	56454	pathovar	True	87.6328	1039	1328	95	below_threshold
Xanthomonas hortorum	strain=CFBP 2533	GCA_021353095.1	56454	56454	pathovar	True	87.5964	1036	1328	95	below_threshold
Xanthomonas bromi	strain=CFBP1976	GCA_002939755.1	56449	56449	type	True	87.3439	985	1328	95	below_threshold
Xanthomonas bromi		GCA_900092025.1	56449	56449	type	True	87.3124	975	1328	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	87.1153	1036	1328	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	87.0876	1014	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:24,564] [INFO] DFAST Taxonomy check result was written to GCF_001010415.1_ASM101041v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:24,565] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:24,565] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:24,565] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f64e99e-db29-4389-8e38-c411dc6942f3/dqc_reference/checkm_data
[2024-01-24 15:18:24,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:24,609] [INFO] Task started: CheckM
[2024-01-24 15:18:24,609] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001010415.1_ASM101041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001010415.1_ASM101041v1_genomic.fna/checkm_input GCF_001010415.1_ASM101041v1_genomic.fna/checkm_result
[2024-01-24 15:19:14,406] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:14,407] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:14,431] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:14,431] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:14,431] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001010415.1_ASM101041v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:14,432] [INFO] Task started: Blastn
[2024-01-24 15:19:14,432] [INFO] Running command: blastn -query GCF_001010415.1_ASM101041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6f64e99e-db29-4389-8e38-c411dc6942f3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001010415.1_ASM101041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:15,865] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:15,869] [INFO] Selected 11 target genomes.
[2024-01-24 15:19:15,869] [INFO] Target genome list was writen to GCF_001010415.1_ASM101041v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:15,878] [INFO] Task started: fastANI
[2024-01-24 15:19:15,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e7d0865-7764-4625-a08b-1b25b0b0089c/GCF_001010415.1_ASM101041v1_genomic.fna.gz --refList GCF_001010415.1_ASM101041v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001010415.1_ASM101041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:29,827] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:29,841] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:29,842] [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_001010415.1	s__Xanthomonas pisi	100.0	1323	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002939865.1	s__Xanthomonas dyei	91.7894	1117	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423585.1	s__Xanthomonas sp001423585	91.3417	1169	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.11	97.14	0.95	0.93	10	-
GCF_001908725.1	s__Xanthomonas vesicatoria	90.6247	1111	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.30	98.65	0.97	0.94	15	-
GCF_001642575.1	s__Xanthomonas floridensis	89.6439	1128	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846205.1	s__Xanthomonas prunicola	88.4066	1057	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_012848175.1	s__Xanthomonas campestris_C	88.234	1028	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454545.1	s__Xanthomonas cassavae	87.9038	1021	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197275.1	s__Xanthomonas campestris_B	87.8568	1019	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	98.71	98.71	0.92	0.92	2	-
GCF_002939785.1	s__Xanthomonas codiaei	87.8109	1068	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900092025.1	s__Xanthomonas bromi	87.2878	978	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:29,843] [INFO] GTDB search result was written to GCF_001010415.1_ASM101041v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:29,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:29,847] [INFO] DFAST_QC result json was written to GCF_001010415.1_ASM101041v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:29,847] [INFO] DFAST_QC completed!
[2024-01-24 15:19:29,847] [INFO] Total running time: 0h1m41s