[2024-01-24 12:39:35,382] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,384] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,385] [INFO] DQC Reference Directory: /var/lib/cwl/stg23973a1f-685c-4cfb-8c88-ef468b6bc6b9/dqc_reference
[2024-01-24 12:39:36,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,600] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg909dd7e5-b241-45e0-91db-066188e6240b/GCF_010093325.1_ASM1009332v1_genomic.fna.gz | prodigal -d GCF_010093325.1_ASM1009332v1_genomic.fna/cds.fna -a GCF_010093325.1_ASM1009332v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:50,826] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:50,827] [INFO] Task started: HMMsearch
[2024-01-24 12:39:50,827] [INFO] Running command: hmmsearch --tblout GCF_010093325.1_ASM1009332v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23973a1f-685c-4cfb-8c88-ef468b6bc6b9/dqc_reference/reference_markers.hmm GCF_010093325.1_ASM1009332v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:51,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:51,088] [INFO] Found 6/6 markers.
[2024-01-24 12:39:51,129] [INFO] Query marker FASTA was written to GCF_010093325.1_ASM1009332v1_genomic.fna/markers.fasta
[2024-01-24 12:39:51,129] [INFO] Task started: Blastn
[2024-01-24 12:39:51,129] [INFO] Running command: blastn -query GCF_010093325.1_ASM1009332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23973a1f-685c-4cfb-8c88-ef468b6bc6b9/dqc_reference/reference_markers.fasta -out GCF_010093325.1_ASM1009332v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:52,065] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:52,070] [INFO] Selected 16 target genomes.
[2024-01-24 12:39:52,070] [INFO] Target genome list was writen to GCF_010093325.1_ASM1009332v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:52,077] [INFO] Task started: fastANI
[2024-01-24 12:39:52,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg909dd7e5-b241-45e0-91db-066188e6240b/GCF_010093325.1_ASM1009332v1_genomic.fna.gz --refList GCF_010093325.1_ASM1009332v1_genomic.fna/target_genomes.txt --output GCF_010093325.1_ASM1009332v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:07,867] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:07,867] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23973a1f-685c-4cfb-8c88-ef468b6bc6b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:07,868] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23973a1f-685c-4cfb-8c88-ef468b6bc6b9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:07,881] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:40:07,881] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:07,882] [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=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	100.0	1520	1522	95	conclusive
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	99.9881	1513	1522	95	conclusive
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	83.0189	845	1522	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	82.5068	825	1522	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	82.4993	807	1522	95	below_threshold
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	82.1052	812	1522	95	below_threshold
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	82.0595	771	1522	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.8349	712	1522	95	below_threshold
Pseudoxanthomonas kalamensis	strain=DSM 18571	GCA_010211745.1	289483	289483	type	True	81.7505	657	1522	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.5639	704	1522	95	below_threshold
Pseudoxanthomonas gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	81.4531	716	1522	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	81.3743	724	1522	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	80.2288	700	1522	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	80.1423	642	1522	95	below_threshold
Xanthomonas hydrangeae	strain=LMG 31884	GCA_905142475.1	2775159	2775159	type	True	79.988	669	1522	95	below_threshold
Xanthomonas citri	strain=ICMP5732	GCA_021474205.1	346	346	pathovar	True	79.86	663	1522	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:07,888] [INFO] DFAST Taxonomy check result was written to GCF_010093325.1_ASM1009332v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:07,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:07,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:07,890] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23973a1f-685c-4cfb-8c88-ef468b6bc6b9/dqc_reference/checkm_data
[2024-01-24 12:40:07,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:07,952] [INFO] Task started: CheckM
[2024-01-24 12:40:07,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093325.1_ASM1009332v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093325.1_ASM1009332v1_genomic.fna/checkm_input GCF_010093325.1_ASM1009332v1_genomic.fna/checkm_result
[2024-01-24 12:40:55,586] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:55,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:55,630] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:55,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:55,631] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093325.1_ASM1009332v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:55,632] [INFO] Task started: Blastn
[2024-01-24 12:40:55,632] [INFO] Running command: blastn -query GCF_010093325.1_ASM1009332v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg23973a1f-685c-4cfb-8c88-ef468b6bc6b9/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093325.1_ASM1009332v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:57,393] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:57,398] [INFO] Selected 16 target genomes.
[2024-01-24 12:40:57,398] [INFO] Target genome list was writen to GCF_010093325.1_ASM1009332v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:57,408] [INFO] Task started: fastANI
[2024-01-24 12:40:57,408] [INFO] Running command: fastANI --query /var/lib/cwl/stg909dd7e5-b241-45e0-91db-066188e6240b/GCF_010093325.1_ASM1009332v1_genomic.fna.gz --refList GCF_010093325.1_ASM1009332v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093325.1_ASM1009332v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:12,203] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:12,228] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:12,229] [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	99.9881	1513	1522	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
GCF_006542425.1	s__Pseudoxanthomonas_A sp006542425	83.1154	836	1522	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_019218945.1	s__Pseudoxanthomonas_A sp019218945	82.9679	861	1522	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_001427635.1	s__Pseudoxanthomonas_A sp001427635	82.6316	854	1522	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	82.526	823	1522	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	82.3609	837	1522	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	82.2686	846	1522	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	82.1876	819	1522	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	82.1725	834	1522	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	82.1053	812	1522	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	82.076	769	1522	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	81.9932	781	1522	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	81.9251	814	1522	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	81.7976	716	1522	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	81.7421	658	1522	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	81.4036	720	1522	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 12:41:12,231] [INFO] GTDB search result was written to GCF_010093325.1_ASM1009332v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:12,231] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:12,235] [INFO] DFAST_QC result json was written to GCF_010093325.1_ASM1009332v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:12,236] [INFO] DFAST_QC completed!
[2024-01-24 12:41:12,236] [INFO] Total running time: 0h1m37s