[2024-01-24 12:40:07,010] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:40:07,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:40:07,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg25a6bf3f-576d-44f1-a683-8126b46cb0f1/dqc_reference
[2024-01-24 12:40:08,332] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:40:08,333] [INFO] Task started: Prodigal
[2024-01-24 12:40:08,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg6c7045ab-977b-43cc-bf34-77fe52a9914f/GCF_010093305.1_ASM1009330v1_genomic.fna.gz | prodigal -d GCF_010093305.1_ASM1009330v1_genomic.fna/cds.fna -a GCF_010093305.1_ASM1009330v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:40:20,878] [INFO] Task succeeded: Prodigal
[2024-01-24 12:40:20,879] [INFO] Task started: HMMsearch
[2024-01-24 12:40:20,879] [INFO] Running command: hmmsearch --tblout GCF_010093305.1_ASM1009330v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25a6bf3f-576d-44f1-a683-8126b46cb0f1/dqc_reference/reference_markers.hmm GCF_010093305.1_ASM1009330v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:40:21,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:40:21,095] [INFO] Found 6/6 markers.
[2024-01-24 12:40:21,132] [INFO] Query marker FASTA was written to GCF_010093305.1_ASM1009330v1_genomic.fna/markers.fasta
[2024-01-24 12:40:21,133] [INFO] Task started: Blastn
[2024-01-24 12:40:21,133] [INFO] Running command: blastn -query GCF_010093305.1_ASM1009330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a6bf3f-576d-44f1-a683-8126b46cb0f1/dqc_reference/reference_markers.fasta -out GCF_010093305.1_ASM1009330v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:22,065] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:22,069] [INFO] Selected 16 target genomes.
[2024-01-24 12:40:22,069] [INFO] Target genome list was writen to GCF_010093305.1_ASM1009330v1_genomic.fna/target_genomes.txt
[2024-01-24 12:40:22,075] [INFO] Task started: fastANI
[2024-01-24 12:40:22,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c7045ab-977b-43cc-bf34-77fe52a9914f/GCF_010093305.1_ASM1009330v1_genomic.fna.gz --refList GCF_010093305.1_ASM1009330v1_genomic.fna/target_genomes.txt --output GCF_010093305.1_ASM1009330v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:36,295] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:36,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25a6bf3f-576d-44f1-a683-8126b46cb0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:36,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25a6bf3f-576d-44f1-a683-8126b46cb0f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:36,309] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:36,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:36,310] [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 sacheonensis	strain=DSM 19373	GCA_010093305.1	443615	443615	type	True	100.0	1325	1327	95	conclusive
Pseudoxanthomonas yeongjuensis	strain=DSM 18204	GCA_010093345.1	377616	377616	type	True	84.8036	887	1327	95	below_threshold
Pseudoxanthomonas gei	strain=KCTC 32298	GCA_010119615.1	1383030	1383030	type	True	83.9277	830	1327	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=DSM 100640	GCA_010093325.1	1073196	1073196	type	True	82.1252	818	1327	95	below_threshold
Pseudoxanthomonas wuyuanensis	strain=CGMCC 1.10978	GCA_900215535.1	1073196	1073196	type	True	82.1193	808	1327	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.7782	667	1327	95	below_threshold
Pseudoxanthomonas beigongshangi	strain=REN9	GCA_016820515.1	2782537	2782537	type	True	81.6845	754	1327	95	below_threshold
Pseudoxanthomonas mexicana	strain=DSM 17121	GCA_010093385.1	128785	128785	type	True	81.4666	724	1327	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	81.4493	716	1327	95	below_threshold
Pseudoxanthomonas japonensis	strain=DSM 17109	GCA_010093445.1	69284	69284	type	True	81.3102	770	1327	95	below_threshold
Xanthomonas hyacinthi	strain=CFBP 1156	GCA_009769165.1	56455	56455	type	True	81.0038	694	1327	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.44	652	1327	95	below_threshold
Luteimonas gilva	strain=H23	GCA_005239095.1	2572684	2572684	type	True	80.2643	630	1327	95	below_threshold
Pseudoxanthomonas dokdonensis	strain=DSM 21858	GCA_001431405.1	344882	344882	type	True	80.2231	624	1327	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	79.8919	613	1327	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	79.8302	602	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:36,312] [INFO] DFAST Taxonomy check result was written to GCF_010093305.1_ASM1009330v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:36,313] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:36,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:36,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25a6bf3f-576d-44f1-a683-8126b46cb0f1/dqc_reference/checkm_data
[2024-01-24 12:40:36,315] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:36,354] [INFO] Task started: CheckM
[2024-01-24 12:40:36,355] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010093305.1_ASM1009330v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010093305.1_ASM1009330v1_genomic.fna/checkm_input GCF_010093305.1_ASM1009330v1_genomic.fna/checkm_result
[2024-01-24 12:41:13,519] [INFO] Task succeeded: CheckM
[2024-01-24 12:41:13,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:41:13,538] [INFO] ===== Completeness check finished =====
[2024-01-24 12:41:13,538] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:41:13,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010093305.1_ASM1009330v1_genomic.fna/markers.fasta)
[2024-01-24 12:41:13,539] [INFO] Task started: Blastn
[2024-01-24 12:41:13,539] [INFO] Running command: blastn -query GCF_010093305.1_ASM1009330v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a6bf3f-576d-44f1-a683-8126b46cb0f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_010093305.1_ASM1009330v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:41:15,240] [INFO] Task succeeded: Blastn
[2024-01-24 12:41:15,244] [INFO] Selected 11 target genomes.
[2024-01-24 12:41:15,244] [INFO] Target genome list was writen to GCF_010093305.1_ASM1009330v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:41:15,250] [INFO] Task started: fastANI
[2024-01-24 12:41:15,250] [INFO] Running command: fastANI --query /var/lib/cwl/stg6c7045ab-977b-43cc-bf34-77fe52a9914f/GCF_010093305.1_ASM1009330v1_genomic.fna.gz --refList GCF_010093305.1_ASM1009330v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010093305.1_ASM1009330v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:25,507] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:25,516] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:41:25,516] [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_010093305.1	s__Pseudoxanthomonas_A sacheonensis	100.0	1325	1327	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_900104085.1	s__Pseudoxanthomonas_A sp900104085	93.6402	1153	1327	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	84.8151	886	1327	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_010119615.1	s__Pseudoxanthomonas_A gei	83.9196	831	1327	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	82.9629	560	1327	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	82.1267	806	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	99.99	99.99	0.99	0.99	2	-
GCA_019218945.1	s__Pseudoxanthomonas_A sp019218945	81.8329	749	1327	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_010211755.1	s__Pseudoxanthomonas_A sangjuensis	81.776	668	1327	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_010093385.1	s__Pseudoxanthomonas_A mexicana	81.4868	722	1327	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	96.97	96.88	0.87	0.86	4	-
GCF_001427585.1	s__Pseudoxanthomonas_A sp001427585	81.3385	750	1327	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	80.2083	626	1327	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 12:41:25,518] [INFO] GTDB search result was written to GCF_010093305.1_ASM1009330v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:25,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:25,522] [INFO] DFAST_QC result json was written to GCF_010093305.1_ASM1009330v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:25,522] [INFO] DFAST_QC completed!
[2024-01-24 12:41:25,522] [INFO] Total running time: 0h1m19s