[2024-01-24 10:47:23,327] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:23,331] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:23,332] [INFO] DQC Reference Directory: /var/lib/cwl/stg1018c2d7-57a3-4b5a-bee2-2b6264dbe835/dqc_reference
[2024-01-24 10:47:26,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:26,183] [INFO] Task started: Prodigal
[2024-01-24 10:47:26,183] [INFO] Running command: gunzip -c /var/lib/cwl/stg84ed304a-0643-469c-80ce-86f7f6f7fc14/GCF_010119615.1_ASM1011961v1_genomic.fna.gz | prodigal -d GCF_010119615.1_ASM1011961v1_genomic.fna/cds.fna -a GCF_010119615.1_ASM1011961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:37,704] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:37,705] [INFO] Task started: HMMsearch
[2024-01-24 10:47:37,705] [INFO] Running command: hmmsearch --tblout GCF_010119615.1_ASM1011961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1018c2d7-57a3-4b5a-bee2-2b6264dbe835/dqc_reference/reference_markers.hmm GCF_010119615.1_ASM1011961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:37,968] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:37,969] [INFO] Found 6/6 markers.
[2024-01-24 10:47:38,005] [INFO] Query marker FASTA was written to GCF_010119615.1_ASM1011961v1_genomic.fna/markers.fasta
[2024-01-24 10:47:38,005] [INFO] Task started: Blastn
[2024-01-24 10:47:38,005] [INFO] Running command: blastn -query GCF_010119615.1_ASM1011961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1018c2d7-57a3-4b5a-bee2-2b6264dbe835/dqc_reference/reference_markers.fasta -out GCF_010119615.1_ASM1011961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:38,942] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:38,946] [INFO] Selected 18 target genomes.
[2024-01-24 10:47:38,947] [INFO] Target genome list was writen to GCF_010119615.1_ASM1011961v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:38,971] [INFO] Task started: fastANI
[2024-01-24 10:47:38,971] [INFO] Running command: fastANI --query /var/lib/cwl/stg84ed304a-0643-469c-80ce-86f7f6f7fc14/GCF_010119615.1_ASM1011961v1_genomic.fna.gz --refList GCF_010119615.1_ASM1011961v1_genomic.fna/target_genomes.txt --output GCF_010119615.1_ASM1011961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:54,134] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:54,135] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1018c2d7-57a3-4b5a-bee2-2b6264dbe835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:54,135] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1018c2d7-57a3-4b5a-bee2-2b6264dbe835/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:54,150] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:54,150] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:54,150] [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 gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	100.0	1126	1126	95	conclusive
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	84.5053	842	1126	95	below_threshold
Pseudoxanthomonas sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	84.0925	809	1126	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	81.676	697	1126	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	81.632	701	1126	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.4566	622	1126	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.2634	645	1126	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	81.2536	630	1126	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_002940605.1	56464	56464	type	True	81.0586	560	1126	95	below_threshold
Xanthomonas theicola	strain=CFBP 4691	GCA_014236795.1	56464	56464	type	True	80.9139	595	1126	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	80.6869	622	1126	95	below_threshold
Xanthomonas massiliensis	strain=SN8	GCA_900018785.1	1720302	1720302	type	True	80.4938	547	1126	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.4493	596	1126	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	80.3211	558	1126	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	80.306	572	1126	95	below_threshold
Stenotrophomonas nematodicola	strain=CPCC 101271	GCA_009467805.1	2656746	2656746	type	True	80.1368	574	1126	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	79.9903	573	1126	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	79.7609	585	1126	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:54,152] [INFO] DFAST Taxonomy check result was written to GCF_010119615.1_ASM1011961v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:54,152] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:54,153] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:54,153] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1018c2d7-57a3-4b5a-bee2-2b6264dbe835/dqc_reference/checkm_data
[2024-01-24 10:47:54,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:54,194] [INFO] Task started: CheckM
[2024-01-24 10:47:54,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010119615.1_ASM1011961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010119615.1_ASM1011961v1_genomic.fna/checkm_input GCF_010119615.1_ASM1011961v1_genomic.fna/checkm_result
[2024-01-24 10:48:31,529] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:31,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:31,552] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:31,553] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:31,553] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010119615.1_ASM1011961v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:31,554] [INFO] Task started: Blastn
[2024-01-24 10:48:31,554] [INFO] Running command: blastn -query GCF_010119615.1_ASM1011961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1018c2d7-57a3-4b5a-bee2-2b6264dbe835/dqc_reference/reference_markers_gtdb.fasta -out GCF_010119615.1_ASM1011961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:33,273] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:33,279] [INFO] Selected 11 target genomes.
[2024-01-24 10:48:33,279] [INFO] Target genome list was writen to GCF_010119615.1_ASM1011961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:33,308] [INFO] Task started: fastANI
[2024-01-24 10:48:33,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg84ed304a-0643-469c-80ce-86f7f6f7fc14/GCF_010119615.1_ASM1011961v1_genomic.fna.gz --refList GCF_010119615.1_ASM1011961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010119615.1_ASM1011961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:42,767] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:42,784] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:42,784] [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_010119615.1	s__Pseudoxanthomonas_A gei	100.0	1126	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_010093345.1	s__Pseudoxanthomonas_A yeongjuensis	84.4962	843	1126	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	84.1193	807	1126	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_004173415.1	s__Pseudoxanthomonas_A sp004173415	84.0426	564	1126	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	83.9045	805	1126	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_900215535.1	s__Pseudoxanthomonas_A wuyuanensis	81.6181	702	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	81.4563	622	1126	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_000513995.1	s__Pseudoxanthomonas sp000513995	80.8599	623	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900018785.1	s__Xanthomonas_B massiliensis	80.4989	546	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Xanthomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014395425.1	s__Thermomonas brevis	80.0664	535	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001014645.1	s__Luteimonas sp001014645	79.5082	514	1126	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:42,786] [INFO] GTDB search result was written to GCF_010119615.1_ASM1011961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:42,787] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:42,791] [INFO] DFAST_QC result json was written to GCF_010119615.1_ASM1011961v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:42,791] [INFO] DFAST_QC completed!
[2024-01-24 10:48:42,791] [INFO] Total running time: 0h1m19s