[2024-01-24 14:47:20,050] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:20,052] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:20,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg22fc14bb-ecaf-462f-9969-6d9f1ad65be3/dqc_reference
[2024-01-24 14:47:21,386] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:21,387] [INFO] Task started: Prodigal
[2024-01-24 14:47:21,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg493a6b9a-ab70-4e06-a19b-da866d112cf8/GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/cds.fna -a GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:36,388] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:36,388] [INFO] Task started: HMMsearch
[2024-01-24 14:47:36,388] [INFO] Running command: hmmsearch --tblout GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg22fc14bb-ecaf-462f-9969-6d9f1ad65be3/dqc_reference/reference_markers.hmm GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:36,747] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:36,749] [INFO] Found 6/6 markers.
[2024-01-24 14:47:36,795] [INFO] Query marker FASTA was written to GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:47:36,796] [INFO] Task started: Blastn
[2024-01-24 14:47:36,796] [INFO] Running command: blastn -query GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg22fc14bb-ecaf-462f-9969-6d9f1ad65be3/dqc_reference/reference_markers.fasta -out GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:37,839] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:37,843] [INFO] Selected 16 target genomes.
[2024-01-24 14:47:37,843] [INFO] Target genome list was writen to GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:47:37,849] [INFO] Task started: fastANI
[2024-01-24 14:47:37,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg493a6b9a-ab70-4e06-a19b-da866d112cf8/GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna.gz --refList GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:54,858] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:54,858] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg22fc14bb-ecaf-462f-9969-6d9f1ad65be3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:54,859] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg22fc14bb-ecaf-462f-9969-6d9f1ad65be3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:54,873] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:47:54,873] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:54,873] [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
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	100.0	1539	1540	95	conclusive
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	99.9762	1516	1540	95	conclusive
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	83.2259	834	1540	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	82.6487	801	1540	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	82.5849	835	1540	95	below_threshold
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	82.1432	803	1540	95	below_threshold
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	82.0001	777	1540	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.9166	725	1540	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	81.7893	664	1540	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.7474	714	1540	95	below_threshold
Pseudoxanthomonas gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	81.5388	706	1540	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	81.4529	729	1540	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.2488	716	1540	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	80.0877	666	1540	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	79.9917	696	1540	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	79.9859	667	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:54,875] [INFO] DFAST Taxonomy check result was written to GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:47:54,876] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:54,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:54,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg22fc14bb-ecaf-462f-9969-6d9f1ad65be3/dqc_reference/checkm_data
[2024-01-24 14:47:54,878] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:54,926] [INFO] Task started: CheckM
[2024-01-24 14:47:54,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/checkm_input GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:48:42,825] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:42,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:42,849] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:42,849] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:42,850] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:48:42,850] [INFO] Task started: Blastn
[2024-01-24 14:48:42,850] [INFO] Running command: blastn -query GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg22fc14bb-ecaf-462f-9969-6d9f1ad65be3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:44,648] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:44,652] [INFO] Selected 16 target genomes.
[2024-01-24 14:48:44,652] [INFO] Target genome list was writen to GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:44,730] [INFO] Task started: fastANI
[2024-01-24 14:48:44,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg493a6b9a-ab70-4e06-a19b-da866d112cf8/GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna.gz --refList GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:01,419] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:01,445] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:01,446] [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_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	100.0	1539	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	83.2177	866	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.15	98.62	0.97	0.96	4	-
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	83.1407	858	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427635.1	s__Pseudoxanthomonas_A sp001427635	82.7073	862	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093445.1	s__Pseudoxanthomonas_A japonensis	82.5976	835	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.78	96.68	0.83	0.68	4	-
GCF_900104255.1	s__Pseudoxanthomonas_A sp900104255	82.4107	845	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	82.3818	857	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014851805.1	s__Pseudoxanthomonas_A sp014851805	82.2365	857	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014852005.1	s__Pseudoxanthomonas_A sp014852005	82.2036	834	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093305.1	s__Pseudoxanthomonas_A sacheonensis	82.1529	802	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863005.1	s__Pseudoxanthomonas_A sp002863005	82.1171	780	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	82.0029	776	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	81.9267	724	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104085.1	s__Pseudoxanthomonas_A sp900104085	81.8989	835	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010211745.1	s__Pseudoxanthomonas_A kalamensis	81.7824	665	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001431405.1	s__Pseudoxanthomonas_A dokdonensis	81.4622	728	1540	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:49:01,448] [INFO] GTDB search result was written to GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:01,448] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:01,452] [INFO] DFAST_QC result json was written to GCF_900215535.1_IMG-taxon_2718217650_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:49:01,452] [INFO] DFAST_QC completed!
[2024-01-24 14:49:01,452] [INFO] Total running time: 0h1m41s