[2024-01-24 13:41:40,948] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:40,950] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:40,950] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f628bc1-c786-46ed-8af7-81695deefb62/dqc_reference
[2024-01-24 13:41:42,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:42,323] [INFO] Task started: Prodigal
[2024-01-24 13:41:42,324] [INFO] Running command: gunzip -c /var/lib/cwl/stga1ce639a-ae6c-4154-a1e1-9c9964c98f05/GCF_015209745.1_ASM1520974v1_genomic.fna.gz | prodigal -d GCF_015209745.1_ASM1520974v1_genomic.fna/cds.fna -a GCF_015209745.1_ASM1520974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:52,317] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:52,317] [INFO] Task started: HMMsearch
[2024-01-24 13:41:52,318] [INFO] Running command: hmmsearch --tblout GCF_015209745.1_ASM1520974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f628bc1-c786-46ed-8af7-81695deefb62/dqc_reference/reference_markers.hmm GCF_015209745.1_ASM1520974v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:52,567] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:52,568] [INFO] Found 6/6 markers.
[2024-01-24 13:41:52,595] [INFO] Query marker FASTA was written to GCF_015209745.1_ASM1520974v1_genomic.fna/markers.fasta
[2024-01-24 13:41:52,596] [INFO] Task started: Blastn
[2024-01-24 13:41:52,596] [INFO] Running command: blastn -query GCF_015209745.1_ASM1520974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f628bc1-c786-46ed-8af7-81695deefb62/dqc_reference/reference_markers.fasta -out GCF_015209745.1_ASM1520974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:53,609] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:53,613] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:53,613] [INFO] Target genome list was writen to GCF_015209745.1_ASM1520974v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:53,626] [INFO] Task started: fastANI
[2024-01-24 13:41:53,626] [INFO] Running command: fastANI --query /var/lib/cwl/stga1ce639a-ae6c-4154-a1e1-9c9964c98f05/GCF_015209745.1_ASM1520974v1_genomic.fna.gz --refList GCF_015209745.1_ASM1520974v1_genomic.fna/target_genomes.txt --output GCF_015209745.1_ASM1520974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:03,110] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:03,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f628bc1-c786-46ed-8af7-81695deefb62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:03,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f628bc1-c786-46ed-8af7-81695deefb62/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:03,128] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:03,128] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:03,128] [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
Lysobacter avium	strain=H23M41	GCA_015209745.1	2781023	2781023	type	True	100.0	950	951	95	conclusive
Lysobacter ciconiae	strain=H21R20	GCA_015209725.1	2781022	2781022	type	True	92.9054	841	951	95	below_threshold
Lysobacter antarcticus	strain=GW1-59	GCA_019802285.1	2862543	2862543	type	True	88.7463	853	951	95	below_threshold
Lysobacter concretionis	strain=Ko07	GCA_000768345.1	262325	262325	type	True	83.3177	644	951	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	82.0885	567	951	95	below_threshold
Vulcaniibacterium tengchongense	strain=DSM 25623	GCA_003814555.1	1273429	1273429	type	True	81.1782	521	951	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	81.1767	433	951	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	81.0872	517	951	95	below_threshold
Lysobacter spongiicola	strain=DSM 21749	GCA_900167055.1	435289	435289	type	True	80.8027	538	951	95	below_threshold
Lysobacter arenosi	strain=R7	GCA_016613475.2	2795387	2795387	type	True	80.5474	509	951	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	80.2216	523	951	95	below_threshold
Lysobacter terrestris	strain=II4	GCA_014489475.1	2865112	2865112	type	True	80.2093	503	951	95	below_threshold
Lysobacter antibioticus	strain=ATCC 29479	GCA_001442535.1	84531	84531	type	True	80.1809	496	951	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:03,130] [INFO] DFAST Taxonomy check result was written to GCF_015209745.1_ASM1520974v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:03,130] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:03,130] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:03,131] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f628bc1-c786-46ed-8af7-81695deefb62/dqc_reference/checkm_data
[2024-01-24 13:42:03,132] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:03,161] [INFO] Task started: CheckM
[2024-01-24 13:42:03,161] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015209745.1_ASM1520974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015209745.1_ASM1520974v1_genomic.fna/checkm_input GCF_015209745.1_ASM1520974v1_genomic.fna/checkm_result
[2024-01-24 13:42:41,014] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:41,016] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:41,033] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:41,034] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:41,034] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015209745.1_ASM1520974v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:41,035] [INFO] Task started: Blastn
[2024-01-24 13:42:41,035] [INFO] Running command: blastn -query GCF_015209745.1_ASM1520974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f628bc1-c786-46ed-8af7-81695deefb62/dqc_reference/reference_markers_gtdb.fasta -out GCF_015209745.1_ASM1520974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:42,846] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:42,850] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:42,851] [INFO] Target genome list was writen to GCF_015209745.1_ASM1520974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:42,905] [INFO] Task started: fastANI
[2024-01-24 13:42:42,905] [INFO] Running command: fastANI --query /var/lib/cwl/stga1ce639a-ae6c-4154-a1e1-9c9964c98f05/GCF_015209745.1_ASM1520974v1_genomic.fna.gz --refList GCF_015209745.1_ASM1520974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015209745.1_ASM1520974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:51,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:51,890] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:51,890] [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_015209765.1	s__Lysobacter sp015209765	97.9849	882	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	98.00	98.00	0.93	0.93	2	conclusive
GCF_015209725.1	s__Lysobacter sp015209725	92.9273	840	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	96.91	96.91	0.94	0.94	2	-
GCF_000855665.1	s__Lysobacter sp000855665	90.8802	814	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768345.1	s__Lysobacter concretionis	83.3312	643	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000768335.1	s__Lysobacter arseniciresistens	82.1242	564	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_907164845.1	s__Lysobacter sp907164845	81.4101	560	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423325.1	s__Lysobacter defluvii	81.099	516	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900167055.1	s__Lysobacter spongiicola	80.8338	535	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016613475.2	s__Lysobacter arenosi	80.5587	509	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489475.1	s__Lysobacter solisilvae	80.2082	499	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308985.1	s__Lysobacter sp017308985	80.045	491	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014395425.1	s__Thermomonas brevis	79.8115	464	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:51,892] [INFO] GTDB search result was written to GCF_015209745.1_ASM1520974v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:51,893] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:51,896] [INFO] DFAST_QC result json was written to GCF_015209745.1_ASM1520974v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:51,897] [INFO] DFAST_QC completed!
[2024-01-24 13:42:51,897] [INFO] Total running time: 0h1m11s